<abstract xml:lang="en" xmlns="http://www.w3.org/1999/xhtml"><p>SSR markers have become the most popular resource for studying population genetic variation in eukaryotes. However, few studies with SSR markers have been carried out with phytoparasitic nematodes. In this study a primary survey on EST-SSRs was made utilizing bioinformatics methods to derive SSRs from expressed sequence tags (ESTs) of 16 species of PPN, which belong to 7 genera and 5 families. The results showed that trinucleotide repeats were the most abundant SSRs in coding ESTs, while tetranucleotide SSRs were predominant in non-coding ESTs and genome sequences. AG/CT, AAC/GTT and (AAAN)n motifs were predominant, and CG/GC, ACT/AGT motifs were scanty in the ESTs of most genera and species. SSRs were more abundant in non-coding ESTs than in coding ESTs. The distribution frequencies of SSR motifs in coding ESTs, non-coding ESTs and genomes are different. Our results will provide useful information for screening SSRs from each genus and species for further genetic study of phytoparastic nematodes.</p></abstract>

SSR markers have become the most popular resource for studying population genetic variation in eukaryotes. However, few studies with SSR markers have been carried out with phytoparasitic nematodes. In this study a primary survey on EST-SSRs was made utilizing bioinformatics methods to derive SSRs from expressed sequence tags (ESTs) of 16 species of PPN, which belong to 7 genera and 5 families. The results showed that trinucleotide repeats were the most abundant SSRs in coding ESTs, while tetranucleotide SSRs were predominant in non-coding ESTs and genome sequences. AG/CT, AAC/GTT and (AAAN)n motifs were predominant, and CG/GC, ACT/AGT motifs were scanty in the ESTs of most genera and species. SSRs were more abundant in non-coding ESTs than in coding ESTs. The distribution frequencies of SSR motifs in coding ESTs, non-coding ESTs and genomes are different. Our results will provide useful information for screening SSRs from each genus and species for further genetic study of phytoparastic nematodes.

SSR data mined from expressed sequence tags of phytoparasitic nematodes

College of Life Sciences, Beijing Normal University, Beijing, 100875, China

Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing, 100081, China

Helminthologia

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

{"article-title":"SSR data mined from expressed sequence tags of phytoparasitic nematodes"}

SSR markers have become the most popular resource for studying population genetic variation in eukaryotes. However, few studies with SSR markers have been...

SSR data mined from expressed sequence tags of phytoparasitic nematodes

Published Online: Feb 13, 2010

Page range: 8 - 19

DOI: https://doi.org/10.2478/s11687-010-0002-2

Keywords
microsatellites, expressed sequence tags, plantparasitic nematodes

© 2010 Institute of Parasitology, SAS, Košice, Slovakia

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

SSR data mined from expressed sequence tags of phytoparasitic nematodes

Published Online: Feb 13, 2010

Page range: 8 - 19

DOI: https://doi.org/10.2478/s11687-010-0002-2

Keywordsmicrosatellites, expressed sequence tags, plantparasitic nematodes

© 2010 Institute of Parasitology, SAS, Košice, Slovakia

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
microsatellites, expressed sequence tags, plantparasitic nematodes