APMicroDB: A microsatellite database of Acyrthosiphon pisum

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 identif...

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Main Authors: Ritika Bishnoi, Deepak Singla
Format: Article
Language:English
Published: Elsevier 2017-06-01
Series:Genomics Data
Online Access:http://www.sciencedirect.com/science/article/pii/S2213596016301726
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spelling doaj-f5e816a5cd7c4b5eb15479a6db733fe02020-11-25T02:16:05ZengElsevierGenomics Data2213-59602017-06-0112C11111510.1016/j.gdata.2017.03.014APMicroDB: A microsatellite database of Acyrthosiphon pisumRitika Bishnoi0Deepak Singla1Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, IndiaCentre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, IndiaPea 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.http://www.sciencedirect.com/science/article/pii/S2213596016301726
collection DOAJ
language English
format Article
sources DOAJ
author Ritika Bishnoi
Deepak Singla
spellingShingle Ritika Bishnoi
Deepak Singla
APMicroDB: A microsatellite database of Acyrthosiphon pisum
Genomics Data
author_facet Ritika Bishnoi
Deepak Singla
author_sort Ritika Bishnoi
title APMicroDB: A microsatellite database of Acyrthosiphon pisum
title_short APMicroDB: A microsatellite database of Acyrthosiphon pisum
title_full APMicroDB: A microsatellite database of Acyrthosiphon pisum
title_fullStr APMicroDB: A microsatellite database of Acyrthosiphon pisum
title_full_unstemmed APMicroDB: A microsatellite database of Acyrthosiphon pisum
title_sort apmicrodb: a microsatellite database of acyrthosiphon pisum
publisher Elsevier
series Genomics Data
issn 2213-5960
publishDate 2017-06-01
description 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.
url http://www.sciencedirect.com/science/article/pii/S2213596016301726
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