De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis.
De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis.
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DOI：
10.1186/1471-2164-13-648
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发表时间：
2012-11-21
期刊：
影响因子：
4.4
通讯作者：
Zhu MY
中科院分区：
文献类型：
--
作者：
Huang HH;Xu LL;Tong ZK;Lin EP;Liu QP;Cheng LJ;Zhu MY
杉木（Cunninghamia lanceolata）是我国重要的用材树种，占我国商品材总产量的20-30%。然而，杉木基因组信息有限，严重阻碍了杉木功能基因组研究和分子育种。最近，转录组测序的重大进展提供了快速和具有成本效益的方法来生成大的表达数据集，这些数据集已被证明是分析具有未确定基因组的非模式生物的转录组的强大工具。在这项研究中，使用Illumina HiSeq™ 2000测序平台分析了来自杉木的9个组织的转录组。获得了大约4000万个配对末端读段，产生了3.62千兆碱基对的测序数据。这些读段被组装成83，248个独特序列（即Unigenes），平均长度为449 bp，总计37.40 Mb。共有73，779个Unigenes被超过5个读段支持，42，663个（57.83%）在NCBI非冗余和Swiss-Prot蛋白质数据库中具有同源物，对应于27，224个独特蛋白质条目。在这些Unigenes中，16，750个被分配到Gene Ontology类，14，877个被聚类到正向组。通过与京都基因和基因组百科全书（KEGG）数据库的BLAST比较，总共21，689个（29.40%）被定位到119条通路。在Unigene数据集中，通过有针对性地搜索其注释，鉴定了编码纤维素和木质素生物合成途径中的酶的大多数基因。并首次发现了一批参与这两条代谢途径的候选基因。克隆了18个与纤维素和木质素生物合成相关的基因，用于实验验证转录组数据。通过比对共发现了49个Unigenes，覆盖了这些选定基因的不同区域。通过qRT-PCR分析它们在不同组织中的表达模式，以探索它们的推定功能。从杉木的深度测序中获得了相当大一部分转录物序列。利用组装的Unigene数据集寻找纤维素和木质素生物合成的候选基因。该转录组数据集将为C.披针形。
Chinese fir (Cunninghamia lanceolata) is an important timber species that accounts for 20–30% of the total commercial timber production in China. However, the available genomic information of Chinese fir is limited, and this severely encumbers functional genomic analysis and molecular breeding in Chinese fir. Recently, major advances in transcriptome sequencing have provided fast and cost-effective approaches to generate large expression datasets that have proven to be powerful tools to profile the transcriptomes of non-model organisms with undetermined genomes. In this study, the transcriptomes of nine tissues from Chinese fir were analyzed using the Illumina HiSeq™ 2000 sequencing platform. Approximately 40 million paired-end reads were obtained, generating 3.62 gigabase pairs of sequencing data. These reads were assembled into 83,248 unique sequences (i.e. Unigenes) with an average length of 449 bp, amounting to 37.40 Mb. A total of 73,779 Unigenes were supported by more than 5 reads, 42,663 (57.83%) had homologs in the NCBI non-redundant and Swiss-Prot protein databases, corresponding to 27,224 unique protein entries. Of these Unigenes, 16,750 were assigned to Gene Ontology classes, and 14,877 were clustered into orthologous groups. A total of 21,689 (29.40%) were mapped to 119 pathways by BLAST comparison against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The majority of the genes encoding the enzymes in the biosynthetic pathways of cellulose and lignin were identified in the Unigene dataset by targeted searches of their annotations. And a number of candidate Chinese fir genes in the two metabolic pathways were discovered firstly. Eighteen genes related to cellulose and lignin biosynthesis were cloned for experimental validating of transcriptome data. Overall 49 Unigenes, covering different regions of these selected genes, were found by alignment. Their expression patterns in different tissues were analyzed by qRT-PCR to explore their putative functions. A substantial fraction of transcript sequences was obtained from the deep sequencing of Chinese fir. The assembled Unigene dataset was used to discover candidate genes of cellulose and lignin biosynthesis. This transcriptome dataset will provide a comprehensive sequence resource for molecular genetics research of C. lanceolata.
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