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The basic helix-loop-helix (bHLH) family of transcription factors is one of the most significant and biggest in plants. It is involved in the regulation of both growth and development, as well as stress response. Numerous members of the bHLH family have been found and characterized in woody plants in recent years. However, no systematic study of the bHLH gene family has been published for Hibiscus hamabo Sieb. et Zucc. In this research, we identified 162 bHLH proteins (HhbHLHs) from the genomic and transcriptomic datasets of H. hamabo, which were phylogenetically divided into 19 subfamilies. According to a gene structural study, the number of exon-introns in HhbHLHs varied between zero and seventeen. MEME research revealed that the majority of HhbHLH proteins contained three conserved motifs, 1, 4, and 5. The examination of promoter cis-elements revealed that the majority of HhbHLH genes had several cis-elements involved in plant growth and development and abiotic stress responses. In addition, the overexpression of HhbHLH2 increased salt and drought stress tolerance in Arabidopsis.
Longjie Ni; Zhiquan Wang; Zekai Fu; Dina Liu; Yunlong Yin; Huogen Li; Chunsun Gu. Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc. International Journal of Molecular Sciences 2021, 22, 8748 .
AMA StyleLongjie Ni, Zhiquan Wang, Zekai Fu, Dina Liu, Yunlong Yin, Huogen Li, Chunsun Gu. Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc. International Journal of Molecular Sciences. 2021; 22 (16):8748.
Chicago/Turabian StyleLongjie Ni; Zhiquan Wang; Zekai Fu; Dina Liu; Yunlong Yin; Huogen Li; Chunsun Gu. 2021. "Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc." International Journal of Molecular Sciences 22, no. 16: 8748.
Terpenoids are important secondary metabolites in plants and are involved in stress responses and pollinator attraction. Geranylgeranyl pyrophosphate synthase (GGPPS) is a key synthase in the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway of terpenoid synthesis, catalyzing the synthesis of diterpenoids. Liriodendron tulipifera is a nectar plant in North America. Little is known about the key genes involved in the biosynthetic pathways of terpenoids, the precursors of most compounds related to nectar, fragrance and coloring in flowers in L. tulipifera. In this study, the LtuGGPPS2 gene and its promoter (LtuGGPPS2-pro) were cloned from L. tulipifera. The results of sequence alignment showed that the LtuGGPPS2 gene is highly homologous to GGPPS genes of other plants. Subcellular localization analysis showed that the LtuGGPPS2 protein localizes to chloroplasts, suggesting that the LtuGGPPS2 gene is probably related to carotenoid and chlorophyll synthesis. Based on tissue expression profiles revealed by RT-qPCR, the expression level of the LtuGGPPS2 gene was highest in petals. These results were consistent with the changes in volatile and nonvolatile terpenoids in the flowers of L. tulipifera. GUS staining to examine the LtuGGPPS2 promoter indicated that it is responsive to hormones. Overexpression of the LtuGGPPS2 gene increased the carotenoid content and GGPPS enzyme activity in Arabidopsis thaliana, indicating that LtuGGPPS2 is the key terpenoid synthase in the flowers of L. tulipifera. Our findings lay a foundation for further functional analysis of the LtuGGPPS2 gene and deeper investigation of the terpenoid biosynthetic pathway in L. tulipifera.
Chengge Zhang; Huanhuan Liu; Yaxian Zong; Zhonghua Tu; Huogen Li. Isolation, expression, and functional analysis of the geranylgeranyl pyrophosphate synthase (GGPPS) gene from Liriodendron tulipifera. Plant Physiology and Biochemistry 2021, 166, 700 -711.
AMA StyleChengge Zhang, Huanhuan Liu, Yaxian Zong, Zhonghua Tu, Huogen Li. Isolation, expression, and functional analysis of the geranylgeranyl pyrophosphate synthase (GGPPS) gene from Liriodendron tulipifera. Plant Physiology and Biochemistry. 2021; 166 ():700-711.
Chicago/Turabian StyleChengge Zhang; Huanhuan Liu; Yaxian Zong; Zhonghua Tu; Huogen Li. 2021. "Isolation, expression, and functional analysis of the geranylgeranyl pyrophosphate synthase (GGPPS) gene from Liriodendron tulipifera." Plant Physiology and Biochemistry 166, no. : 700-711.
