A comprehensive collection of chicken cDNAs
A comprehensive collection of chicken cDNAs
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DOI：
10.1016/s0960-9822(02)01296-4
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发表时间：
2002-11-19
期刊：
影响因子：
9.2
通讯作者：
Hubbard, SJ
中科院分区：
文献类型：
--
作者：
Boardman, PE;Sanz-Ezquerro, J;Hubbard, SJ
鸟类在许多生物学科中扮演着核心角色，特别是生态学，进化和行为。鸡作为一种模式脊椎动物，也是发育生物学家、免疫学家、细胞生物学家和遗传学家的重要实验系统。然而，鸡的基因组资源落后于其他模式生物，只有1845个非冗余全长鸡cDNA序列目前存放在EMBL数据库。我们描述了一个大规模的表达序列标签（EST）项目，旨在基因发现鸡（www.chick.umist.ac.uk）。总共有339，314个EST已经从21种不同的胚胎和成体组织产生的64个cDNA文库中测序。这些被聚类并组装成85，486个连续序列（重叠群）。我们发现至少38%的重叠群在其他生物中具有直系同源物，并确定了13，000个新鸡基因的上限。剩余的重叠群可能包括新的禽类特异性或快速进化的基因。重叠群与已知鸡基因和直系同源物的比较表明，30%包括含有起始密码子的cDNA，20%的重叠群代表全长cDNA序列。使用这个数据集，我们估计鸡总共有大约35，000个基因，这表明这个数字可能是脊椎动物的一个特征。
Birds have played a central role in many biological disciplines, particularly ecology, evolution, and behavior. The chicken, as a model vertebrate, also represents an important experimental system for developmental biologists, immunologists, cell biologists, and geneticists. However, genomic resources for the chicken have lagged behind those for other model organisms, with only 1845 nonredundant full-length chicken cDNA sequences currently deposited in the EMBL databank. We describe a large-scale expressed-sequence-tag (EST) project aimed at gene discovery in chickens (http://www.chick.umist.ac.uk). In total, 339,314 ESTs have been sequenced from 64 cDNA libraries generated from 21 different embryonic and adult tissues. These were clustered and assembled into 85,486 contiguous sequences (contigs). We find that a minimum of 38% of the contigs have orthologs in other organisms and define an upper limit of 13,000 new chicken genes. The remaining contigs may include novel avian specific or rapidly evolving genes. Comparison of the contigs with known chicken genes and orthologs indicates that 30% include cDNAs that contain the start codon and 20% of the contigs represent full-length cDNA sequences. Using this dataset, we estimate that chickens have approximately 35,000 genes in total, suggesting that this number may be a characteristic feature of vertebrates.