Tuesday, October 9, 2018

Characteristics of SSR Markers in #FlocculariaLuteo-virens by #RNA -Sequencing by Zhanling Xie in BJSTR

Abstract

Simple sequence repeats (SSRs) in Transcript and Unigene of #FlocculariaLuteo-virens were determined by #RNA sequencing. There were 4, 715 SSRs in 38, 988 Transcript sequences and 2, 910 SSRs in 22, 122 Unigene sequences using de novo sequencing, respectively. Mononucleotides showed the highest frequency of 26.16% in Transcript, and the ratio of #mononucleotides was A>T>G>C; while in Unigene, #dinucleotides showed the highest of 59.27%, and the ratio of dinucleotides was TG/GT>AC/CA>AT/TA>AG/GA. The SSR with 10 repeats was the most abundant in #Transcript (26.36%), while that with six repeats was the most abundant in Unigene (22.71%). Motif A had the highest frequency of 17.50% and 11.65% in Transcript and Unigene, while Motif C had the lowest frequency of l 1.10% and 1.08% in Transcript and Unigene, respectively. For the PCR products, seven primers were screened and tested from the motifs, the result were in consistent with RNA sequencing results.




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