Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals.
Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals.
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DOI：
10.1093/gbe/evr041
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发表时间：
2011
影响因子：
3.3
通讯作者：
Venkatesh B
中科院分区：
文献类型：
--
作者：
Kai W;Kikuchi K;Tohari S;Chew AK;Tay A;Fujiwara A;Hosoya S;Suetake H;Naruse K;Brenner S;Suzuki Y;Venkatesh B
红鳍东方鲀（Takifugu rubripes）的紧凑基因组已被广泛用作了解脊椎动物基因组进化的参考基因组。然而，河豚基因组组装的片段化性质限制了其用于脊椎动物基因组结构的比较。为了将装配体的邻近性扩展到染色体水平，我们已经生成了一个全面的河豚遗传图谱，并将装配体的支架锚定到河豚的22条染色体上。该图谱由1，220个微卫星标记组成，为覆盖86%基因组组装的697个支架提供锚点（http：//www.fugu-sg.org/）。整合的基因组图谱显示，与其他脊椎动物相比，河豚鱼的重组率较高，并且河豚鱼的重组率在性别和染色体之间存在很大的差异。我们使用了扩展的组装，探讨最近的重排事件的谱系中的河豚，河豚，青鳉和比较它们与重排在三种哺乳动物（人类，小鼠和负鼠）的谱系。在这两种河豚中，河豚经历的染色体重排比河豚少。基因顺序在三种硬骨鱼中比在哺乳动物中更高度保守，这主要是由于硬骨鱼中染色体间重排率较低。这些结果提供了新的见解硬骨鱼和哺乳动物之间的基因组进化的不同模式。该图为脊椎动物的比较基因组学研究提供了宝贵的资源，也为阐明近500年来进化的近25种东方鲀表型多样性的遗传基础提供了宝贵的资源。
The compact genome of fugu (Takifugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of fugu and anchored the scaffolds of the assembly to the 22 chromosomes of fugu. The map consists of 1,220 microsatellite markers that provide anchor points to 697 scaffolds covering 86% of the genome assembly (http://www.fugu-sg.org/). The integrated genome map revealed a higher recombination rate in fugu compared with other vertebrates and a wide variation in the recombination rate between sexes and across chromosomes of fugu. We used the extended assembly to explore recent rearrangement events in the lineages of fugu, Tetraodon, and medaka and compared them with rearrangements in three mammalian (human, mouse, and opossum) lineages. Between the two pufferfishes, fugu has experienced fewer chromosomal rearrangements than Tetraodon. The gene order is more highly conserved in the three teleosts than in mammals largely due to a lower rate of interchromosomal rearrangements in the teleosts. These results provide new insights into the distinct patterns of genome evolution between teleosts and mammals. The consolidated genome map and the genetic map of fugu are valuable resources for comparative genomics of vertebrates and for elucidating the genetic basis of the phenotypic diversity of ∼25 species of Takifugu that evolved within the last 5 My.
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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：
9.8
作者：
Hillier LW;Miller RD;Baird SE;Chinwalla A;Fulton LA;Koboldt DC;Waterston RH
通讯作者：
Waterston RH
影响因子：
7
作者：
Beye, Martin;Gattermeier, Irene;Page, Robert E., Jr.
通讯作者：
Page, Robert E., Jr.
影响因子：
7
作者：
Hill, Matthew M.;Broman, Karl W.;Sidow, Arend
通讯作者：
Sidow, Arend
影响因子：
3.3
作者：
Kai, W;Kikuchi, K;Suzuki, Y
通讯作者：
Suzuki, Y