Transcriptome of Xenopus andrei, an octoploid frog, during embryonic development.
Transcriptome of Xenopus andrei, an octoploid frog, during embryonic development.
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DOI：
10.1016/j.dib.2018.05.017
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发表时间：
2018-08
期刊：
影响因子：
1.2
通讯作者：
Saha MS
中科院分区：
文献类型：
--
作者：
Pownall ME;Cutler RR;Saha MS
虽然多倍性发生在整个鱼类和两栖类谱系中，但爪蟾属表现出多倍性的高发生率，26个已知物种中有25个是多倍体。然而，转录组信息目前只有一个这些物种，四倍体非洲爪蟾。非洲爪蟾，非洲爪蟾属内的一个二倍体物种，提供了一个机会，评估一个新的多倍体转录组在脊椎动物的发展。在从未受精卵到游泳蝌蚪阶段的九个不同发育阶段产生RNA-Seq数据，并且将原始FASTQ文件保存在NCBI SRA数据库（登录号SRP 134281）中。此外，将来自所有9个阶段的RNA-seq数据合并，以使用Trinity创建转录组的从头组装，并已保存在NCBI GEO数据库中（登录号GSE 111639）。据我们所知，这代表了第一个发表的一个二倍体脊椎动物转录组的组装。总共组装了849 Mb，这导致在具有630个碱基的重叠群N50的组装体中鉴定出1，650，048个转录物。这种RNA-Seq和转录组数据对于比较非洲爪蟾物种的多倍体转录组以及理解脊椎动物全基因组复制和多倍性的进化意义将是有价值的。
Although polyploidy occurs throughout the fish and amphibian lineages, the Xenopus genus exhibits a high incidence of polyploidy, with 25 out of the 26 known species being polyploid. However, transcriptomic information is currently available for only one of these species, the tetraploid Xenopus laevis. Xenopus andrei, an octoploid species within the Xenopus genus, offers an opportunity for assessing a novel polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through swimming tadpole stages and raw FASTQ files were deposited in the NCBI SRA database (accession number SRP134281). Additionally, RNA-seq data from all nine stages were pooled to create a de novo assembly of the transcriptome using Trinity and has been deposited in the NCBI GEO database (accession number GSE111639). To our knowledge, this represents the first published assembly of an octoploid vertebrate transcriptome. In total, 849 Mb were assembled, which led to the identification of 1,650,048 transcripts in the assembly with a contig N50 of 630 bases. This RNA-Seq and transcriptome data will be valuable for comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication and polyploidy in vertebrates.
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DOI：
10.1083/jcb.201502016
发表时间：
2015-05-25
期刊：
The Journal of cell biology
影响因子：
--
作者：
Schoenfelder KP;Fox DT
通讯作者：
Fox DT
影响因子：
48
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影响因子：
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通讯作者：
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影响因子：
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影响因子：
3.7
作者：
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通讯作者：
Blackburn, David C.