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Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens.

ABSTRACT: Viola is a large genus with worldwide distribution and many traits not currently exemplified in model plants including unique breeding systems and the production of cyclotides. Here we report de novo genome assembly and transcriptomic analyses of the non-model species Viola pubescens using short-read DNA sequencing data and RNA-Seq from eight diverse tissues. First, V. pubescens genome size was estimated through flow cytometry, resulting in an approximate haploid genome of 455 Mbp. Next, the draft V. pubescens genome was sequenced and assembled resulting in 264,035,065 read pairs and 161,038 contigs with an N50 length of 3,455 base pairs (bp). RNA-Seq data were then assembled into tissue-specific transcripts. Together, the DNA and transcript data generated 38,081 ab initio gene models which were functionally annotated based on homology to Arabidopsis thaliana genes and Pfam domains. Gene expression was visualized for each tissue via principal component analysis and hierarchical clustering, and gene co-expression analysis identified 20 modules of tissue-specific transcriptional networks. Some of these modules highlight genetic differences between chasmogamous and cleistogamous flowers and may provide insight into V. pubescens' mixed breeding system. Orthologous clustering with the proteomes of A. thaliana and Populus trichocarpa revealed 8,531 sequences unique to V. pubescens, including 81 novel cyclotide precursor sequences. Cyclotides are plant peptides characterized by a stable, cyclic cystine knot motif, making them strong candidates for drug scaffolding and protein engineering. Analysis of the RNA-Seq data for these cyclotide transcripts revealed diverse expression patterns both between transcripts and tissues. The diversity of these cyclotides was also highlighted in a maximum likelihood protein cladogram containing V. pubescens cyclotides and published cyclotide sequences from other Violaceae and Rubiaceae species. Collectively, this work provides the most comprehensive sequence resource for Viola, offers valuable transcriptomic insight into V. pubescens, and will facilitate future functional genomics research in Viola and other diverse plant groups.

SUBMITTER: Sternberger AL

PROVIDER: S-EPMC6384259 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens.

Sternberger Anne L AL Bowman Megan J MJ Kruse Colin P S CPS Childs Kevin L KL Ballard Harvey E HE Wyatt Sarah E SE

Frontiers in plant science 20190215

Viola is a large genus with worldwide distribution and many traits not currently exemplified in model plants including unique breeding systems and the production of cyclotides. Here we report de novo genome assembly and transcriptomic analyses of the non-model species Viola pubescens using short-read DNA sequencing data and RNA-Seq from eight diverse tissues. First, V. pubescens genome size was estimated through flow cytometry, resulting in an approximate haploid geno ...[more]

PMID: 30828342

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Project description:The liver is the center for uptake, synthesis, packaging, and secretion of lipids and lipoproteins. The research on lipid metabolism in pigs is limited. The objective of the present study is to identify the genes related to lipid metabolism and oxidative stress in pigs by using transcriptomic analysis. Liver segments were collected from 60 Jinhua pigs for the determination of liver lipid content. The 7 pigs with the highest and lowest liver lipid content were set as group H and group L, respectively. Liver segments and serum samples were collected from each pig of the H and L groups for RNA sequencing and the determination of triglycerides (TG) content and high-density lipoprotein cholesterol (HDL) content, respectively. The HDL content in the serum of pigs in the H group was significantly higher than the L group (P < 0.05). From transcriptomic sequencing, 6162 differentially expressed genes (DEGs) were identified, among which 2962 were upregulated and 3200 downregulated genes with the increase in the liver content of Jinhua pigs. After GO enrichment and KEGG analyses, lipid modification, cellular lipid metabolic process, cholesterol biosynthetic process, fatty acid metabolic process, oxidoreduction coenzyme metabolic process, oxidoreductase activity, acting on CH-OH group of donors, response to oxidative stress, nonalcoholic fatty liver disease (NAFLD), sphingolipid metabolism, and oxidative phosphorylation pathways were involved in lipid metabolism and oxidative stress in Jinhua pigs. For further validation, we selected 10 DEGs including 7 upregulated genes (APOE, APOA1, APOC3, LCAT, CYP2E1, GPX1, and ROMO1) and 4 downregulated genes (PPARA, PPARGC1A, and TXNIP) for RT-qPCR verification. To validate these results in other pig species, we analyzed these 10 DEGs in the liver of Duroc×Landrace×Yorkshire pigs. Similar expression patterns of these 10 DEGs were observed. These data would provide an insight to understand the gene functions regulating lipid metabolism and oxidative stress and would potentially provide theoretical basis for the development of strategies to modulate lipid metabolism and even control human diabetes and obesity by gene regulations.

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Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens.

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Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in <i>Viola pubescens</i>.

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