A gene-based SNP resource and linkage map for the copepod Tigriopus californicus.
A gene-based SNP resource and linkage map for the copepod Tigriopus californicus.
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DOI：
10.1186/1471-2164-12-568
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发表时间：
2011-11-21
期刊：
影响因子：
4.4
通讯作者：
Edmands S
中科院分区：
文献类型：
--
作者：
Foley BR;Rose CG;Rundle DE;Leong W;Moy GW;Burton RS;Edmands S
到目前为止，在甲壳类动物中开发的基因组资源还很少。鉴于该类群在数量上的丰富性以及分类学和生态多样性，这种缺乏在桡足类中尤为明显。斑腿虎非常适合作为遗传模式的桡足类动物，在环境压力和生殖隔离方面一直是广泛研究的对象。因此，我们着手开发一个广泛有用的遗传标记小组，并构建一个密度足够高的连锁图谱，用于在加州叉尾轮虫的区间作图框架中进行数量性状基因座检测--这在桡足类中尚属首次。用190个单核苷酸多态性(SNPs)对我们的定位群体F2代幼虫进行了基因分型。构建的连锁图谱平均标记间距离为1.8 cM，最大标记间距离为10.3 cM。所有的标记都被组装成连锁群，这12个连锁群对应于卡氏锥虫的12条已知染色体。我们估计总基因组大小为401.0 cM，总覆盖率为73.7%。75%的作图标记在另外9个加州锥虫种群中被检测到。在已有的模式节肢动物基因组中，我们能够偶然地显示出更多的共同定位的同源物对，比预期的要多，这表明膜翅目和桡足目之间保存了大范围的同源关系。我们的研究提供了大量跨越所有染色体的连锁标记。这些标记中的许多也在加州锥虫的多个种群以及该属的另外两个物种中被发现。我们开发的基因组资源将使我们能够绘制该物种和密切相关物种的整个地理范围的图谱。这一连锁图谱将促进基因组测序、测绘和组装成一个具有生态和分类学意义的群体，目前正在为该群体开发基因组资源。
As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development.
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影响因子：
4.4
作者：
Koyama T;Asakawa S;Katagiri T;Shimizu A;Fagutao FF;Mavichak R;Santos MD;Fuji K;Sakamoto T;Kitakado T;Kondo H;Shimizu N;Aoki T;Hirono I
通讯作者：
Hirono I
影响因子：
2.4
作者：
BURTON, RS;FELDMAN, MW;SWISHER, SG
通讯作者：
SWISHER, SG
影响因子：
4.9
作者：
Edmands, S
通讯作者：
Edmands, S
影响因子：
2.1
作者：
Harrison, J. S.;Edmands, S.
通讯作者：
Edmands, S.
影响因子：
2.6
作者：
HUMES, AG
通讯作者：
HUMES, AG