龙胆科植物基因组中简单序列重复的挖掘

Mining of simple sequence repeats in the Genome of Gentianaceae.

作者信息

Sathishkumar R, Lakshmi P T V, Annamalai A, Arunachalam V

机构信息

Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.

出版信息

Pharmacognosy Res. 2011 Jan;3(1):19-29. doi: 10.4103/0974-8490.79111.

DOI:10.4103/0974-8490.79111

PMID:21731391

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3119266/

Abstract

Simple sequence repeats (SSRs) or short tandem repeats are short repeat motifs that show high level of length polymorphism due to insertion or deletion mutations of one or more repeat types. Here, we present the detection and abundance of microsatellites or SSRs in nucleotide sequences of Gentianaceae family. A total of 545 SSRs were mined in 4698 nucleotide sequences downloaded from the National Center for Biotechnology Information (NCBI). Among the SSR sequences, the frequency of repeat type was about 429 -mono repeats, 99 -di repeats, 15 -tri repeats, and 2 --hexa repeats. Mononucleotide repeats were found to be abundant repeat types, about 78%, followed by dinucleotide repeats (18.16%) among the SSR sequences. An attempt was made to design primer pairs for 545 identified SSRs but these were found only for 169 sequences.

摘要

简单序列重复（SSRs）或短串联重复是短重复基序，由于一种或多种重复类型的插入或缺失突变而表现出高度的长度多态性。在此，我们展示了龙胆科核苷酸序列中微卫星或SSRs的检测及丰度情况。从美国国立生物技术信息中心（NCBI）下载的4698个核苷酸序列中总共挖掘出545个SSRs。在这些SSR序列中，重复类型的频率约为429个单核苷酸重复、99个二核苷酸重复、15个三核苷酸重复和2个六核苷酸重复。单核苷酸重复被发现是丰富的重复类型，在SSR序列中约占78%，其次是二核苷酸重复（18.16%）。我们尝试为545个已鉴定的SSRs设计引物对，但仅为169个序列成功设计出引物对。