Hibiscus hamabo Siebold & Zuccarini (H. hamabo) is tolerant to salt and drought conditions, but the molecular mechanisms that underlie this stress tolerance remain unclear. In this study, the transcriptome of H. hamabo roots was investigated under NaCl or PEG treatment. A total of 20,513 and 27,516 significantly changed known genes at 6 h and 24 h, respectively, were detected between the salt or drought treatments and the control libraries. Among these, there were 3845 and 7430 overlapping genes under the two stresses at 6 h and 24 h, respectively. Based on the analysis of enriched KEGG pathways and clustering of expression patterns, the DEGs that were continuously up- or down-regulated under both salt and drought treatments were mainly enriched in MAPK signaling pathway, transcription factors, transporters and other pathways. The transcriptome expression profiles of H. hamabo provide a genetic resource for identifying common regulatory factors involved in responses to different abiotic stresses. In addition, the identified factors may be useful to developing genetic breeding strategies for the Malvaceae.
Zhiquan Wang; Longjie Ni; Jianfeng Hua; Liangqin Liu; Yunlong Yin; Huogen Li; Chunsun Gu. Transcriptome Analysis Reveals Regulatory Framework for Salt and Drought Tolerance in Hibiscus hamabo Siebold & Zuccarini. Forests 2021, 12, 454 .
AMA StyleZhiquan Wang, Longjie Ni, Jianfeng Hua, Liangqin Liu, Yunlong Yin, Huogen Li, Chunsun Gu. Transcriptome Analysis Reveals Regulatory Framework for Salt and Drought Tolerance in Hibiscus hamabo Siebold & Zuccarini. Forests. 2021; 12 (4):454.
Chicago/Turabian StyleZhiquan Wang; Longjie Ni; Jianfeng Hua; Liangqin Liu; Yunlong Yin; Huogen Li; Chunsun Gu. 2021. "Transcriptome Analysis Reveals Regulatory Framework for Salt and Drought Tolerance in Hibiscus hamabo Siebold & Zuccarini." Forests 12, no. 4: 454.
Liriodendron plants have been cultivated in many regions of the world for both wood production and landscape ornamentation. Hybrid Liriodendron varieties show obvious growth and resistance heterosis; thus, interspecies hybridization and heterosis utilization constitute the major breeding strategy for Liriodendron plants. Choosing superior crossing parents/combinations and predicting the heterosis of potential hybrid combinations will greatly improve breeding efficiency and accelerate the breeding process. To explore the relationships between genetic parameters and heterosis, we investigated dynamic changes in the genetic parameters of growth traits with age by testing 57 progeny combinations derived from six cross types in Liriodendron. Tree height (H) and diameter at breast height (DBH) were under intermediate to strong genetic control and varied among combinations, indicating that parent-pair selection or combination selection is feasible. Both heritability and combining ability (general combining ability, GCA; specific combining ability, SCA) changed with age, with narrow-sense heritability fluctuating greatly in the early stage and increasing in the late stage, and the combining abilities varied among combinations. Additionally, the GCA of Liriodendron chinense parents was higher than that of Liriodendron tulipifera and hybrid Liriodendron parents, and the SCA of L. tulipifera × L. chinense combinations fluctuated less than that of other combinations. Further, midparent heterosis (MPH) and SCA were significantly positively correlated, suggesting that SCA could be a suitable criterion for predicting growth heterosis. Our findings provide useful clues for selecting parent pairs/combinations and predicting heterosis, which will accelerate Liriodendron tree breeding and shed light on cross-breeding in other plants.
Hui Xia; Weijie Si; Ziyuan Hao; Weiping Zhong; Shenghua Zhu; Zhonghua Tu; Chengge Zhang; Huogen Li. Dynamic changes in the genetic parameters of growth traits with age and their associations with heterosis in hybrid Liriodendron. Tree Genetics & Genomes 2021, 17, 1 -18.
AMA StyleHui Xia, Weijie Si, Ziyuan Hao, Weiping Zhong, Shenghua Zhu, Zhonghua Tu, Chengge Zhang, Huogen Li. Dynamic changes in the genetic parameters of growth traits with age and their associations with heterosis in hybrid Liriodendron. Tree Genetics & Genomes. 2021; 17 (2):1-18.
Chicago/Turabian StyleHui Xia; Weijie Si; Ziyuan Hao; Weiping Zhong; Shenghua Zhu; Zhonghua Tu; Chengge Zhang; Huogen Li. 2021. "Dynamic changes in the genetic parameters of growth traits with age and their associations with heterosis in hybrid Liriodendron." Tree Genetics & Genomes 17, no. 2: 1-18.
