Background: Saposhnikovia divaricata (Turcz.) Schischk. is a perennial herb whose dried roots are commonly used as a source of traditional medicines. To elucidate the organelle-genome-based phylogeny of Saposhnikovia species and the transfer of DNA between organelle genomes, we sequenced and characterised the mitochondrial genome (mitogenome) of S. divaricata. Results: The mitogenome of S. divaricata is a circular molecule of 293,897 bp. The nucleotide composition of the mitogenome is as follows: A, 27.73%; T, 27.03%; C, 22.39%; and G, 22.85. The entire gene content is 45.24%. A total of 31 protein-coding genes, 20 tRNAs and 4 rRNAs, including one pseudogene (rpl16), were annotated in the mitogenome. Phylogenetic analysis of the organelle genomes from S. divaricata and 10 related species produced congruent phylogenetic trees. Selection pressure analysis revealed that most of the mitochondrial genes of related species are highly conserved. Moreover, 2 and 46 RNA-editing sites were found in the chloroplast genome (cpgenome) and mitogenome protein-coding regions, respectively. Finally, a comparison of the cpgenome and the mitogenome assembled from the same dataset revealed 10 mitochondrial DNA fragments with sequences similar to those in the repeat regions of the cpgenome, suggesting that the repeat regions might be transferred into the mitogenome. Conclusions: In this study, we assembled and annotated the mitogenome of S. divaricata. This study provides valuable information on the taxonomic classification and molecular evolution of members of the family Apiaceae.

Background: Sugarcane (Saccharum officinarum) is one of the most valuable feedstocks for sugar production. In addition to the production of industrial raw materials such as alcohol, papermaking, the fiber of livestock feed, respectively, sugarcane can produce bioactive compounds such as anthocyanins. Elucidation of the anthocyanin biosynthesis pathway is critical for the molecular breeding of sugarcane varieties with favorable traits. We aimed to identify candidate genes involved in anthocyanin biosynthesis by transcriptomic and metabolomic analyses. Results: Three varieties of sugarcane displaying different colors were used in this study: FN15 (greed rind), ROC22 (red rind), and Badila (purple rind). Sample materials were subjected to metabolomic analysis using UPLC-Q-TOF/MS and RNA-seq analysis. The metabolomic profiling results showed Cyanidin, Cyanidin (6’-malonylglucoside), Cyanidin O-glucoside, and Peonidin O-glucoside were the main components responsible for the rind color. Then, through RNA-seq analysis, we identified a total of 3137, 3302, 3014 differentially expressed genes (DEGs) between the rind and pith tissues for the corresponding varieties Badila rind, ROC22, and FN15. We then compared the expression levels of genes among the rind tissues from the three varieties. We identified 2901, 2821, and 3071 DEGs between Badila rind vs. ROC22 rind, Badila rind vs. FN15 rind, ROC22 rind vs. FN15 rind, respectively. We identified two enriched pathways, including phenylpropanoid biosynthesis and flavonoid biosynthesis. Sequencing similarity search identified a total of 50 unigenes belonging to 15 enzyme families as putative genes involved in anthocyanin biosynthesis in sugarcane rind. Seven of them were identified as candidate genes related to anthocyanin biosynthesis in the rind of sugarcane through co-localization analysis with the anthocyanin content in sugarcane. In total, 25 unigenes were selected and subjected to RT-qPCR analysis, and qRT-PCR results were consistent with those obtained with the RNA-Seq experiments. Conclusions: We proposed a pathway for anthocyanin biosynthesis in sugarcane rind. This is the first report on the biosynthesis of anthocyanin in sugarcane using the combined transcriptomic and metabolomic methods. The results obtained from this study will lay the foundation for breeding purple pith sugarcane varieties with high anthocyanin contents.

Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.

Sugarcane yellow leaf disease severely affects sugarcane production. As a viral disease, the pathogen sugarcane yellow leaf virus can only be transmitted by aphid vectors rather than mechanical means. To understand the sugarcane responses to ScYLV infection, the corresponding transcriptomic profile of ScYLV-infected and ScYLV-free plants were analyzed with RNA-Seq technology. In this study, Melanaphis sacchari was used as the vector to transmit ScYLV to the susceptible sugarcane cultivar CP72-1210 and transcriptome was sequenced as well as differentially expressed genes between disease-infected and non-infected sugarcane plants were investigated. A total of 1,22,593 genes were assembled, of which 1,630 genes were differentially expressed. Among DEGs, 1,622 were upregulated and eight were downregulated that were further annotated with GO, KEGG, KOG, PFAM, SwissProt, and Nr databases. The expression levels of DEGs in the three KEGG pathways, namely endocytosis, PEX protein synthesis, and endoplasmic reticulum stress response to viral protein synthesis were observed. Interestingly, it was found that the yellow leaf virus could induce the formation of autophagosomes by LC3, promoted by ER stress, and may be related to the replication of viral RNA. We tested 63 DEGs in this research. The qRT-PCR results showed that two were downregulated and 45 were upregulated in response to the ScYLV infection. This study will not only offer an overall comprehension of sugarcane responses to ScYLV infection at the gene expression level but also increase the chances to block the transmission of ScYLV for use in further molecular biology techniques and will aid in increasing the resistance of plants against ScYLV.

Codonopsis pilosulasubsp.tangshenis one of the most important medicinal herbs used in traditional Chinese medicine. Correct identification of materials fromC.pilosulasubsp.tangshenis critical to ensure the efficacy and safety of the associated medicines. Traditional DNA molecular markers could distinguishCodonopsisspecies well, so we need to develop super or specific molecular markers. In this study, we reported the plastome ofCodonopsis pilosulasubsp.tangshen(Oliv.) D.Y. Hong conducted phylogenomic and comparative analyses in theCodonopsisgenus for the first time. The entire length of theCodonopsis pilosulasubsp.tangshenplastome was 170,672 bp. There were 108 genes in the plastome, including 76 protein-coding genes, 28 transfer RNA (tRNA), and four ribosomal RNA (rRNA) genes. Comparative analysis indicated thatCodonopsis pilosulasubsp.tangshenhad an unusual large inversion in the large single-copy (LSC) region compared with the other threeCodonopsisspecies. And there were two dispersed repeat sequences at both ends of the inverted regions, which might mediate the generation of this inversion. We found five hypervariable regions among the fourCodonopsisspecies. PCR amplification and Sanger sequencing experiments demonstrated that two hypervariable regions could distinguish three medicinalCodonopsisspecies. Results obtained from this study will support taxonomic classification, discrimination, and molecular evolutionary studies ofCodonopsisspecies.