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Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinale trihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.
Yan Tong; Hui Huang; Yuhua Wang. Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale. Sustainability 2021, 13, 2826 .
AMA StyleYan Tong, Hui Huang, Yuhua Wang. Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale. Sustainability. 2021; 13 (5):2826.
Chicago/Turabian StyleYan Tong; Hui Huang; Yuhua Wang. 2021. "Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale." Sustainability 13, no. 5: 2826.
Akebia trifoliata subsp. australis is a well-known medicinal and potential woody oil plant in China. The limited genetic information available for A. trifoliata subsp. australis has hindered its exploitation. Here, a high-quality chromosome-level genome sequence of A. trifoliata subsp. australis is reported. The de novo genome assembly of 682.14 Mb was generated with a scaffold N50 of 43.11 Mb. The genome includes 25,598 protein-coding genes, and 71.18% (485.55 Mb) of the assembled sequences were identified as repetitive sequences. An ongoing massive burst of long terminal repeat (LTR) insertions, which occurred ~1.0 million years ago, has contributed a large proportion of LTRs in the genome of A. trifoliata subsp. australis. Phylogenetic analysis shows that A. trifoliata subsp. australis is closely related to Aquilegia coerulea and forms a clade with Papaver somniferum and Nelumbo nucifera, which supports the well-established hypothesis of a close relationship between basal eudicot species. The expansion of UDP-glucoronosyl and UDP-glucosyl transferase gene families and β-amyrin synthase-like genes and the exclusive contraction of terpene synthase gene families may be responsible for the abundant oleanane-type triterpenoids in A. trifoliata subsp. australis. Furthermore, the acyl-ACP desaturase gene family, including 12 stearoyl-acyl-carrier protein desaturase (SAD) genes, has expanded exclusively. A combined transcriptome and fatty-acid analysis of seeds at five developmental stages revealed that homologs of SADs, acyl-lipid desaturase omega fatty acid desaturases (FADs), and oleosins were highly expressed, consistent with the rapid increase in the content of fatty acids, especially unsaturated fatty acids. The genomic sequences of A. trifoliata subsp. australis will be a valuable resource for comparative genomic analyses and molecular breeding.
Hui Huang; Juan Liang; Qi Tan; Linfeng Ou; Xiaolin Li; Caihong Zhong; Huilin Huang; Ian Max Møller; Xianjin Wu; Songquan Song. Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis. Horticulture Research 2021, 8, 1 -15.
AMA StyleHui Huang, Juan Liang, Qi Tan, Linfeng Ou, Xiaolin Li, Caihong Zhong, Huilin Huang, Ian Max Møller, Xianjin Wu, Songquan Song. Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis. Horticulture Research. 2021; 8 (1):1-15.
Chicago/Turabian StyleHui Huang; Juan Liang; Qi Tan; Linfeng Ou; Xiaolin Li; Caihong Zhong; Huilin Huang; Ian Max Møller; Xianjin Wu; Songquan Song. 2021. "Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis." Horticulture Research 8, no. 1: 1-15.
Dendrobium catenatum is a member of epiphytic orchids with extensive range of pharmacological properties and ornamental values. Superoxide dismutase (SOD), a key member of antioxidant system, plays a vital role in protecting plants against oxidative damage caused by various biotic and abiotic stresses. So far, little is known about the SOD gene family in D. catenatum. In this study, eight SOD genes, including four Cu/ZnSODs, three FeSODs and one MnSOD, were identified in D. catenatum genome. Phylogenetic analyses of SOD proteins in D. catenatum and several other species revealed that these SOD proteins can be assigned to three subfamilies based on their metal co-factors. Moreover, the similarities in conserved motifs and gene structures in the same subfamily corroborated their classification and inferred evolutionary relationships. There were many hormone and stress response elements in DcaSODs, of which light responsiveness elements was the largest group. All DcaSODs displayed tissue-specific expression patterns and exhibited abundant expression levels in flower and leaf. According to public RNA-seq data and qRT-PCR analysis showed that the almost DcaSODs, except for DcaFSD2, were highly expressed under cold and drought treatments. Under heat, light, and salt stresses, DcaCSD1, DcaCSD2, DcaCSD3 were always significantly up-regulated, which may play a vital role in coping with various stresses. The expression levels of DcaFSD1 and DcaFSD2 were promoted by high light, suggesting their important roles in light response. These findings provided valuable information for further research on DcaSODs in D. catenatum.
Hui Huang; Hui Wang; Yan Tong; Yuhua Wang. Insights into the Superoxide Dismutase Gene Family and Its Roles in Dendrobium catenatum under Abiotic Stresses. Plants 2020, 9, 1452 .
AMA StyleHui Huang, Hui Wang, Yan Tong, Yuhua Wang. Insights into the Superoxide Dismutase Gene Family and Its Roles in Dendrobium catenatum under Abiotic Stresses. Plants. 2020; 9 (11):1452.
