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...
Main Authors: | , |
---|---|
Format: | Article |
Language: | English |
Published: |
Elsevier
2017-06-01
|
Series: | Genomics Data |
Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596016301726 |
id |
doaj-f5e816a5cd7c4b5eb15479a6db733fe0 |
---|---|
record_format |
Article |
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 |
work_keys_str_mv |
AT ritikabishnoi apmicrodbamicrosatellitedatabaseofacyrthosiphonpisum AT deepaksingla apmicrodbamicrosatellitedatabaseofacyrthosiphonpisum |
_version_ |
1724892967949303808 |