Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource
We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were compl...
Main Authors: | , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2018-03-01
|
Series: | Frontiers in Plant Science |
Subjects: | |
Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2018.00401/full |
id |
doaj-6318079c3c094247919e4c0e0e53b9ca |
---|---|
record_format |
Article |
spelling |
doaj-6318079c3c094247919e4c0e0e53b9ca2020-11-24T22:26:34ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-03-01910.3389/fpls.2018.00401350273Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web ResourceEzio Portis0Sergio Lanteri1Lorenzo Barchi2Flavio Portis3Luisa Valente4Laura Toppino5Giuseppe L. Rotino6Alberto Acquadro7Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, ItalyDipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, ItalyDipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, ItalyYebokey, Turin, ItalyYebokey, Turin, ItalyCREA-GB, Research Centre for Genomics and Bioinformatics, Lodi, ItalyCREA-GB, Research Centre for Genomics and Bioinformatics, Lodi, ItalyDipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, ItalyWe have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an intervening block of <100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an “Eggplant Microsatellite DataBase” (EgMiDB) which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an in silico PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions.http://journal.frontiersin.org/article/10.3389/fpls.2018.00401/fulldatabaseeggplantgenomemicrosatelliteSolanum melongenaSSR |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ezio Portis Sergio Lanteri Lorenzo Barchi Flavio Portis Luisa Valente Laura Toppino Giuseppe L. Rotino Alberto Acquadro |
spellingShingle |
Ezio Portis Sergio Lanteri Lorenzo Barchi Flavio Portis Luisa Valente Laura Toppino Giuseppe L. Rotino Alberto Acquadro Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource Frontiers in Plant Science database eggplant genome microsatellite Solanum melongena SSR |
author_facet |
Ezio Portis Sergio Lanteri Lorenzo Barchi Flavio Portis Luisa Valente Laura Toppino Giuseppe L. Rotino Alberto Acquadro |
author_sort |
Ezio Portis |
title |
Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource |
title_short |
Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource |
title_full |
Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource |
title_fullStr |
Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource |
title_full_unstemmed |
Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource |
title_sort |
comprehensive characterization of simple sequence repeats in eggplant (solanum melongena l.) genome and construction of a web resource |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2018-03-01 |
description |
We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an intervening block of <100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an “Eggplant Microsatellite DataBase” (EgMiDB) which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an in silico PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions. |
topic |
database eggplant genome microsatellite Solanum melongena SSR |
url |
http://journal.frontiersin.org/article/10.3389/fpls.2018.00401/full |
work_keys_str_mv |
AT ezioportis comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource AT sergiolanteri comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource AT lorenzobarchi comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource AT flavioportis comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource AT luisavalente comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource AT lauratoppino comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource AT giuseppelrotino comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource AT albertoacquadro comprehensivecharacterizationofsimplesequencerepeatsineggplantsolanummelongenalgenomeandconstructionofawebresource |
_version_ |
1725752876437864448 |