Chicago/Turabian StyleHui Huang; Hui Wang; Yan Tong; Yuhua Wang. 2020. "Insights into the Superoxide Dismutase Gene Family and Its Roles in Dendrobium catenatum under Abiotic Stresses." Plants 9, no. 11: 1452.
Akebia trifoliata subsp. australis (Diels) T.Shimizu is a medicinal plant in China. Here, the complete chloroplast (cp) genome sequence of A. trifoliata subsp. australis was assembled and characterized as a resource for future genetic studies. The whole cp genome was 157,952 bp in length, containing of a large single-copy (LSC) region of 86,596 bp, a small single-copy (SSC) region of 19,060 bp, and two inverted repeat (IR) regions of 26,148 bp. The new sequence possessed total 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The nucleotide composition was asymmetric (30.3% A, 19.7% C, 19.0% G and 31.0% T) with an overall GC content of 38.7%. The maximum likelihood phylogenetic analysis based on 10 cp genomes indicated that A. trifoliata subsp. australis was closely related to Akebia trifoliata subsp. trifoliata. However, Akebia quinata was closely related to Stauntonia obovatifoliola.
Aqiao Yu; Qi Tan; Jing Chen; Hui Huang. The complete chloroplast genome of Akebia trifoliata subsp. australis (Lardizabalaceae), a medicinal plant in China. Mitochondrial DNA Part B 2020, 5, 3333 -3334.
AMA StyleAqiao Yu, Qi Tan, Jing Chen, Hui Huang. The complete chloroplast genome of Akebia trifoliata subsp. australis (Lardizabalaceae), a medicinal plant in China. Mitochondrial DNA Part B. 2020; 5 (3):3333-3334.
Chicago/Turabian StyleAqiao Yu; Qi Tan; Jing Chen; Hui Huang. 2020. "The complete chloroplast genome of Akebia trifoliata subsp. australis (Lardizabalaceae), a medicinal plant in China." Mitochondrial DNA Part B 5, no. 3: 3333-3334.
Aquilegia barnebyi, belonging to the genus Aquilegia (Ranunculaceae), is a member of basal eudicot species. In this study, we obtained the complete chloroplast (cp) genome of A. barnebyi. The genome size is 161,954 bp with a GC content of 38.98%. A total of 113 unique genes including 79 protein-coding genes, 30 tRNA genes, four rRNA genes were annotated. The large single-copy region and small single-copy region contains 91,250 bp and 17,359 bp, respectively. The inverted repeat regions are 26,671 bp in length. The phyologenetic analysis indicated that A. barnebyi had a close relationship with A. coerulea. And four species in genus Aquilegia formed a monophyletic group with high support value. The availability of A. barnebyi cp genomic resources will greatly helpful for taxonomy, phylogeny and conservation genetic studies of basal eudicot specie.
Hui Huang. The complete chloroplast genome of Aquilegia barnebyi, a basal eudicot species. Mitochondrial DNA Part B 2020, 5, 1060 -1061.
AMA StyleHui Huang. The complete chloroplast genome of Aquilegia barnebyi, a basal eudicot species. Mitochondrial DNA Part B. 2020; 5 (1):1060-1061.
Chicago/Turabian StyleHui Huang. 2020. "The complete chloroplast genome of Aquilegia barnebyi, a basal eudicot species." Mitochondrial DNA Part B 5, no. 1: 1060-1061.
The complete chloroplast genome sequence of Aquilegia rockii was assembled and characterized as a resource for future genetic studies. With a total length of 162,123 bp, the chloroplast genome comprised of a large single-copy (LSC) region of 91,337 bp, a small single-copy (SSC) region of 17,376 bp, and 2 inverted repeat (IR) regions of 26,705 bp. A total of 117 unique genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 32 tRNA genes. The maximum likelihood phylogenetic analysis based on 18 cp genomes indicated that A. rockii is sister to the clade formed by Semiaquilegia adoxoides and Urophysa rockii.
Fei Yu; Yu-Chen Zhao; Hui Huang. The complete chloroplast genome of aquilegia rockii, an endemic herb plant in Western China. Mitochondrial DNA Part B 2019, 4, 1737 -1738.
AMA StyleFei Yu, Yu-Chen Zhao, Hui Huang. The complete chloroplast genome of aquilegia rockii, an endemic herb plant in Western China. Mitochondrial DNA Part B. 2019; 4 (1):1737-1738.
Chicago/Turabian StyleFei Yu; Yu-Chen Zhao; Hui Huang. 2019. "The complete chloroplast genome of aquilegia rockii, an endemic herb plant in Western China." Mitochondrial DNA Part B 4, no. 1: 1737-1738.