Iris lactea var. chinensis (I. lactea var. chinensis) is a perennial herb halophyte with salt and drought tolerance. In this study, full-length transcripts of I. lactea var. chinensis were sequenced using the PacBio RSII sequencing platform. Moreover, the transcriptome was investigated under NaCl or polyethylene glycol (PEG) stress. Approximately 30.89 G subreads were generated and 31,195 unigenes were obtained by clustering the same isoforms by the PacBio RSII platform. A total of 15,466 differentially expressed genes (DEGs) were obtained under the two stresses using the Illumina platform. Among them, 9266 and 8390 DEGs were obtained under high concentrations of NaCl and PEG, respectively. In total, 3897 DEGs with the same expression pattern under the two stresses were obtained. The transcriptome expression profiles of I. lactea var. chinensis under NaCl or PEG stress obtained in this study may provide a resource for the same and different response mechanisms against different types of abiotic stress. Furthermore, the stress-related genes found in this study can provide data for future molecular breeding.
Longjie Ni; Zhiquan Wang; Jinbo Guo; Xiaoxiao Pei; Liangqin Liu; Huogen Li; Haiyan Yuan; Chunsun Gu. Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis. Genes 2021, 12, 434 .
AMA StyleLongjie Ni, Zhiquan Wang, Jinbo Guo, Xiaoxiao Pei, Liangqin Liu, Huogen Li, Haiyan Yuan, Chunsun Gu. Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis. Genes. 2021; 12 (3):434.
Chicago/Turabian StyleLongjie Ni; Zhiquan Wang; Jinbo Guo; Xiaoxiao Pei; Liangqin Liu; Huogen Li; Haiyan Yuan; Chunsun Gu. 2021. "Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis." Genes 12, no. 3: 434.
Alternative splicing (AS) plays pivotal roles in regulating plant growth and development, flowering, biological rhythms, signal transduction, and stress responses. However, no studies on AS have been performed in Liriodendron chinense, a deciduous tree species that has high economic and ecological value. In this study, we used multiple tools and algorithms to analyze transcriptome data derived from seven tissues via hybrid sequencing. Although only 17.56% (8,503/48,408) of genes in L. chinense were alternatively spliced, these AS genes occurred in 37,844 AS events. Among these events, intron retention was the most frequent AS event, producing 1,656 PTC-containing and 3,310 non-PTC-containing transcripts. Moreover, 183 long noncoding RNAs (lncRNAs) also underwent AS events. Furthermore, weighted gene coexpression network analysis (WGCNA) revealed that there were great differences in the activities of transcription and post-transcriptional regulation between pistils and leaves, and AS had an impact on many physiological and biochemical processes in L. chinense, such as photosynthesis, sphingolipid metabolism, fatty acid biosynthesis and metabolism. Moreover, our analysis showed that the features of genes may affect AS, as AS genes and non-AS genes had differences in the exon/intron length, transcript length, and number of exons/introns. In addition, the structure of AS genes may impact the frequencies and types of AS because AS genes with more exons or introns tended to exhibit more AS events, and shorter introns tended to be retained, whereas shorter exons tended to be skipped. Furthermore, eight AS genes were verified, and the results were consistent with our analysis. Overall, this study reveals that AS and gene interaction are mutual—on one hand, AS can affect gene expression and translation, while on the other hand, the structural characteristics of the gene can also affect AS. This work is the first to comprehensively report on AS in L. chinense, and it can provide a reference for further research on AS in L. chinense.
Zhonghua Tu; Yufang Shen; Shaoying Wen; Yaxian Zong; Huogen Li. Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense. Frontiers in Plant Science 2020, 11, 1 .
AMA StyleZhonghua Tu, Yufang Shen, Shaoying Wen, Yaxian Zong, Huogen Li. Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense. Frontiers in Plant Science. 2020; 11 ():1.
Chicago/Turabian StyleZhonghua Tu; Yufang Shen; Shaoying Wen; Yaxian Zong; Huogen Li. 2020. "Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense." Frontiers in Plant Science 11, no. : 1.
Background: Adaptive genetic differentiation is a hotspot in the research of speciation mechanisms in evolutionary biology. Genomic resources are important for detecting ecological adaptive evolution of non-model plants. Using RNA-seq for non-model plants is a good approach to obtain their genomic resources. The combination of population transcriptome resources and environmental data can provide insights into the genetic mechanism of adaptive genetic differentiation.Results: Based on the population transcriptome data, we investigated the spatial distribution of genetic variations in Liriodendron to detect relationships between ecological factors and genetic differentiation. Environmental data and genetic variations from 17 populations were integrated to detect the population structure, adaptive genes and key environmental factors that shape the population genetic structure by landscape genetic approach. Here, we identified 16592 high-quality single nucleotide polymorphisms (SNPs). The population structure analysis results showed that 17 populations were divided into three groups: L. tulipifera, eastern group and western group of L. chinense. Redundancy analysis and latent factor mixed model analysis suggested that precipitation seasonality, precipitation in the driest quarter, diurnal temperature, and solar radiation in May were closely associated with the adaptive genetic differentiation of Liriodendron. Ecological niche differentiation analysis implied significant ecological niche divergence between L. chinense and L. tulipifera habitats. In total, 858 environment-related loci were identified, which were associated with 464 genes. Pathway enrichment analysis revealed that these genes were significantly enriched in multiple biological pathways. Related studies confirmed that these biological pathways play vital roles in plant growth, development, stress, immune response and photosynthesis.Conclusions: Our research provided empirical evidence that environmental factors may play a key role in driving adaptive genetic differentiation of species. Furthermore, the combination of population transcriptome resources and environmental datasets provides new insights into the study of adaptive genetic differentiation of species.
