Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis)
Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis)
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日本落叶松 (Larix leptolepis) 体细胞胚胎的转录组分析和计算机分析
DOI：
10.1007/s00299-012-1277-1
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发表时间：
2012-09-01
影响因子：
6.2
通讯作者：
Qi, Liwang
中科院分区：
文献类型：
--
作者：
Zhang, Yuan;Zhang, Shougong;Qi, Liwang
日本落叶松（Larix leptolepis）是重要的生态经济树种，主要分布在中国东北、日本和欧洲。然而，由于胚败育率高而导致开花不稳定和种质资源贫乏，阻碍了落叶松物种的育种。体细胞胚胎发生（SE）是生产L.在一些实施方案中，本发明涉及具有所需特性的鳞翅目昆虫，例如全能性的表达、合成种子的制备和遗传转化。然而，该物种的公共基因组资源有限。我们从454个测序的L. leptolepisomatic胚胎，产生572，403个高质量读数。这些读段被组装成70，927个独特序列（UniGenes），包括32，321个重叠群和38，606个单例。去除低质量序列后，使用UniProtKB程序注释了65，115个UniGenes。基于它们与已知蛋白质的序列相似性，来自664个物种的30，372个匹配序列估计代表大约19，000个独特基因。基因本体分析显示，21，324个UniGenes被分配到51个类别。通过京都基因百科全书和基因组作图，25，773个转录本与160个生化途径相关。进一步的分析筛选出4个信号转导途径代表的337酶和17个次生代谢产物。计算机模拟分析表明，落叶松中有207个UniESTs与其它模式植物中的MAPKs基因同源，可能参与了SE的调控。本研究为落叶松体细胞胚胎发生过程中的转录组研究提供了初步的信息，为今后的研究奠定了良好的基础。获得了超过59万条序列，并构建了深覆盖EST数据库。
Japanese larch (Larix leptolepis) is an ecologically and economically important species mainly grown in northeastern China, Japan and Europe. However, erratic flowering and poor germplasm resources caused by high embryo abortion rates have hampered breeding ofLarixspecies. Somatic embryogenesis (SE) is an effective tool for the production ofL. leptolepiswith desirable characteristics, such as expression of totipotency, preparation of synthetic seeds, and genetic transformation. However, public genomic resources for this species are limited. We sequenced 591,759 raw expressed sequence tags (ESTs) from a 454 sequencing cDNA library ofL. leptolepissomatic embryos, resulting in 572,403 high-quality reads. These reads were assembled into 70,927 unique sequences (UniGenes), including 32,321 contigs and 38,606 singletons. After removal of low-quality sequences, 65,115 UniGenes were annotated using the UniProtKB program. Based on their sequence similarity with known proteins, the matched 30,372 sequences from 664 species were estimated to represent approximately 19,000 unique genes. Gene ontology analysis revealed 21,324 UniGenes assigned to 51 categories. By Kyoto Encyclopedia of Genes and Genomes mapping, 25,773 transcripts were associated with 160 biochemical pathways. Further analysis screened four signal transduction pathways represented by 337 enzymes and 17 secondary metabolites. In silico analysis reveals that 207 UniESTs inLarixare homologous to MAPKs genes identified from other model plants, which may be involved in regulating SE development. This study provides an initial insight into theLarixtranscriptomes of the pro-embryogenic mass and is a sound basis for future studies.Key messageWe constructed a large, full-length 454 sequencing cDNA library ofLarix leptolepisduring somatic embryogenesis. More than 590,000 sequences were obtained and a deep-coverage EST database was constructed.