Jung Won Yong, Lee Sang Sook, Kim Chul Wook, Kim Hyun-Soon, Min Sung Ran, Moon Jae Sun, Kwon Suk-Yoon, Jeon Jae-Heung, Cho Hye Sun
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea; Animal Material Engineering, Gyeongnam National University of Science and Technology, Jinju, Korea.
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
PLoS One. 2014 Nov 6;9(11):e111982. doi: 10.1371/journal.pone.0111982. eCollection 2014.
Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a source of fructans (inulin) for pharmaceutical applications in diabetes and obesity prevention. However, transcriptomic and genomic data for Jerusalem artichoke remain scarce. In this study, Illumina RNA sequencing (RNA-Seq) was performed on samples from Jerusalem artichoke leaves, roots, stems and two different tuber tissues (early and late tuber development). Data were used for de novo assembly and characterization of the transcriptome. In total 206,215,632 paired-end reads were generated. These were assembled into 66,322 loci with 272,548 transcripts. Loci were annotated by querying against the NCBI non-redundant, Phytozome and UniProt databases, and 40,215 loci were homologous to existing database sequences. Gene Ontology terms were assigned to 19,848 loci, 15,434 loci were matched to 25 Clusters of Eukaryotic Orthologous Groups classifications, and 11,844 loci were classified into 142 Kyoto Encyclopedia of Genes and Genomes pathways. The assembled loci also contained 10,778 potential simple sequence repeats. The newly assembled transcriptome was used to identify loci with tissue-specific differential expression patterns. In total, 670 loci exhibited tissue-specific expression, and a subset of these were confirmed using RT-PCR and qRT-PCR. Gene expression related to inulin biosynthesis in tuber tissue was also investigated. Exsiting genetic and genomic data for H. tuberosus are scarce. The sequence resources developed in this study will enable the analysis of thousands of transcripts and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke.
菊芋（Helianthus tuberosus L.）长期以来一直作为蔬菜种植，并且是用于预防糖尿病和肥胖症的医药用途中果聚糖（菊粉）的来源。然而，菊芋的转录组学和基因组数据仍然匮乏。在本研究中，对菊芋叶片、根、茎以及两种不同块茎组织（块茎早期和晚期发育阶段）的样本进行了Illumina RNA测序（RNA-Seq）。数据用于转录组的从头组装和表征。总共生成了206,215,632条双末端 reads。这些 reads 被组装成66,322个位点，包含272,548条转录本。通过与NCBI非冗余数据库、植物基因组数据库（Phytozome）和通用蛋白质数据库（UniProt）进行比对来注释位点，40,215个位点与现有数据库序列同源。基因本体论术语被分配到19,848个位点，15,434个位点与25个真核生物直系同源群分类相匹配，11,844个位点被分类到142条京都基因与基因组百科全书通路中。组装的位点还包含了一万零七百七十八个潜在的简单序列重复。新组装的转录组用于鉴定具有组织特异性差异表达模式的位点。总共670个位点表现出组织特异性表达，其中一部分通过逆转录聚合酶链反应（RT-PCR）和实时定量逆转录聚合酶链反应（qRT-PCR）得到了验证。还研究了块茎组织中与菊粉生物合成相关的基因表达。菊芋现有的遗传和基因组数据匮乏。本研究开发的序列资源将有助于对数千条转录本进行分析，从而加速菊芋的分子标记辅助育种研究以及菊粉生物合成的研究。
