R V Sreedhar, Kumari Priya, Rupwate Sunny D, Rajasekharan Ram, Srinivasan Malathi
CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore-560 065, Karnataka, India.
CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore-560 065, Karnataka, India; Academy of Scientific and Innovative Research, CSIR, New Delhi-110 025, India.
PLoS One. 2015 Apr 13;10(4):e0123580. doi: 10.1371/journal.pone.0123580. eCollection 2015.
Chia (Salvia hispanica L.), a member of the mint family (Lamiaceae), is a rediscovered crop with great importance in health and nutrition and is also the highest known terrestrial plant source of heart-healthy omega-3 fatty acid, alpha linolenic acid (ALA). At present, there is no public genomic information or database available for this crop, hindering research on its genetic improvement through genomics-assisted breeding programs. The first comprehensive analysis of the global transcriptome profile of developing Salvia hispanica L. seeds, with special reference to lipid biosynthesis is presented in this study. RNA from five different stages of seed development was extracted and sequenced separately using the Illumina GAIIx platform. De novo assembly of processed reads in the pooled transcriptome using Trinity yielded 76,014 transcripts. The total transcript length was 66,944,462 bases (66.9 Mb), with an average length of approximately 880 bases. In the molecular functions category of Gene Ontology (GO) terms, ATP binding and nucleotide binding were found to be the most abundant and in the biological processes category, the metabolic process and the regulation of transcription-DNA-dependent and oxidation-reduction process were abundant. From the EuKaryotic Orthologous Groups of proteins (KOG) classification, the major category was "Metabolism" (31.97%), of which the most prominent class was 'carbohydrate metabolism and transport' (5.81% of total KOG classifications) followed by 'secondary metabolite biosynthesis transport and catabolism' (5.34%) and 'lipid metabolism' (4.57%). A majority of the candidate genes involved in lipid biosynthesis and oil accumulation were identified. Furthermore, 5596 simple sequence repeats (SSRs) were identified. The transcriptome data was further validated through confirmative PCR and qRT-PCR for select lipid genes. Our study provides insight into the complex transcriptome and will contribute to further genome-wide research and understanding of chia. The identified novel UniGenes will facilitate gene discovery and creation of genomic resource for this crop.
奇亚籽（Salvia hispanica L.）是薄荷科（唇形科）的一员，是一种重新被发现的作物，在健康和营养方面具有重要意义，也是已知的对心脏有益的ω-3脂肪酸——α-亚麻酸（ALA）的最高陆地植物来源。目前，这种作物没有公开的基因组信息或数据库，这阻碍了通过基因组辅助育种计划对其进行遗传改良的研究。本研究首次对发育中的Salvia hispanica L.种子的全球转录组图谱进行了全面分析，特别关注脂质生物合成。从种子发育的五个不同阶段提取RNA，并使用Illumina GAIIx平台分别进行测序。使用Trinity对合并转录组中的处理后读数进行从头组装，产生了76,014个转录本。转录本总长度为66,944,462个碱基（66.9 Mb），平均长度约为880个碱基。在基因本体论（GO）术语的分子功能类别中，发现ATP结合和核苷酸结合最为丰富；在生物过程类别中，代谢过程以及转录 - DNA依赖性调节和氧化还原过程较为丰富。从真核生物直系同源蛋白组（KOG）分类来看，主要类别是“代谢”（31.97%），其中最突出的类别是“碳水化合物代谢和运输”（占总KOG分类的5.81%），其次是“次生代谢物生物合成、运输和分解代谢”（5.34%）和“脂质代谢”（4.57%）。鉴定出了大多数参与脂质生物合成和油脂积累的候选基因。此外，还鉴定出了5596个简单序列重复（SSR）。通过对选定脂质基因进行验证性PCR和qRT-PCR，进一步验证了转录组数据。我们的研究为复杂的转录组提供了见解，并将有助于对奇亚籽进行进一步的全基因组研究和理解。所鉴定的新型单基因将有助于该作物的基因发现和基因组资源的创建。
