APMicroDB: A microsatellite database of Acyrthosiphon pisum

Genomics Data Pub Date : 2017-06-01 DOI:10.1016/j.gdata.2017.03.014

Ritika Bishnoi , Deepak Singla

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引用次数: 1

Abstract

Pea aphids represent a complex genetic system that could be used for QTL analysis, genetic diversity and population genetics studies. Here, we described the development of first microsatellite repeat database of the pea aphid (APMicroDB), accessible at “http://deepaklab.com/aphidmicrodb”. We identified 3,40,233 SSRs using MIcroSAtellite (MISA) tool that was distributed in 14,067 (out of 23,924) scaffold of the pea aphid. We observed 89.53% simple repeats of which 73.41% were mono-nucleotide, followed by di-nucleotide repeats. This database stored information about the repeats kind, GC content, motif type (mono - hexa), genomic location etc. We have also incorporated the primer information derived from Primer3 software of the 250bp flanking region of the identified marker. Blast tool is also provided for searching the user query sequence for identified marker and their primers. This work has an immense use for scientific community working in the field of agricultural pest management, QTL mapping, and host-pathogen interaction analysis.

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APMicroDB:一个微卫星数据库

豌豆蚜虫是一个复杂的遗传系统，可用于QTL分析、遗传多样性和群体遗传学研究。在这里，我们描述了豌豆蚜虫的第一个微卫星重复数据库(APMicroDB)的开发，可访问“http://deepaklab.com/aphidmicrodb”。我们使用MIcroSAtellite (MISA)工具鉴定了340233个SSRs，分布在14067个(23924个)豌豆蚜虫支架中。其中单核苷酸重复数占73.41%，其次是双核苷酸重复数。该数据库存储了重复序列类型、GC含量、基序类型(单六元)、基因组位置等信息。我们还结合了从Primer3软件中得到的鉴定标记250bp侧翼区域的引物信息。还提供Blast工具，用于在用户查询序列中搜索已识别的标记物及其引物。这项工作对农业有害生物管理、QTL定位和宿主-病原体相互作用分析等领域的科学界工作具有巨大的应用价值。

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Genomics Data

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12 weeks