Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.).
Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.).
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使用 RNA-Seq 组装具有超过 13,000 个全长表达基因的玫瑰转录组，并开发玫瑰 (Rosa L.) 的 WagRhSNP 68k Axiom SNP 阵列。
DOI：
10.3389/fpls.2015.00249
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发表时间：
2015
影响因子：
5.6
通讯作者：
Smulders MJ
中科院分区：
文献类型：
--
作者：
Koning-Boucoiran CF;Esselink GD;Vukosavljev M;van 't Westende WP;Gitonga VW;Krens FA;Voorrips RE;van de Weg WE;Schulz D;Debener T;Maliepaard C;Arens P;Smulders MJ
为了开发一个通用的和大的SNP阵列的玫瑰，我们开始挖掘EST从不同的玫瑰种质。为此，使用Illumina配对末端测序从四倍体切花和花园玫瑰中产生含有约7亿个读段的RNA-Seq文库，并使用454测序从二倍体多花蔷薇中产生含有约7亿个读段的RNA-Seq文库。进行单独的从头组装，以确定单核苷酸多态性（SNP）内和玫瑰品种之间。选择四倍体玫瑰之间的SNP来构建基因分型阵列，所述基因分型阵列可用于基于来自切花玫瑰和花园玫瑰的四倍体种质的育种程序中的遗传作图和标记-性状关联发现。总共有68，893个SNP被包括在WagRhSNP Axiom阵列上。接下来，进行直向同源性引导的组装以构建非冗余玫瑰转录组数据库。在草莓（Fragaria vesca L.）基因组其中13，390个似乎含有全长编码区。这一新建立的转录组资源大大增加了目前可用的序列资源的蔷薇科一般和属蔷薇特别。
In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
Hansen KD;Brenner SE;Dudoit S
通讯作者：
Dudoit S
影响因子：
4.4
作者：
Kim J;Park JH;Lim CJ;Lim JY;Ryu JY;Lee BW;Choi JP;Kim WB;Lee HY;Choi Y;Kim D;Hur CG;Kim S;Noh YS;Shin C;Kwon SY
通讯作者：
Kwon SY
影响因子：
3.7
作者：
Chagné D;Crowhurst RN;Troggio M;Davey MW;Gilmore B;Lawley C;Vanderzande S;Hellens RP;Kumar S;Cestaro A;Velasco R;Main D;Rees JD;Iezzoni A;Mockler T;Wilhelm L;Van de Weg E;Gardiner SE;Bassil N;Peace C
通讯作者：
Peace C
影响因子：
4.4
作者：
Dubois A;Carrere S;Raymond O;Pouvreau B;Cottret L;Roccia A;Onesto JP;Sakr S;Atanassova R;Baudino S;Foucher F;Le Bris M;Gouzy J;Bendahmane M
通讯作者：
Bendahmane M