Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
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DOI：
10.1371/journal.pone.0019315
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发表时间：
2011-04-26
期刊：
影响因子：
3.7
通讯作者：
Blaxter ML
中科院分区：
文献类型：
--
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
限制性位点相关DNA（RAD）测序是一种强大的新方法，用于在许多个体的基因组中进行靶向测序。这种方法具有广泛的潜力，非模式生物的遗传分析，包括基因型-表型关联作图，遗传地理学，群体遗传学和支架基因组组装通过连锁图谱。我们构建了一个RAD文库，使用基因组DNA从小菜蛾（小菜蛾）回交分离杀虫剂多杀菌素的抗性。在单个Illumina GAIIx泳道上对24个个体进行测序（51个碱基配对末端读数）。利用雌性鳞翅目昆虫同源染色体中缺乏交换的优势，将3，177个母系遗传的RAD等位基因分配到31条染色体上，从而能够鉴定多杀菌素抗性和W/Z性染色体。将每个RAD等位基因的配对末端读段组装成重叠群，并使用BLAST与家蚕的基因组（n = 28）进行比较，揭示了28个同源匹配加上3个预期的融合/断裂事件，这解释了染色体数目的差异。 全基因组连锁图（1292 cM）推断与2,878分离RAD等位基因遗传自回交父亲，产生染色体和位置特异性测序RAD标记。在这里，我们已经使用RAD测序构建了一个没有以前的基因组数据的生物体的遗传连锁图谱从头。木霉菌与B连锁群的比较分析。家蚕染色体首次表明，遗传同线现象在大鳞翅目昆虫以外普遍存在。RAD测序是一种功能强大的系统，能够快速生成非模型生物体的染色体特异性数据。
Restriction-site associated DNA (RAD) sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis of non-model organisms including genotype-phenotype association mapping, phylogeography, population genetics and scaffolding genome assemblies through linkage mapping. We constructed a RAD library using genomic DNA from a Plutella xylostella (diamondback moth) backcross that segregated for resistance to the insecticide spinosad. Sequencing of 24 individuals was performed on a single Illumina GAIIx lane (51 base paired-end reads). Taking advantage of the lack of crossing over in homologous chromosomes in female Lepidoptera, 3,177 maternally inherited RAD alleles were assigned to the 31 chromosomes, enabling identification of the spinosad resistance and W/Z sex chromosomes. Paired-end reads for each RAD allele were assembled into contigs and compared to the genome of Bombyx mori (n = 28) using BLAST, revealing 28 homologous matches plus 3 expected fusion/breakage events which account for the difference in chromosome number. A genome-wide linkage map (1292 cM) was inferred with 2,878 segregating RAD alleles inherited from the backcross father, producing chromosome and location specific sequenced RAD markers. Here we have used RAD sequencing to construct a genetic linkage map de novo for an organism that has no previous genome data. Comparative analysis of P. xyloxtella linkage groups with B. mori chromosomes shows for the first time, genetic synteny appears common beyond the Macrolepidoptera. RAD sequencing is a powerful system capable of rapidly generating chromosome specific data for non-model organisms.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
4.4
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
通讯作者：
Hayes PM
影响因子：
7
作者：
Miller, Michael R.;Dunham, Joseph P.;Johnson, Eric A.
通讯作者：
Johnson, Eric A.
影响因子：
3.8
作者：
Fujii, Tsuguru;Abe, Hiroaki;Shimada, Toru
通讯作者：
Shimada, Toru
DOI：
10.1073/pnas.0910413107
发表时间：
2010-04-27
影响因子：
11.1
作者：
d'Alencon, E.;Sezutsu, H.;Feyereisen, R.
通讯作者：
Feyereisen, R.