The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry).
The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry).
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DOI：
10.1093/gigascience/giy010
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发表时间：
2018-04-01
期刊：
影响因子：
9.2
通讯作者：
Sargent DJ
中科院分区：
文献类型：
--
作者：
Buti M;Moretto M;Barghini E;Mascagni F;Natali L;Brilli M;Lomsadze A;Sonego P;Giongo L;Alonge M;Velasco R;Varotto C;Šurbanovski N;Borodovsky M;Ward JA;Engelen K;Cavallini A;Cestaro A;Sargent DJ
委陵菜属与草莓属关系密切，是经济上重要的草莓属。微花委陵菜是一种不发育浆果但与野草莓具有许多形态和生态特征的物种。这些相似之处使薇甘菊成为比较基因组学研究的一个有吸引力的选择。维斯卡本研究对薇甘菊基因组进行了测序和注释，并利用开花和结果不同发育阶段的RNA-Seq数据进行了一系列基因预测。一个327 Mbp的序列和注释的薇甘菊的基因组，跨越2674个序列重叠群，N50大小为335，712，估计覆盖80%的总基因组大小的物种。委陵菜属的基因组比草莓属的基因组大，但恢复的序列支架在微同线水平上与委陵菜属的基因组显著共线。vesca，它最近的序列亲属。总共预测了33，602个基因，并且95.1%的基准通用单拷贝直向同源基因在所呈现的序列内是完整的。因此，我们认为，基因组的大多数基因丰富的区域已经测序。比较花和果实发育阶段的RNA-Seq数据，揭示了薇甘菊和F.所提供的数据是草莓属和蔷薇科浆果发育的未来研究的宝贵资源，它们也揭示了该家族基因组大小和组织的进化。
The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca. In this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced. Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca.The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
GDR（酒渣鼻科的基因组数据库）：酒渣鼻基因组学和遗传学数据的综合网络数据库。
影响因子：
14.9
作者：
Jung S;Staton M;Lee T;Blenda A;Svancara R;Abbott A;Main D
通讯作者：
Main D
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
7.4
作者：
Fang, SC;Fernandez, DE
通讯作者：
Fernandez, DE
影响因子：
14.9
作者：
Huala, E;Dickerman, AW;Rhee, SY
通讯作者：
Rhee, SY