scholarly journals Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum

Nature ◽  
2004 ◽  
Vol 428 (6986) ◽  
pp. 942-945 ◽  
Author(s):  
Joshua B. Plotkin ◽  
Jonathan Dushoff ◽  
Hunter B. Fraser
Keyword(s):  
Genome Sequence ◽  
Single Genome ◽  
Single Genome Sequence

scholarly journals IDSSR: An Efficient Pipeline for Identifying Polymorphic Microsatellites from a Single Genome Sequence

2019 ◽  
Vol 20 (14) ◽  
pp. 3497 ◽  
Author(s):  
Xuan-Min Guang ◽  
Jin-Quan Xia ◽  
Jian-Qing Lin ◽  
Jun Yu ◽  
Qiu-Hong Wan ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Experimental Validation ◽  
High Reliability ◽  
Molecular Ecology ◽  
Polymorphic Ssrs ◽  
Screening Experiments ◽  
Single Genome ◽  
New Strategy ◽  
Nucleotide Insertions ◽  
Single Genome Sequence

Simple sequence repeats (SSRs) are known as microsatellites, and consist of tandem 1–6-base motifs. They have become one of the most popular molecular markers, and are widely used in molecular ecology, conservation biology, molecular breeding, and many other fields. Previously reported methods identify monomorphic and polymorphic SSRs and determine the polymorphic SSRs via experimental validation, which is potentially time-consuming and costly. Herein, we present a new strategy named insertion/deletion (INDEL) SSR (IDSSR) to identify polymorphic SSRs by integrating SSRs with nucleotide insertions/deletions (INDEL) solely based on a single genome sequence and the sequenced pair-end reads. These INDEL indexes and polymorphic SSRs were identified, as well as the number of repeats, repeat motifs, chromosome location, annealing temperature, and primer sequences, enabling future experimental approaches to determine the correctness and polymorphism. Experimental validation with the giant panda demonstrated that our method has high reliability and stability. The efficient SSR pipeline would help researchers obtain high-quality genetic markers for plants and animals of interest, save labor, and reduce costly marker-screening experiments. IDSSR is freely available at https://github.com/Allsummerking/IDSSR.

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