Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations.
Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations.
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DOI：
10.1111/1755-0998.12301
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发表时间：
2015-03
影响因子：
7.7
通讯作者：
Munshi-South J
中科院分区：
文献类型：
--
作者：
Harris SE;O'Neill RJ;Munshi-South J
基因组资源是重要的和可获得的研究非模式物种的不同自然种群的进化变化。我们利用两个下一代测序（NGS）平台，454和SOLiD 5500 XL，组装低覆盖率的白足小鼠（白足鼠），一个广泛和丰富的本地啮齿动物在北美东部的转录组。我们对来自纽约市城市人群和附近未受干扰的保护区农村人群的多个个体的肝脏mRNA转录物进行了测序，并使用1，080，065，954 SOLiD 5500 XL（75 bp）读数和3，052，640 454 GS FLX +读数组装了参考转录组。参考品含有40，908个重叠群，N50 = 1，044 bp，总含量为30.06 Mb。从与小家鼠（39.96%注释）Uniprot数据库的比较中注释重叠群。我们使用侧翼引物鉴定了104，655个高质量单核苷酸多态性（SNP）和65个单序列重复（SSR）。我们还使用标准化的读段计数来鉴定群体之间10个基因中推定的基因表达差异。与农村人群相比，城市人群中有19个重叠群显著差异表达，基因功能注释通常与蛋白质的翻译和修饰以及参与免疫应答的基因相关。在这项研究中产生的个人转录组将被用来调查城市化的进化反应。参考转录组提供了一个宝贵的资源，为科学界使用北美Peromyscus物种作为生态遗传学和适应的新兴模式系统。
Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of non-model species. We utilized two Next Generation Sequencing (NGS) platforms, 454 and SOLiD 5500XL, to assemble low coverage transcriptomes of the white-footed mouse (Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver mRNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby, and assembled a reference transcriptome using 1,080,065,954 SOLiD 5500XL (75 bp) reads and 3,052,640 454 GS FLX + reads. The reference contained 40,908 contigs with a N50 = 1,044 bp and a total content of 30.06 Megabases (Mb). Contigs were annotated from comparisons to Mus musculus (39.96% annotated) Uniprot databases. We identified 104,655 high quality single nucleotide polymorphisms (SNPs) and 65 single sequence repeats (SSRs) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 10 genes between populations. There were 19 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using North American Peromyscus species as emerging model systems for ecological genetics and adaptation.
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影响因子：
10.7
作者：
Chapman MA;Hiscock SJ;Filatov DA
通讯作者：
Filatov DA
影响因子：
7.7
作者：
De Wit, Pierre;Pespeni, Melissa H.;Palumbi, Stephen R.
通讯作者：
Palumbi, Stephen R.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
7.7
作者：
Faircloth, Brant C.
通讯作者：
Faircloth, Brant C.
影响因子：
5.8
作者：
Conesa, A;Götz, S;Robles, M
通讯作者：
Robles, M