Yufang Shen; Hui Xia; Zhonghua Tu; Yaxian Zong; Lichun Yang; Huogen Li. Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics. 2020, 1 .
AMA StyleYufang Shen, Hui Xia, Zhonghua Tu, Yaxian Zong, Lichun Yang, Huogen Li. Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics. . 2020; ():1.
Chicago/Turabian StyleYufang Shen; Hui Xia; Zhonghua Tu; Yaxian Zong; Lichun Yang; Huogen Li. 2020. "Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics." , no. : 1.
Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .
Zhonghua Tu; Yufang Shen; Shaoying Wen; Huanhuan Liu; Lingmin Wei; Huogen Li. Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing. 2020, 1 .
AMA StyleZhonghua Tu, Yufang Shen, Shaoying Wen, Huanhuan Liu, Lingmin Wei, Huogen Li. Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing. . 2020; ():1.
Chicago/Turabian StyleZhonghua Tu; Yufang Shen; Shaoying Wen; Huanhuan Liu; Lingmin Wei; Huogen Li. 2020. "Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing." , no. : 1.
Liriodendron chinense is a common ornamental tree that has attractive leaves, which is a valuable trait for use in landscape architecture. In this work, we aimed to identify the potential genes that control and regulate the development of L. chinense leaf lobes. Based on the transcriptome data for the leaf developmental stages we previously generated, two candidate genes were identified in this study. KNOTTED-LIKE HOMEOBOX(KNOX), encoding homeobox family proteins, play a large role in leaf lobe and leaf complexity regulation. Here, two full length KNOX genes from L. chinense were amplified and named LcKNOX1 and LcKNOX6 according to their sequence similarities with the respective Arabidopsis thaliana KNOX family genes. Overexpression vectors were constructed and subsequently transformed into wild type (WT) A. thaliana. Additionally, LcKNOX6 was expressed in tobacco leaves to examine its subcellular localization, and the 35S::LcKNOX6 transgenic A. thaliana leaf cells were imaged with the use of SEM. The expression of several genes that participate in KNOX gene regulation were validated by quantitative real-time PCR. The results show that LcKNOX1 produces almost the same phenotype as that found in WT A. thaliana. Notably, the LcKNOX6-1 lines presented deep leaf lobes that were similar to L. chinense leaf lobes. Two 35S::LcKNOX6 lines induced an abnormal growth phenotype whose seeds were abortive. In short, these results indicate that the LcKNOX6 gene might affect leaf development in A. thaliana and provide insights into the regulation of L. chinense leaf shaping.
Jikai Ma; Guoguo Mei; Huanhuan Liu; Huogen Li. Overexpression of a Novel LcKNOX Transcription Factor from Liriodendron chinense Induces Lobed Leaves in Arabidopsis thaliana. Forests 2019, 11, 33 .
AMA StyleJikai Ma, Guoguo Mei, Huanhuan Liu, Huogen Li. Overexpression of a Novel LcKNOX Transcription Factor from Liriodendron chinense Induces Lobed Leaves in Arabidopsis thaliana. Forests. 2019; 11 (1):33.
Chicago/Turabian StyleJikai Ma; Guoguo Mei; Huanhuan Liu; Huogen Li. 2019. "Overexpression of a Novel LcKNOX Transcription Factor from Liriodendron chinense Induces Lobed Leaves in Arabidopsis thaliana." Forests 11, no. 1: 33.
Background Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02–79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.
Huanhuan Liu; Jikai Ma; Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. BMC Plant Biology 2019, 19, 1 -18.
AMA StyleHuanhuan Liu, Jikai Ma, Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. BMC Plant Biology. 2019; 19 (1):1-18.
Chicago/Turabian StyleHuanhuan Liu; Jikai Ma; Huogen Li. 2019. "Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion." BMC Plant Biology 19, no. 1: 1-18.
