PMC:3820681 / 22597-24109 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3820681","sourcedb":"PMC","sourceid":"3820681","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3820681","text":"ORF identification and SSR discovery\nThe “getorf” function of EMBOSS software was used to identify the ORFs of the assembled sequences. Of the 134,684 assembled C. fluminea unigene sequences, 105,737 (78.50%) had an ORF longer than 100 bp, with an average length of 445 bp (min length = 102, max length = 11,592, Figure 4).\n10.1371/journal.pone.0079516.g004 Figure 4 ORF lengths of the C. fluminea transriptome. The application of marker-assisted selection (MAS) or genome-wide marker-assisted selection (G-MAS) can be employed in the C. fluminea breeding program. Currently, a limited collection of genetic markers is available for C. fluminea. In this study, simple sequence repeats (SSRs) were identified. The putative and filtered SSRs C. fluminea are shown in Table S5. In total, 2,151 SSRs were identified from the assembled sequences (Table 4). Of 1,547 SSR-containing sequences, 340 SSRs were present in compound form, and 452 sequences contained more than one SSR. The most frequent repeat motifs were tri-nucleotides, which accounted for 57.83% of all SSRs, followed by di-nucleotides (31.38%), tetra-nucleotides (7.53%), penta-nucleotides (3.11%) and hexa-nucleotides (0.14%). These SSRs would be top candidates for marker development and very helpful for further research involving population genetic structuring, relatedness, genetic or genomic studies on this species.\n10.1371/journal.pone.0079516.t004 Table 4 Summary of simple sequence repeat (SSR) types in the C. fluminea transcriptome.\n\nI","divisions":[{"label":"Title","span":{"begin":0,"end":36}},{"label":"Figure caption","span":{"begin":324,"end":414}},{"label":"Title","span":{"begin":368,"end":412}},{"label":"Table caption","span":{"begin":1387,"end":1511}},{"label":"Title","span":{"begin":1430,"end":1509}}],"tracks":[]}