Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes.
Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes.
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DOI：
10.1186/1471-2164-14-49
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发表时间：
2013-01-23
期刊：
影响因子：
4.4
通讯作者：
Kusumi K
中科院分区：
文献类型：
--
作者：
Eckalbar WL;Hutchins ED;Markov GJ;Allen AN;Corneveaux JJ;Lindblad-Toh K;Di Palma F;Alföldi J;Huentelman MJ;Kusumi K
绿色变色龙蜥蜴（Anolis carolinensis）是进化遗传学、发育、神经生物学、生理学、行为和生态学实验室和野外研究的关键物种。作为第一个非鸟类爬行动物基因组测序，A.卡罗莱纳也是一个主要的爬行动物模型与其他脊椎动物的基因组进行比较。Ensembl和NCBI的公共数据库已经提供了变色龙基因组的第一代基因注释，其主要依赖于与相关物种的序列保守性。基于组织特异性转录组的第二代注释将为分子研究提供有价值的资源。在这里，我们提供了一个注释的A。carolinensis基因组的基础上从头组装的深转录组的14个成人和胚胎组织。这个修订后的注释描述了59，373个转录本，而Ensembl和NCBI目前的转录本分别为16，533和18，939个，以及22，962个预测的蛋白质编码基因。这个修订注释的一个关键改进是覆盖了非翻译区（UTR）序列，79%和59%的转录本分别含有5'和3' UTR。基因组序列与目前的A. carolinensis build（Anocar2.0）的基因组覆盖率低于70%，我们鉴定了16，542个未定位的转录本，代表6，695个直系同源物。将组织特异性转录组序列并入A. Carolinensis基因组注释显著提高了其用于比较和功能研究的效用。增加的UTR覆盖率允许更准确地预测蛋白质序列和调控分析。这个修订的注释也提供了一个成人和胚胎组织特异性基因表达图谱。
The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies. Here we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5’ and 3’ UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage. Incorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
12.3
作者：
Haas, Brian J.;Salzberg, Steven L.;Zhu, Wei;Pertea, Mihaela;Allen, Jonathan E.;Orvis, Joshua;White, Owen;Buell, C. Robin;Wortman, Jennifer R.
通讯作者：
Wortman, Jennifer R.
DOI：
10.4061/2011/274975
发表时间：
2011-01-01
期刊：
International Journal of Evolutionary Biology
影响因子：
--
作者：
Grassa, Christopher J.;Kulathinal, Rob J.
通讯作者：
Kulathinal, Rob J.
影响因子：
3.3
作者：
Fujita MK;Edwards SV;Ponting CP
通讯作者：
Ponting CP
影响因子：
3.3
作者：
Janes DE;Chapus C;Gondo Y;Clayton DF;Sinha S;Blatti CA;Organ CL;Fujita MK;Balakrishnan CN;Edwards SV
通讯作者：
Edwards SV