home > bioproject > PRJDB2225
identifier PRJDB2225
type bioproject
sameAs
sra-study  DRP000455
organism Cryptomeria japonica
title Analysis of microsatellites on expressed sequence tags and development of EST-SSR markers for a conifer, Cryptomeria japonica - A scheme for the second generation
description We collected 141,097 and 1,333,444 sequence reads by Sanger and pyrosequencing method, respectively. After trimming contaminant and low quality sequences 118,319 Sanger and 1,201,150 pyrosequencing reads were passed to the MIRA assembler, which resulted in 81,284 contigs for which SSR analyses were conducted. We found 4,119 SSRs in 3,694 (4.54 %) contigs, showing lower frequency than that in seven other plant species in gene index (5.4 - 21.9 %). Average GC percent of these contigs were 41.55 %, a value higher than those for whole contigs (40.23 %). Although tri-SSRs were the most common, AT motif (655 or 46.3 % of di-SSRs) had the highest frequency, following AAG motif (342 or 25.9 % in tri-SSRs). Most (72.8 %) of tri-SSRs resided in coding regions, while 55.6 % of di-SSRs were in non-coding regions where higher frequency of AT motif was found in 3’ untranslated regions. Gene ontology (GO) annotations showed six GO terms were significantly over-represented within SSR-containing contigs. Forty-four EST-SSR markers were developed from 192 prime pairs by two pipelines read2Marker and CMiB combining several open tools. Markers resulting from both pipelines showed no differences in PCR success rate and polymorphisms, while expected PCR product size and number of SSR repeats showed significant effects on PCR success and polymorphisms, respectively. EST-SSR markers showed lower polymorphisms than genomic SSRs. none provided
data type DDBJ SRA Study
publication
22507374
external link
properties 
{...}
dbXrefs
sra-run  DRR001377DRR001378DRR001379
sra-submission  DRA000446
biosample  SAMD00009375
sra-study  DRP000455
sra-sample  DRS000986
sra-experiment  DRX000973
distribution JSONJSON-LD
status public
visibility unrestricted-access
dateCreated 2014-05-12T00:46:27+0000
dateModified 2014-05-12T00:46:27+0000
datePublished 2014-05-12T00:46:27+0000