Afrobatrachian mitochondrial genomes: genome reorganization, gene rearrangement mechanisms, and evolutionary trends of duplicated and rearranged genes.
Afrobatrachian mitochondrial genomes: genome reorganization, gene rearrangement mechanisms, and evolutionary trends of duplicated and rearranged genes.
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DOI：
10.1186/1471-2164-14-633
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发表时间：
2013-09-21
期刊：
影响因子：
4.4
通讯作者：
Sumida M
中科院分区：
文献类型：
--
作者：
Kurabayashi A;Sumida M
线粒体基因组重组很少在近亲动物中发现，但在蛙属青蛙中发现了剧烈的重组。三个主要的蛙类分类群（Natatanura，Microhylidae和Afrobatrachia）的系统发育关系一直是有问题的，并为Afrobatrachians的有丝分裂基因组信息一直没有。线粒体（mt）基因重排的几种分子模型已被提出，但观察证据一直不足以评估他们。此外，重排mt基因的进化趋势还没有得到很好的理解。为了获得这些问题的分子和系统发育的见解，我们分析了MT基因组的四个非洲蟾物种（短头adspersus，半marmoratus，Hyperolius marmoratus，和Trichobatrachus robustus），并进行分子系统发育分析。此外，我们还寻找了两种预期的进化模式，在重新排列的mt基因的类人猿。广泛重组mt基因组中有许多重复和重排的基因被发现在三个分析的四个非洲Batrachians。事实上，短头龙拥有脊椎动物中最大的已知mt基因组。尽管这些物种的重复和重排基因的类型不同，但普遍存在非串联拷贝基因位于串联拷贝区域内的基因重排模式，而且12S和16S三重核糖体RNA区域的非相邻拷贝之间存在协同进化。基于有丝分裂基因组学数据的系统发育分析支持非洲Batrachia和Microhylidae之间的密切关系，其1亿年前的估计分歧与非洲大陆上非洲Batrachians的现今特有性一致。非洲两栖动物mt数据支持mt基因重排的第一串联和第二非串联重复模型以及重复mt区域协同进化的重组模型。我们还表明，特定的核苷酸取代和重复和重排的mt基因预期的组成模式没有发生，这表明没有不利的利用这些基因的系统发育推断。
Mitochondrial genomic (mitogenomic) reorganizations are rarely found in closely-related animals, yet drastic reorganizations have been found in the Ranoides frogs. The phylogenetic relationships of the three major ranoid taxa (Natatanura, Microhylidae, and Afrobatrachia) have been problematic, and mitogenomic information for afrobatrachians has not been available. Several molecular models for mitochondrial (mt) gene rearrangements have been proposed, but observational evidence has been insufficient to evaluate them. Furthermore, evolutionary trends in rearranged mt genes have not been well understood. To gain molecular and phylogenetic insights into these issues, we analyzed the mt genomes of four afrobatrachian species (Breviceps adspersus, Hemisus marmoratus, Hyperolius marmoratus, and Trichobatrachus robustus) and performed molecular phylogenetic analyses. Furthermore we searched for two evolutionary patterns expected in the rearranged mt genes of ranoids. Extensively reorganized mt genomes having many duplicated and rearranged genes were found in three of the four afrobatrachians analyzed. In fact, Breviceps has the largest known mt genome among vertebrates. Although the kinds of duplicated and rearranged genes differed among these species, a remarkable gene rearrangement pattern of non-tandemly copied genes situated within tandemly-copied regions was commonly found. Furthermore, the existence of concerted evolution was observed between non-neighboring copies of triplicated 12S and 16S ribosomal RNA regions. Phylogenetic analyses based on mitogenomic data support a close relationship between Afrobatrachia and Microhylidae, with their estimated divergence 100 million years ago consistent with present-day endemism of afrobatrachians on the African continent. The afrobatrachian mt data supported the first tandem and second non-tandem duplication model for mt gene rearrangements and the recombination-based model for concerted evolution of duplicated mt regions. We also showed that specific nucleotide substitution and compositional patterns expected in duplicated and rearranged mt genes did not occur, suggesting no disadvantage in employing these genes for phylogenetic inference.
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影响因子：
16.8
作者：
Dowton, M;Campbell, NJH
通讯作者：
Campbell, NJH
影响因子：
14.9
作者：
Abascal F;Zardoya R;Telford MJ
通讯作者：
Telford MJ
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
10.7
作者：
Fonseca, Miguel M.;Posada, David;Harris, D. James
通讯作者：
Harris, D. James
DOI：
10.1073/pnas.1112487109
发表时间：
2012-04-03
影响因子：
11.1
作者：
Crottini, Angelica;Madsen, Ole;Vences, Miguel
通讯作者：
Vences, Miguel