Insights into corn genes derived from large-scale cDNA sequencing.
Insights into corn genes derived from large-scale cDNA sequencing.
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源自大规模cDNA测序的玉米基因的见解。
DOI：
10.1007/s11103-008-9415-4
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发表时间：
2009-01
影响因子：
5.1
通讯作者：
Feldmann, Kenneth A.
中科院分区：
文献类型：
--
作者：
Alexandrov, Nickolai N.;Brover, Vyacheslav V.;Freidin, Stanislav;Troukhan, Maxim E.;Tatarinova, Tatiana V.;Zhang, Hongyu;Swaller, Timothy J.;Lu, Yu-Ping;Bouck, John;Flavell, Richard B.;Feldmann, Kenneth A.
我们展示了玉米转录组的大部分，包括代表来自53个文库的484，032个cDNA克隆的EST和36，565个完全测序的cDNA克隆，其中31，552个克隆是非冗余的。这些和其他先前测序的转录本已与现有的基因组序列进行了比对，并为这一主要作物物种的基因结构和启动子特征提供了新的见解。我们发现，虽然每个基因的平均内含子数在玉米和拟南芥中大致相同，但玉米基因有更多的选择性剪接异构体。对编码区核苷酸组成的分析表明，玉米基因以及其他禾本科（禾本科）基因可根据编码密码子第三位氨基酸的GC含量分为两类。许多在第三位具有较低GC含量的转录物具有双子叶植物同源物，但高GC含量的转录物往往对禾本科植物更具特异性。高GC含量类别也富含无内含子基因。这表明，在植物中的一个可识别的基因类与禾本科分歧。此外，由于这些基因中的许多似乎来自不含内含子的祖先基因，这种进化差异可能是来自物种的水平基因转移的结果，不仅具有不同的密码子使用，而且可能没有内含子，也许在植物王国之外。通过将本文所述的cDNA与GenBank中的玉米mRNA的非冗余集合进行比较，我们估计在玉米中存在约50，000个不同的蛋白质编码基因。本研究的所有序列数据已提交给DDBJ/GenBank/EMBL，登录号为EU 940701-EU 977132（FLI cDNA）和FK 944382-FL 482108（EST）。本文的在线版本（doi：10.1007/s11103-008-9415-4）包含补充材料，可供授权用户使用。
We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA clones, out of which 31,552 clones are non-redundant. These and other previously sequenced transcripts have been aligned with available genome sequences and have provided new insights into the characteristics of gene structures and promoters within this major crop species. We found that although the average number of introns per gene is about the same in corn and Arabidopsis, corn genes have more alternatively spliced isoforms. Examination of the nucleotide composition of coding regions reveals that corn genes, as well as genes of other Poaceae (Grass family), can be divided into two classes according to the GC content at the third position in the amino acid encoding codons. Many of the transcripts that have lower GC content at the third position have dicot homologs but the high GC content transcripts tend to be more specific to the grasses. The high GC content class is also enriched with intronless genes. Together this suggests that an identifiable class of genes in plants is associated with the Poaceae divergence. Furthermore, because many of these genes appear to be derived from ancestral genes that do not contain introns, this evolutionary divergence may be the result of horizontal gene transfer from species not only with different codon usage but possibly that did not have introns, perhaps outside of the plant kingdom. By comparing the cDNAs described herein with the non-redundant set of corn mRNAs in GenBank, we estimate that there are about 50,000 different protein coding genes in Zea. All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701–EU977132 (FLI cDNA) and FK944382-FL482108 (EST). The online version of this article (doi:10.1007/s11103-008-9415-4) contains supplementary material, which is available to authorized users.
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