Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
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DOI：
10.1371/journal.pgen.1000740
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发表时间：
2009-11
期刊：
影响因子：
4.5
通讯作者：
Yu Y
中科院分区：
文献类型：
--
作者：
Soderlund C;Descour A;Kudrna D;Bomhoff M;Boyd L;Currie J;Angelova A;Collura K;Wissotski M;Ashley E;Morrow D;Fernandes J;Walbot V;Yu Y
全长cDNA（FLcDNA）测序确定了单个基因转录本的精确一级结构。从代表27种B73组织和非生物胁迫处理的两个文库中，对27455个高质量的FLcDNA进行了测序。平均转录本长度为1.44kb，其中包括分别为218个碱基和321个碱基的5′和3′非翻译区（UTR），8.6%的FLcDNA编码预测的少于100个氨基酸的蛋白质。大约94%的FLcDNA严格定位到玉米基因组。尽管该基因组近三分之二由转座元件（TEs）组成，但只有5.6%的FLcDNA在编码区或UTR区域包含TE序列。大约7.2%的FLcDNA是假定的转录因子，这表明罕见转录本在我们的FLcDNA集合中得到了很好的富集。蛋白质相似性搜索确定了1737个在水稻、高粱、拟南芥或杨树注释基因中不存在的玉米转录本。严格的FLcDNA组装产生了24467个非冗余序列，其中88%有非玉米蛋白质匹配。这些FLcDNA还与来自其他项目的GenBank中的41759个FLcDNA进行了组装，使用半严格参数从该项目中识别出13368个潜在独特的非冗余序列。该项目产生的文库、表达序列标签（ESTs）和FLcDNA序列是公开可用的。注释的EST和FLcDNA组装可通过玉米FLcDNA网络资源（www.maizecdna.org）获取。
为了配合玉米B73基因组测序的完成，我们从代表大多数组织和常见非生物胁迫条件下基因转录本的两个玉米B73文库中对27455个全长cDNA（FLcDNA）进行了测序。通过将FLcDNA与测序的基因组进行比对，FLcDNA有助于确定基因的外显子/内含子结构；我们94%的FLcDNA与玉米基因组比对上了。将27455个FLcDNA与水稻、高粱、拟南芥和杨树的基因序列进行比较；在所有四组中发现了22874个，1737个是玉米特有的。玉米基因组的三分之二由一种称为“转座元件”的重复序列组成；只有5.6%的FLcDNA序列包含与这些重复序列同源的任何片段。除了我们的集合外，还有另外三组玉米FLcDNA，总共69306个基因转录本，其中许多来自不同的玉米品系（即FLcDNA通常只有微小差异，反映了分化）。我们使用允许大多数等位基因和近期分化的基因转录本比对在一起的参数将它们组装在一起，结果产生了46739个独特的基因转录本。
Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5′ and 3′ UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org). To complement the completion of sequencing the maize B73 genome, we sequenced 27,455 full-length cDNAs (FLcDNA) from two maize B73 libraries representing the gene transcripts from most tissues and common abiotic stress conditions. The FLcDNAs are beneficial in determining the exon/intron structure of genes by aligning them to the sequenced genome; 94% of our FLcDNAs aligned to the maize genome. The 27,455 FLcDNAs were compared to gene sequences for rice, sorghum, Arabidopsis, and poplar; 22,874 were found in all four sets, and 1,737 were unique to maize. Two-thirds of the maize genome is composed of a type of repetitive sequence called “transposable elements”; only 5.6% of the FLcDNA sequence contained any segment homologous to these repeats. In addition to our set, there are three other sets of maize FLcDNAs for a total of 69,306 gene transcripts, where many of them are from different maize lines (i.e. FLcDNAs often have only slight differences reflecting divergence). We assembled these together using parameters that would allow most alleles and recently diverged gene transcripts to align together, resulting in 46,739 unique gene transcripts.
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