Background: Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood. Methods: In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results: L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions: We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.
Huanhuan Liu; Jikai Ma; Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. 2019, 1 .
AMA StyleHuanhuan Liu, Jikai Ma, Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. . 2019; ():1.
Chicago/Turabian StyleHuanhuan Liu; Jikai Ma; Huogen Li. 2019. "Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion." , no. : 1.
Flower colour and colour patterns are crucial traits for ornamental species; thus, a comprehensive understanding of their genetic basis is extremely significant for plant breeders. The tulip tree (Liriodendron tulipifera Linn.) is well known for its flowers, odd leave shape and tree form. However, the genetic basis of its colour inheritance remains unknown. In this study, a putative plastid terminal oxidase gene (LtuPTOX) was identified from L. tulipifera based on multiple databases of differentially expressed genes at various developmental stages. Then, the full-length cDNA of LtuPTOX was derived from tepals and leaves using RACE (rapid amplification of cDNA ends) approaches. Furthermore, gene structure and phylogenetic analyses of PTOX as well as AOXs (alternative oxidases), another highly similar homologue in the AOX family, were used to distinguish between the two subfamilies of genes. In addition, transient transformation and qPCR methods were used to determine the subcellular localization and tissue expression pattern of the LtuPTOX gene. Moreover, the expression of LtuPTOX as well as pigment contents was investigated to illustrate the function of this gene during the formation of orange bands on petals. The results showed that the LtuPTOX gene encodes a 358-aa protein that contains a complete AOX domain (PF01786). Accordingly, the Liriodendron PTOX and AOX genes were identified as only paralogs since they were rather similar in sequence. LtuPTOX showed chloroplast localization and was expressed in coloured organs such as petals and leaves. Additionally, an increasing pattern of LtuPTOX transcripts leads to carotenoid accumulation on the orange-band during flower bud development. Taken together, our results suggest that LtuPTOX is involved in petal carotenoid metabolism and orange band formation in L. tulipifera. The identification of this potentially involved gene will lay a foundation for further uncovering the genetic basis of flower colour in L. tulipifera.
Ziyuan Hao; Yaxian Zong; Huanhuan Liu; Zhonghua Tu; Huogen Li. Cloning, Characterization and Functional Analysis of the LtuPTOX Gene, a Homologue of Arabidopsis thaliana IMMUTANS Derived from Liriodendron tulipifera. Genes 2019, 10, 878 .
AMA StyleZiyuan Hao, Yaxian Zong, Huanhuan Liu, Zhonghua Tu, Huogen Li. Cloning, Characterization and Functional Analysis of the LtuPTOX Gene, a Homologue of Arabidopsis thaliana IMMUTANS Derived from Liriodendron tulipifera. Genes. 2019; 10 (11):878.
Chicago/Turabian StyleZiyuan Hao; Yaxian Zong; Huanhuan Liu; Zhonghua Tu; Huogen Li. 2019. "Cloning, Characterization and Functional Analysis of the LtuPTOX Gene, a Homologue of Arabidopsis thaliana IMMUTANS Derived from Liriodendron tulipifera." Genes 10, no. 11: 878.
Background Nectar is a major flower attractant and reward for insects for pollination. Liriodendron , a genus of the Magnoliaceae family, has only two relict species, L. chinense and L. tulipifera , that are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of the nectary, the mechanism of nectar secretion and the molecular mechanism involved in nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and the change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select definitive samples for next research. Transcriptome sequencing was performed on the top and middle parts of the immature nectary and the middle parts of the mature nectary and the postsecreted nectary in L. tulipifera . We evaluated the expression profiles of 21 DEGs that were closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results The L. tulipifera nectary is a starch-storing nectary and is located in the top and middle parts of L . tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by analyzing six different pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions We evaluated the nectary development and secretion process comprehensively and identified many related candidate genes in L. tulipifera . These findings suggest that the nectary may play important roles in flavonoid synthesis and petal color presentation.
Huanhuan Liu; Jikai Ma; Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. 2019, 1 .
AMA StyleHuanhuan Liu, Jikai Ma, Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. . 2019; ():1.
Chicago/Turabian StyleHuanhuan Liu; Jikai Ma; Huogen Li. 2019. "Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion." , no. : 1.
