通过内含子保守模式解析深层动物分化
Resolution of a deep animal divergence by the pattern of intron conservation.
作者信息
Roy Scott William, Gilbert Walter
机构信息
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
出版信息
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4403-8. doi: 10.1073/pnas.0409891102. Epub 2005 Mar 15.
Abstract
The relationship between three biologically important groups, arthropods, nematodes, and deuterostomes, remains unresolved. It is unknown whether arthropods are more closely related to nematodes (consistent with the "ecdysozoa" hypothesis) or to deuterostomes (consistent with "coelomata"). We present a method in which we use the pattern of spliceosomal intron conservation to develop a series of inequalities that characterize each possible relationship. We find that only the ecdysozoa grouping satisfies these predictions, with P < 10(-6). Simulations show that our method, unlike some previous methods, is largely insensitive to rate variation between branches.
摘要
节肢动物、线虫和后口动物这三个具有重要生物学意义的类群之间的关系仍未明确。目前尚不清楚节肢动物与线虫的关系更为密切（这与“蜕皮动物”假说相符）还是与后口动物关系更为密切（这与“体腔动物”假说相符）。我们提出了一种方法，利用剪接体内含子保守模式来建立一系列不等式，以描述每种可能的关系。我们发现只有蜕皮动物分组满足这些预测，P值小于10的负6次方。模拟结果表明，与之前的一些方法不同，我们的方法在很大程度上不受分支间速率变化的影响。
相似文献
1
Resolution of a deep animal divergence by the pattern of intron conservation.通过内含子保守模式解析深层动物分化
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4403-8. doi: 10.1073/pnas.0409891102. Epub 2005 Mar 15.
2
Rare genomic characters do not support Coelomata: intron loss/gain.罕见的基因组特征不支持真体腔动物：内含子的缺失/获得。
Mol Biol Evol. 2008 Apr;25(4):620-3. doi: 10.1093/molbev/msn035. Epub 2008 Feb 14.
3
Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata.罕见的编码序列变化与蜕皮动物门一致，而非与真体腔动物一致。
Mol Biol Evol. 2007 Aug;24(8):1604-7. doi: 10.1093/molbev/msm105. Epub 2007 May 24.
4
The evolution of protostome GATA factors: molecular phylogenetics, synteny, and intron/exon structure reveal orthologous relationships.原口动物GATA因子的进化：分子系统发育、共线性和内含子/外显子结构揭示直系同源关系。
BMC Evol Biol. 2008 Apr 15;8:112. doi: 10.1186/1471-2148-8-112.
5
Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation.通过对内含子保守模式的严格分析，对动物体腔动物进化枝的支持。
Mol Biol Evol. 2007 Nov;24(11):2583-92. doi: 10.1093/molbev/msm207. Epub 2007 Sep 24.
6
Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda.后生动物线粒体基因组学：关于具腿无脊椎动物，泛节肢动物共同起源的证据。
Genome Biol Evol. 2010 Jul 12;2:425-40. doi: 10.1093/gbe/evq030.
7
Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan.有丝分裂基因组学和系统发育基因组学揭示了鳃曳虫是现存的蜕皮动物祖先模型。
Evol Dev. 2006 Nov-Dec;8(6):502-10. doi: 10.1111/j.1525-142X.2006.00123.x.
8
Genome-scale evidence of the nematode-arthropod clade.线虫-节肢动物进化枝的基因组规模证据。
Genome Biol. 2005;6(5):R41. doi: 10.1186/gb-2005-6-5-r41. Epub 2005 Apr 28.
9
Evidence for a clade of nematodes, arthropods and other moulting animals.线虫、节肢动物和其他蜕皮动物进化枝的证据。
Nature. 1997 May 29;387(6632):489-93. doi: 10.1038/387489a0.
10
Phylogeny of Nematoda and Cephalorhyncha derived from 18S rDNA.基于18S核糖体DNA推导的线虫纲和头吻纲系统发育
J Mol Evol. 1998 Nov;47(5):597-605. doi: 10.1007/pl00006416.
引用本文的文献
1
Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments.利用预测的 2b-RAD 片段对 21 种果蝇进行全基因组系统发育分析。
PeerJ. 2013 Dec 23;1:e226. doi: 10.7717/peerj.226.
2
Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications.三种蚊子基因中外显子含量与密码子使用偏性之间的拮抗关系：功能和进化意义。
Evol Appl. 2013 Nov;6(7):1079-89. doi: 10.1111/eva.12088. Epub 2013 Jul 24.
