A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.
A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.
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DOI：
10.1101/gr.141689.112
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发表时间：
2013-01
期刊：
影响因子：
7
通讯作者：
Andolfatto P
中科院分区：
文献类型：
--
作者：
Hu TT;Eisen MB;Thornton KR;Andolfatto P
我们使用1.42亿对短读段序列和先前发表的菌株w501的数据创建了一个新的果蝇基因组组装体。我们的组装代表了更高质量的基因组序列，具有更大的覆盖范围，更少的错误组装，并且通过几个指数，更少的序列错误。这个基因组参考序列的进化分析揭示了有趣的模式的谱系特异性的分歧，是从以前报道的不同。具体来说，我们发现果蝇的进化速度比D。simulans在所有注释的位点类别，包括在最小内含子中发现的pupernetally中性进化位点。这可能与D.黑腹鱼，我们还发现了显着的异质性，在不同类别的网站，与历史上的差异，有效的人口规模为两个物种的进化速度。与以前的研究结果相反，我们发现X染色体的非同义和大多数非编码DNA位点的进化速度明显快于常染色体，而同义位点的进化速度明显慢于常染色体。puppet中性位点的X/A差异的情况下，基因本体论和性别偏见的表达模式的鲁棒性表明，部分隐性有益突变可能包括物种之间观察到的非编码DNA分歧的很大一部分。我们的结果对于解释不同质量基因组的进化分析具有更普遍的影响。
We create a new assembly of the Drosophila simulans genome using 142 million paired short-read sequences and previously published data for strain w501. Our assembly represents a higher-quality genomic sequence with greater coverage, fewer misassemblies, and, by several indexes, fewer sequence errors. Evolutionary analysis of this genome reference sequence reveals interesting patterns of lineage-specific divergence that are different from those previously reported. Specifically, we find that Drosophila melanogaster evolves faster than D. simulans at all annotated classes of sites, including putatively neutrally evolving sites found in minimal introns. While this may be partly explained by a higher mutation rate in D. melanogaster, we also find significant heterogeneity in rates of evolution across classes of sites, consistent with historical differences in the effective population size for the two species. Also contrary to previous findings, we find that the X chromosome is evolving significantly faster than autosomes for nonsynonymous and most noncoding DNA sites and significantly slower for synonymous sites. The absence of a X/A difference for putatively neutral sites and the robustness of the pattern to Gene Ontology and sex-biased expression suggest that partly recessive beneficial mutations may comprise a substantial fraction of noncoding DNA divergence observed between species. Our results have more general implications for the interpretation of evolutionary analyses of genomes of different quality.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
64.8
作者：
Fay, JC;Wyckoff, GJ;Wu, CI
通讯作者：
Wu, CI
种群基因组学：果蝇果蝇中多态性和差异的全基因组分析。
影响因子：
9.8
作者：
Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
通讯作者：
Langley, Charles H.
影响因子：
12.3
作者：
Kelley DR;Schatz MC;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
4.3
作者：
Bradley RK;Roberts A;Smoot M;Juvekar S;Do J;Dewey C;Holmes I;Pachter L
通讯作者：
Pachter L