Liriodendron chinense (Hemsl.), a Tertiary relic tree, is mainly distributed in subtropical China. The causes of the geographical distribution pattern of this species are poorly understood. In this study, we inferred historical dispersal routes and glacial refugia of this species by combining genetic data (chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and nuclear DNA (nDNA)) and geospatial data (climate and geology) with the methods of landscape genetics. Additionally, based on sequence variation at multiple loci, we employed GenGIS and Barrier software to analyze L. chinense population genetic structure. Dispersal corridors and historical gene flow between the eastern and western populations were detected, and they were located in mountainous regions. Based on species distribution model (SDMs), the distribution patterns in paleoclimatic periods were consistent with the current pattern, suggesting the presence of multiple refuges in multiple mountainous regions in China. The genetic structure analysis clustered most eastern populations into a clade separated from the western populations. Additionally, a genetic barrier was detected between the eastern and western populations. The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations. Due to Quaternary climatic fluctuations, the habitats and dispersal corridors were frequently inhabited by warm-temperate evergreen forests, which may have fragmented L. chinense habitats and exacerbated the differentiation of eastern and western populations. Ultimately, populations retreated to multiple isolated mountainous refugia, shaping the current geographical distribution pattern. These dispersal corridors and montane refugia suggested that the mountains in subtropical China play a crucial role in the conservation of genetic resources and migration of subspecies or related species in this region.
Yufang Shen; Yanli Cheng; Kangqin Li; Huogen Li. Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense. Forests 2019, 10, 565 .
AMA StyleYufang Shen, Yanli Cheng, Kangqin Li, Huogen Li. Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense. Forests. 2019; 10 (7):565.
Chicago/Turabian StyleYufang Shen; Yanli Cheng; Kangqin Li; Huogen Li. 2019. "Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense." Forests 10, no. 7: 565.
Ten candidate reference genes were examined in Hibiscus hamabo Sieb. et Zucc. ACT and SKIP are proposed as good reference genes for gene studies in Hibiscus hamabo Sieb. et Zucc. Because of its sensitivity and rapidness, quantitative real-time PCR (qRT-PCR) is currently extensively used to analyze gene-expression patterns. Selecting suitable reference genes to normalize qRT-PCR results is essential. Hibiscus hamabo Sieb. et Zucc. (H. hamabo) is a semi-mangrove plant that is widely used for the ecological restoration of saline-alkali land and coastal afforestation owing to its excellent salt tolerance. However, suitable reference genes used for the normalization of H. hamabo qRT-PCR data have not been selected or verified. Here, we tested the expression stabilities of ten candidate reference genes in different H. hamabo tissues under a set of abiotic stresses (salt, drought, high temperature, and low temperature) and hormonal treatments (methyl jasmonate, abscisic acid, and salicylic acid) using three statistical algorithms, i.e., NormFinder, geNorm, and BestKeeper. Actin (ACT) and ski-interacting protein (SKIP) can be regarded as good choices as reference genes in studying gene expression of H. hamabo. In addition, the qRT-PCR analysis of the NAC (NAM/ATAF1/2/CUC2) target gene’s expression pattern under NaCl-treated conditions confirmed the suitability of selected reference genes. Here, we used qRT-PCR technology to provide a stable reference gene list for H. hamabo gene-expression studies.
Longjie Ni; Zhiquan Wang; Liangqin Liu; Jinbo Guo; Huogen Li; Chunsun Gu. Selection and verification of candidate reference genes for gene expression by quantitative RT-PCR in Hibiscus hamabo Sieb.et Zucc. Trees 2019, 33, 1591 -1601.
AMA StyleLongjie Ni, Zhiquan Wang, Liangqin Liu, Jinbo Guo, Huogen Li, Chunsun Gu. Selection and verification of candidate reference genes for gene expression by quantitative RT-PCR in Hibiscus hamabo Sieb.et Zucc. Trees. 2019; 33 (6):1591-1601.
Chicago/Turabian StyleLongjie Ni; Zhiquan Wang; Liangqin Liu; Jinbo Guo; Huogen Li; Chunsun Gu. 2019. "Selection and verification of candidate reference genes for gene expression by quantitative RT-PCR in Hibiscus hamabo Sieb.et Zucc." Trees 33, no. 6: 1591-1601.
Background Nectar is a major flower attractant and reward for insects for pollination. Liriodendron, a genus of the Magnoliaceae family, has only two relict species, L. chinense and L. tulipifera, that are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of the nectary, the mechanism of nectar secretion and the molecular mechanism involved in nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and the change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select definitive samples for next research. Transcriptome sequencing was performed on the top and middle parts of the immature nectary and the middle parts of the mature nectary and the postsecreted nectary in L. tulipifera. We evaluated the expression profiles of 22 DEGs that were closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results The L. tulipifera nectary is a starch-storing nectary and is located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by analyzing six different pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 22 candidate genes. Conclusions We evaluated the nectary development and secretion process comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that the nectary may play important roles in flavonoid synthesis and petal color presentation.