Tea-specialized metabolites contribute to rich flavors and healthy function of tea. Their accumulation patterns and underlying regulatory mechanism are significantly different under different nitrogen (N) conditions during adaptation stage. Here, we find that flavonoids associated with tea flavor are dominated by different metabolic and transcriptional responses among the four N conditions (N-deficiency, nitrate, ammonia, and nitric oxide). Nitrogen-deficiency tea plants accumulate diverse flavonoids, corresponding with higher expression of hub genes including F3H, FNS, UFGT, bHLH35, and bHLH36. Compared with N-deficiency, N-supply tea plants significantly increase proline, glutamine, and theanine, which are also associated with tea flavor, especially under NH4+-supply. As NH4+-tolerant species, tea plant exploits the adaptive strategy by substantial accumulation of amino acids including theanine to adapt excess NH4+, which attributes to, at least in part, efficient N transport and assimilation, and active protein degradation. A distinct divergence of N reallocation in young shoots of tea plant under different N sources contributes to diverse tea flavor.
Hui Huang; Qiuyang Yao; Enhua Xia; Lizhi Gao. Metabolomics and Transcriptomics Analyses Reveal Nitrogen Influences on the Accumulation of Flavonoids and Amino Acids in Young Shoots of Tea Plant (Camellia sinensis L.) Associated with Tea Flavor. Journal of Agricultural and Food Chemistry 2018, 66, 9828 -9838.
AMA StyleHui Huang, Qiuyang Yao, Enhua Xia, Lizhi Gao. Metabolomics and Transcriptomics Analyses Reveal Nitrogen Influences on the Accumulation of Flavonoids and Amino Acids in Young Shoots of Tea Plant (Camellia sinensis L.) Associated with Tea Flavor. Journal of Agricultural and Food Chemistry. 2018; 66 (37):9828-9838.
Chicago/Turabian StyleHui Huang; Qiuyang Yao; Enhua Xia; Lizhi Gao. 2018. "Metabolomics and Transcriptomics Analyses Reveal Nitrogen Influences on the Accumulation of Flavonoids and Amino Acids in Young Shoots of Tea Plant (Camellia sinensis L.) Associated with Tea Flavor." Journal of Agricultural and Food Chemistry 66, no. 37: 9828-9838.
Camellia taliensis is one of the most important wild relatives of cultivated tea tree, C. sinensis. The species extensively occupies mountainous habitats representing a wide-range abiotic tolerance and biotic resistance and thus harbors valuable gene resources that may greatly benefit genetic improvement of cultivated tea tree. However, owning to a large genome size of ~3 Gb and structurally complex genome, there are fairly limited genetic information and particularly few genomic resources publicly available for this species. To better understand the key pathways determining tea flavor and enhance tea tree breeding programs, we performed a high-throughput transcriptome sequencing for C. taliensis. In this study, approximate 241.5 million high-quality paired-end reads, accounting for ~24 Gb of sequence data, were generated from tender shoots, young leaves, flower buds and flowers using Illumina HiSeq 2000 platform. De novo assembly with further processing and filtering yielded a set of 67,923 transcripts with an average length of 685 bp and an N50 of 995 bp. Based on sequence similarity searches against public databases, a total of 39,475 transcripts were annotated with gene descriptions, conserved protein domains or gene ontology (GO) terms. Candidate genes for major metabolic pathways involved in tea quality were identified and experimentally validated using RT-qPCR. Further gene expression profiles showed that they are differentially regulated at different developmental stages. To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species. Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis. We reported the first large-coverage transcriptome datasets for C. taliensis using the next-generation sequencing technology. Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future.
Hai-Bin Zhang; En-Hua Xia; Hui Huang; Jian-Jun Jiang; Ben-Ying Liu; Li-Zhi Gao. De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response. BMC Genomics 2015, 16, 1 -14.
AMA StyleHai-Bin Zhang, En-Hua Xia, Hui Huang, Jian-Jun Jiang, Ben-Ying Liu, Li-Zhi Gao. De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response. BMC Genomics. 2015; 16 (1):1-14.
Chicago/Turabian StyleHai-Bin Zhang; En-Hua Xia; Hui Huang; Jian-Jun Jiang; Ben-Ying Liu; Li-Zhi Gao. 2015. "De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response." BMC Genomics 16, no. 1: 1-14.
Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species. The eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences. Despite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang’s taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia.
Hui Huang; Chao Shi; Yuan Liu; Shu-Yan Mao; Li-Zhi Gao. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evolutionary Biology 2014, 14, 151 -151.
AMA StyleHui Huang, Chao Shi, Yuan Liu, Shu-Yan Mao, Li-Zhi Gao. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evolutionary Biology. 2014; 14 (1):151-151.
Chicago/Turabian StyleHui Huang; Chao Shi; Yuan Liu; Shu-Yan Mao; Li-Zhi Gao. 2014. "Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships." BMC Evolutionary Biology 14, no. 1: 151-151.