Simple sequence repeats mining using computational approach in chloroplast genome of Marchantia polymorpha

Simple sequence repeats (SSRs) consist of short repeat motifs of 1-6 nucleotides and are found in DNA sequences.The present study was conducted to detect SSRs in chloroplast genome of Tetraphis pellucida (Accession number: NC_024291), downloaded from the National Center for Biotechnology Information (NCBI). The sequence was mined with the help of MISA, a Perl script, to detect SSRs. The length of SSRs defined as ≥12 for mono, di, tri and tetranucleotide, ≥15 for pentanucleotide and ≥18 for hexanucleotide repeats. In total, 41 perfect microsatellites were identified in 127.489 kb sequence mined. An average length of 13.56 bp was calculated for mined SSRs with a density of 1 SSR/3.04 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 20 nt. Dinucleotides (14, 34.15%) were the most frequent repeat type, followed by tetranucleotides (10, 24.39%), trinucleotides (7, 17.07%), mononucleotides (6, 14.63%) and pentanucleotide (4, 9.76%) repeats. Hexanucleotide repeats were completely absent in chloroplast genome of Tetraphis pellucida. The mined SSRs can be used to develop molecular markers and genetic diversity studies in Tetraphis species.

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Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

Ecology and Evolution ◽

10.1002/ece3.8151 ◽

2021 ◽

Author(s):

Ming Zhu ◽

Peipei Feng ◽

Jingyao Ping ◽

Jinye Li ◽

YingJuan Su ◽

...

Keyword(s):

Chloroplast Genome ◽

Simple Sequence Repeats ◽

Phylogenetic Significance ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Genus Level ◽

Simple Sequence

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A Low Mutation Rate For Chloroplast Microsatellites

Genetics ◽

10.1093/genetics/153.2.943 ◽

1999 ◽

Vol 153 (2) ◽

pp. 943-947

Author(s):

Jim Provan ◽

Nicole Soranzo ◽

Neil J Wilson ◽

David B Goldstein ◽

Wayne Powell

Keyword(s):

Chloroplast Genome ◽

Mutation Rate ◽

Simple Sequence Repeats ◽

Mutation Rates ◽

Chloroplast Microsatellites ◽

Ssr Loci ◽

Nuclear Ssr ◽

Monomorphic Population ◽

Simple Sequence ◽

Pinus Torreyana

Abstract We used chloroplast simple sequence repeats (cpSSRs) to examine whether there is any variation present in the chloroplast genome of Pinus torreyana (Parry ex Carrière) that may previously not have been detected using RFLPs. Analysis of 17 cpSSR loci showed no variation, which is consistent with previous cpRFLP work and confirms that the species is descended from an original, highly monomorphic population following a bottleneck. This lack of biological variation in the chloroplast genome of P. torreyana allowed us to estimate the mutation rates at cpSSR loci as between 3.2 × 10-5 and 7.9 × 10-5. This estimate is lower than published mutation rates at nuclear SSR loci but higher than substitution rates elsewhere in the chloroplast genome.

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The Complete Chloroplast Genome Sequence of Four Plant Species, Their SSR Identification and Phylogenetic Analysis

10.20944/preprints202110.0246.v1 ◽

2021 ◽

Author(s):

Yueyi Zhu ◽

Xianwen Zhang ◽

Guopeng Li ◽

Jiqian Xiang ◽

Jinghua Su ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Molecular Markers ◽

Chloroplast Genome ◽

Simple Sequence Repeats ◽

Genetic Information ◽

Phylogenetic Trees ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes ◽

Chloroplast Genome Sequence ◽

Simple Sequence

The chloroplast genome is conservative and stable, which can be employed to resolve genotypes. Currently, published nuclear sequences and molecular markers failed to differentiate the species from taxa robustly, including Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. In this study, the four chloroplast genomes were characterized, and then their simple sequence repeats (SSRs) and phylogenetic positions were analyzed. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. Moreover, the chloroplast genomes contained typical four regions. Six classes of SSR were identified from the four chloroplast genomes, in which mononucleotide was the class with the most members. The types of the repeats were various within individual classes of SSR. Phylogenetic trees indicated that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed under family Ocimeae. Additionally, R. bambusarum and R. henryi were clustered together, whereas they did not belong to the same species due to the differing SSR features. This research would provide evidence for resolving the species and contributed new genetic information for further study.

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