Huanhuan Liu; Jikai Ma; Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. 2019, 1 .
AMA StyleHuanhuan Liu, Jikai Ma, Huogen Li. Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. . 2019; ():1.
Chicago/Turabian StyleHuanhuan Liu; Jikai Ma; Huogen Li. 2019. "Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion." , no. : 1.
The precision and reliability of reverse transcription quantitative polymerase chain reaction (RT-qPCR) depend mainly on suitable reference genes; however, reference genes have not yet been identified for Liriodendron chinense (Hemsl.) Sarg. In this study, the expression stability of 15 candidate reference genes, ACT7, ACT97, UBQ1, eIF2, eIF3, HIS, BIG, AGD11, EFG, GAPDH, CYP, RPL25, UBC, RPB1, and TUB, was tested across multiple organs of L. chinense using four algorithms, geNorm, NormFinder, BestKeeper, and RefFinder. To understand the difference between the selected reference genes and the unsuitable candidate reference genes, the expression level of a target gene, LcPAT7, was normalized across various plant samples. ACT97 and eIF3 represented the best combination across all samples tested, while AGD11 and UBQ1 were unsuitable for normalization in this case. In the vegetative organ subset, ACT97, ACT7, and GAPDH showed the highest expression stability. For floral organs, UBC and eIF3 were the most stable reference genes. Unsuitable reference genes underestimated the expression levels of a target gene, LcPAT7. This study identified two reference genes (ACT97 and eIF3) for the precise and reliable normalization of L. chinense RT-qPCR data across various organs. Our work provides an effective framework for quantifying gene expression in L. chinense.
Zhonghua Tu; Ziyuan Hao; Weiping Zhong; Huogen Li. Identification of Suitable Reference Genes for RT-qPCR Assays in Liriodendron chinense (Hemsl.) Sarg. Forests 2019, 10, 441 .
AMA StyleZhonghua Tu, Ziyuan Hao, Weiping Zhong, Huogen Li. Identification of Suitable Reference Genes for RT-qPCR Assays in Liriodendron chinense (Hemsl.) Sarg. Forests. 2019; 10 (5):441.
Chicago/Turabian StyleZhonghua Tu; Ziyuan Hao; Weiping Zhong; Huogen Li. 2019. "Identification of Suitable Reference Genes for RT-qPCR Assays in Liriodendron chinense (Hemsl.) Sarg." Forests 10, no. 5: 441.
Liriodendron is a genus of Magnoliaceae, which consists of two relict species, Liriodendron chinense and L. tulipifera. Although the morphologies are highly similar, the two species exhibit different adaptive capacity. Dehydrins (DHNs) are abiotic stresses resistant proteins in planta, which are associated with adaptive evolution. To better understand the evolution divergence between L. chinense and L. tulipifera and how DHN genes are associated with adaptation evolution, we firstly investigated the DNA polymorphisms of the LcDHN-like gene in 21 L. chinense and 6 L. tulipifera populations. A 707 bp LcDHN-like gene was cloned, which included a 477 bp open reading frame (ORF) and coding 158 amino acids. 311 LcDHN-like gDNA sequences were obtained from 70 L. chinense and 35 L. tulipifera individuals. The AMOVA and phylogenetic relationship analysis showed significant differences between the two species. A higher genetic diversity was observed in L. tulipifera compared to L. chinense, in consistent with the higher adaptive capacity of L. tulipifera. Our data also suggested that the LcDHN-like genes’ polymorphisms were under neutral mutation and purifying selection model in the L. chinense and L. tulipifera populations, respectively. The distinct expanding range and rate between the two species, haplotypes shared only in L.chinense’s nearby populations, and wide dispersals in L. tulipifera could contribute to the obscure east-west separation in L. chinense and entirely unordered phylogeny in L. tulipifera. The completely separated nonsynonymous substitution at position 875 and the higher range scope of aliphatic index in L. tulipifera populations may be related with its higher adaptive capacity. Taken together, our study suggests LcDHN-like gene is a potential mark gene responsible for adaptive evolution divergence in Liriodendron. Significant differences and completely distinct haplogroups between L. chinense and L. tulipifera showed that the two species have evolved into different directions. The more widely distribution, earlier haplogroups divergence events, and richer SNPs variations in L. tulipifera could imply its stronger adaptation in this species. And potential effect of the allelic variations in LcDHN-like gene may reflect the difference of water stress and chill tolerance between L. chinense and L. tulipifera, which could provide some information for further adaption evolution studies of Liriodendron.
