Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis
Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis
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使用 RNA-seq 鉴定两种甘薯基因型的基因并利用挖掘分析类胡萝卜素生物合成
DOI：
10.1016/j.sajb.2017.01.003
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发表时间：
2017-03
影响因子：
3.1
通讯作者：
Liming Zhang
中科院分区：
文献类型：
--
作者：
Zhen Qin;Aixian Li;Fuyun Hou;Qingmei Wang;Shunxu Dong;Liming Zhang
甘薯是淀粉和胡萝卜素含量高的重要粮食作物。然而，关于这些作物的分子生物学研究是有限的。本文选取两个甘薯品种（正薯20号和罗薯8号）进行转录组分析。在田间条件下，使用带有PE125的Illumina Hiseq 2500平台对这些甘薯（块茎根、茎和叶）进行从头RNA测序。测序结果约为34.4 G核苷酸碱基。组装后，鉴定出176,167个转录本和109,401个统一基因。使用不同的数据库对41,729个（Nr）、21,004个（Nt）、12,524个（KO）、29,444个（SwissProt）、30,212个（PFAM）、31,304个（GO）和14,349个（KOG）序列进行了功能注释，共鉴定出47,749个注释序列。简单重复序列（SSRs）分析在8334个单基因上发现了9549个SSR位点。KEGG分析发现55个和78个基因分别参与类胡萝卜素和萜类主干生物合成途径。其中，正树20号和罗树8号分别有20个和10个差异表达基因。通过qRT-PCR验证了8个差异表达的unique基因。因此，我们准备并分析了两个甘薯品种的转录组数据，因为之前的基因组信息有限。这一新的序列信息将提高对这一重要健康作物的现有认识，并为进一步的生物学研究提供有价值的见解。
Sweetpotatoes are important food crops with high starch and high carotene content. However, studies concerning the molecular biology of these crops are limited. In this paper, we selected two varieties of sweetpotato (Zhengshu 20 and Luoxushu 8) for transcriptome analysis. De novo RNA sequencing of these sweetpotatoes (tuberous roots, stems and leaves) under field conditions was performed using an Illumina Hiseq 2500 platform with PE125. Approximately 34.4 G nucleotide bases were sequenced. Following assembly, 176,167 transcripts and 109,401 unigenes were identified. 41,729 (Nr), 21,004 (Nt), 12,524 (KO), 29,444 (SwissProt), 30,212 (PFAM), 31,304 (GO), and 14,349 (KOG) unigenes were functionally annotated using different databases, and a total of 47,749 annotated sequences were identified. Simple sequence repeats (SSRs) analyses revealed 9549 SSR loci on the 8334 unigenes. The KEGG analysis uncovered 55 and 78 unigenes involved in the carotenoid and terpenoid backbone biosynthesis pathways, respectively. Among these genes, 20 and 10 differentially expressed unigenes were observed in the Zhengshu 20 and Luoxushu 8, respectively. Eight differentially expressed unigenes were validated by qRT-PCR. Thus, we prepared and analyzed the transcriptome data of the two sweetpotato varieties, for which prior genomic information was limited. This new sequence information will improve the current knowledge in this important and healthy crop and provide valuable insight for further biological research.
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