Artificially designed hybrids facilitate efficient generation of high-resolution linkage maps.
Artificially designed hybrids facilitate efficient generation of high-resolution linkage maps.
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DOI：
10.1038/s41598-018-34431-6
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发表时间：
2018-10-31
影响因子：
4.6
通讯作者：
Asakawa S
中科院分区：
文献类型：
--
作者：
Yoshitake K;Igarashi Y;Mizukoshi M;Kinoshita S;Mitsuyama S;Suzuki Y;Saito K;Watabe S;Asakawa S
当对真核生物基因组进行测序时，连锁图谱对于构建组装和/或验证染色体的支架是必不可少的。然而，目前构建连锁图谱的方法受到标记密度和成本效益的限制，特别是对于野生生物。我们现在设计了一种基于人工产生的杂交生物的新策略，以较低的成本获得超高密度的基因组标记，并建立高度精确的连锁图谱。我们还开发了具有低深度连锁分析（SELDLA）的新型分析管道Scaffold Extender，用于数据处理以生成连锁图和草图基因组。利用SELDLA，同时获得了两种河豚的连锁图谱和改良基因组，分别是红鳍东鲀（Takifugu rubripes）和棘鳍东鲀（Takifugu stictonotus）。该策略适用于广泛的有性繁殖生物，因此可以加速各种生物的全基因组分析，包括鱼类，软体动物，两栖动物，昆虫，植物，甚至哺乳动物。
When sequencing eukaryotic genomes, linkage maps are indispensable for building scaffolds to assemble and/or to validate chromosomes. However, current approaches to constructing linkage maps are limited by marker density and cost-effectiveness, especially for wild organisms. We have now devised a new strategy based on artificially generated hybrid organisms to acquire ultrahigh-density genomic markers at reduced cost and build highly accurate linkage maps. We have also developed the novel analysis pipeline Scaffold Extender with Low Depth Linkage Analysis (SELDLA) for data processing to generate linkage maps and draft genomes. Using SELDLA, linkage maps and improved genomes for two species of pufferfish, Takifugu rubripes and Takifugu stictonotus, were obtained simultaneously. The strategy is applicable to a wide range of sexually reproducing organisms, and could, therefore, accelerate the whole genome analysis of various organisms including fish, mollusks, amphibians, insects, plants, and even mammals.
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影响因子：
3.5
作者：
Zhang X;Mizukoshi M;Zhang H;Tan E;Igarashi Y;Suzuki Y;Mitsuyama S;Kinoshita S;Saito K;Watabe S;Asakawa S
通讯作者：
Asakawa S
DOI：
10.1093/dnares/dsw001
发表时间：
2016-04
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Bodénès C;Chancerel E;Ehrenmann F;Kremer A;Plomion C
通讯作者：
Plomion C
影响因子：
4.4
作者：
Liu N;Li M;Hu X;Ma Q;Mu Y;Tan Z;Xia Q;Zhang G;Nian H
通讯作者：
Nian H
影响因子：
7
作者：
Kielbasa, Szymon M.;Wan, Raymond;Frith, Martin C.
通讯作者：
Frith, Martin C.
影响因子：
16.6
作者：
Campbell, Christopher L.;Furlotte, Nicholas A.;Eriksson, Nick;Hinds, David;Auton, Adam
通讯作者：
Auton, Adam