Yanli Cheng; Huogen Li. Interspecies evolutionary divergence in Liriodendron, evidence from the nucleotide variations of LcDHN-like gene. BMC Evolutionary Biology 2018, 18, 195 .
AMA StyleYanli Cheng, Huogen Li. Interspecies evolutionary divergence in Liriodendron, evidence from the nucleotide variations of LcDHN-like gene. BMC Evolutionary Biology. 2018; 18 (1):195.
Chicago/Turabian StyleYanli Cheng; Huogen Li. 2018. "Interspecies evolutionary divergence in Liriodendron, evidence from the nucleotide variations of LcDHN-like gene." BMC Evolutionary Biology 18, no. 1: 195.
The leaf, a photosynthetic organ that plays an indispensable role in plant development and growth, has a certain ability to adapt to the environment and exhibits tremendous diversity among angiosperms. Liriodendron chinense, an ancestral angiosperm species, is very popular in landscaping. The leaf of this species has two lobes and resembles a Qing Dynasty Chinese robe; thus, leaf shape is the most valuable ornamental trait of the tree. In this work, to determine the candidate genes associated with leaf development in L. chinense, scanning electron microscopy (SEM) was employed to distinguish the developmental stages of tender leaves. Four stages were clearly separated, and transcriptome sequencing was performed for two special leaf stages. Altogether, there were 48.23 G clean reads in the libraries of the two leaf developmental stages, and 48,107 assembled unigenes were annotated with five databases. Among four libraries, 3118 differentially expressed genes (DEGs) were enriched in expression profiles. We selected ten DEGs associated with leaf development and validated their expression patterns via quantitative real-time PCR (qRT-PCR) assays. Most validation results were closely correlated with the RNA-sequencing data. Taken together, we examined the dynamic process of leaf development and indicated that several transcription factors and phytohormone metabolism genes may participate in leaf shape development. The transcriptome data analysis presented in this work aims to provide basic insights into the mechanisms mediating leaf development, and the results serve as a reference for the genetic breeding of ornamental traits in L. chinense.
Jikai Ma; Lingmin Wei; Jiayu Li; Huogen Li. The Analysis of Genes and Phytohormone Metabolic Pathways Associated with Leaf Shape Development in Liriodendron chinense via De Novo Transcriptome Sequencing. Genes 2018, 9, 577 .
AMA StyleJikai Ma, Lingmin Wei, Jiayu Li, Huogen Li. The Analysis of Genes and Phytohormone Metabolic Pathways Associated with Leaf Shape Development in Liriodendron chinense via De Novo Transcriptome Sequencing. Genes. 2018; 9 (12):577.
Chicago/Turabian StyleJikai Ma; Lingmin Wei; Jiayu Li; Huogen Li. 2018. "The Analysis of Genes and Phytohormone Metabolic Pathways Associated with Leaf Shape Development in Liriodendron chinense via De Novo Transcriptome Sequencing." Genes 9, no. 12: 577.
Houpoëa officinalis is a traditional Chinese medical plant, which has significantly declined in the past decades because of human influence and habitat fragmentation. Twelve expressed sequence tag SSR (EST-SSR) markers developed from the EST sequence of H. officinalis were used to analyse the genetic diversity and structure of fourteen natural populations. The results indicated that moderate genetic diversity and high genetic differentiation existed in this plant (Ho = 0.600, Fst = 0.327). STRUCTURE and UPGMA analyses showed that H. officinalis populations could be divided into 3 different groups, and the west group had higher genetic diversity than the central and east groups. The historical migration rates among the groups were low and unsymmetrical, and there was no significant correlation between Nei’s genetic distance and geographic distance. According to the genetic consequences, conservation strategies (in situ or ex situ, artificial pollination) should be carried out in all populations to preserve genetic diversity.
Xu Yang; Zhiling Yang; Huogen Li. Genetic Diversity, Population Genetic Structure and Protection Strategies for Houpoëa officinalis (Magnoliaceae), an Endangered Chinese Medical Plant. Journal of Plant Biology 2018, 61, 159 -168.
AMA StyleXu Yang, Zhiling Yang, Huogen Li. Genetic Diversity, Population Genetic Structure and Protection Strategies for Houpoëa officinalis (Magnoliaceae), an Endangered Chinese Medical Plant. Journal of Plant Biology. 2018; 61 (3):159-168.
Chicago/Turabian StyleXu Yang; Zhiling Yang; Huogen Li. 2018. "Genetic Diversity, Population Genetic Structure and Protection Strategies for Houpoëa officinalis (Magnoliaceae), an Endangered Chinese Medical Plant." Journal of Plant Biology 61, no. 3: 159-168.