3
The impact of paralogy on phylogenomic studies - a case study on annelid relationships.并系同源对系统基因组学研究的影响——以环节动物亲缘关系为例。
PLoS One. 2013 May 7;8(5):e62892. doi: 10.1371/journal.pone.0062892. Print 2013.
4
Insights into bilaterian evolution from three spiralian genomes.从三个螺旋体基因组中洞察两侧对称动物的演化。
Nature. 2013 Jan 24;493(7433):526-31. doi: 10.1038/nature11696. Epub 2012 Dec 19.
5
Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information.利用互信息分析原口动物内含子模式中的系统发育信号。
Theory Biosci. 2013 Jun;132(2):93-104. doi: 10.1007/s12064-012-0173-0. Epub 2012 Dec 18.
6
In silico characterization and comparative genomic analysis of the Culex quinquefasciatus glutathione S-transferase (GST) supergene family.黄库蚊谷胱甘肽 S-转移酶（GST）超级基因家族的计算机特征描述和比较基因组分析。
Parasitol Res. 2011 Oct;109(4):1165-77. doi: 10.1007/s00436-011-2364-x. Epub 2011 Apr 15.
7
The fibrillar collagen family.纤维胶原家族。
Int J Mol Sci. 2010 Jan 28;11(2):407-426. doi: 10.3390/ijms11020407.
8
Wagner and Dollo: a stochastic duet by composing two parsimonious solos.瓦格纳与多洛：通过谱写两首简约的独奏曲构成的一曲随机二重奏。
Syst Biol. 2008 Oct;57(5):772-84. doi: 10.1080/10635150802434394.
9
Exalign: a new method for comparative analysis of exon-intron gene structures.Exalign：一种用于外显子-内含子基因结构比较分析的新方法。
Nucleic Acids Res. 2008 May;36(8):e47. doi: 10.1093/nar/gkn153. Epub 2008 Apr 8.
10
Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax.人类疟疾的起源：罕见的基因组变化和完整的线粒体基因组证实了恶性疟原虫与其他哺乳动物寄生虫的关系，但使间日疟原虫的起源变得复杂。
Mol Biol Evol. 2008 Jun;25(6):1192-8. doi: 10.1093/molbev/msn069. Epub 2008 Mar 21.
本文引用的文献
1
The position of the Arthropoda in the phylogenetic system.节肢动物在系统发育系统中的位置。
J Morphol. 1998 Dec;238(3):263-285. doi: 10.1002/(SICI)1097-4687(199812)238:3<263::AID-JMOR1>3.0.CO;2-L.
2
A phylogeny of caenorhabditis reveals frequent loss of introns during nematode evolution.秀丽隐杆线虫的系统发育揭示了线虫进化过程中内含子的频繁丢失。
Genome Res. 2004 Jul;14(7):1207-20. doi: 10.1101/gr.2639304.
3
Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications.陆地植物线粒体基因nad1中内含子的分布：系统发育和分子进化意义
Mol Phylogenet Evol. 2004 Jul;32(1):246-63. doi: 10.1016/j.ympev.2003.12.013.
4
Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin.蜕皮动物系统发育与贝叶斯推断：首次使用近乎完整的28S和18S rRNA基因序列对节肢动物及其亲属进行分类。
Mol Phylogenet Evol. 2004 Apr;31(1):178-91. doi: 10.1016/j.ympev.2003.07.013.
5
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.真体腔动物而非蜕皮动物：来自全基因组系统发育分析的证据。
Genome Res. 2004 Jan;14(1):29-36. doi: 10.1101/gr.1347404.
6
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution.真核生物进化过程中内含子位置的显著跨界保守性以及大量谱系特异性内含子的丢失和获得。
Curr Biol. 2003 Sep 2;13(17):1512-7. doi: 10.1016/s0960-9822(03)00558-x.
7
Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain.哺乳动物基因内含子位置的大规模比较显示存在内含子丢失但无增加。
Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7158-62. doi: 10.1073/pnas.1232297100. Epub 2003 May 30.
8
Large-scale comparison of intron positions among animal, plant, and fungal genes.动物、植物和真菌基因内含子位置的大规模比较。
Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16128-33. doi: 10.1073/pnas.242624899. Epub 2002 Nov 20.
9
The evolution of spliceosomal introns.剪接体内含子的进化。
Curr Opin Genet Dev. 2002 Dec;12(6):701-10. doi: 10.1016/s0959-437x(02)00360-x.
10
The origin and evolution of model organisms.模式生物的起源与进化。
Nat Rev Genet. 2002 Nov;3(11):838-49. doi: 10.1038/nrg929.
Zotero 插件