In Silico Comparative Analysis of Simple Sequence Repeats in Chloroplast Genomes of Genus Nymphaea

Kumar, Sumit; Shanker, Asheesh

doi:10.37398/jsr.2020.640127

Cited by 3 publications

(3 citation statements)

References 27 publications

(24 reference statements)

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“…Earlier, mtSSRs were identified in various plants including order Hypnales (Anand et al, 2019), Aneura pinguis (L.) Dumort (Kumar & Shanker, 2020a), and Orthotrichum (Kumar et al, 2020). Apart from these, SSRs were also mined in chloroplast genomes of Arabidopsis (Kumar & Shanker, 2018a) and Nymphaea (Kumar & Shanker, 2020c). In all these studies, the distribution of mono-/hexanucleotide repeat motifs also varied from species to species, which is congruent with the present study.…”

Section: Discussionsupporting

confidence: 91%

“…Other repeat motifs and identical repeat motifs showing no significant similarity of flanking sequences with any of the species in the same genus were considered as unique microsatellites (Kumar & Shanker, 2020a, 2020c. A schematic representation to detect common, polymorphic, and unique microsatellites is presented in Fig 4.…”

Section: Detection Of Common Polymorphic and Unique Mtssrsmentioning

confidence: 99%

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pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites

2022

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Microsatellites, also termed as simple sequence repeats, are repetitive tracts in a DNA sequence, typically consisting of one to six nucleotides. These repeats are found in all genomes and play key roles in phylogeny and species identification. Microsatellites are highly polymorphic, and their length may differ from species to species. There are several online resources dedicated to mitochondria; however, comprehensive information is not available about the length variation of mitochondrial microsatellites. Therefore, to explore it between species among a genus, we have developed a database named pSATdb (polymorphic microSATellites database; https://lms.snu.edu.in/pSATdb/). pSATdb contains 28,710 perfect microsatellites identified across 5,976 mitochondrial genome (mt-genome) sequences from 1,576 genera which includes 1,535 (5,846 mt-genome) and 41 (130 mt-genome) genera of Metazoa and Viridiplantae, respectively. pSATdb is the only database which provides genus-wise information about the length variation of mitochondrial microsatellites. Because of the emerging role of microsatellites in genomics studies, the identified common, polymorphic, and unique microsatellites stored in pSATdb will be effectively useful in various studies including genetic diversity, mapping, marker-assisted selection, and comparative population studies.

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Section: Discussionsupporting

confidence: 91%

Section: Detection Of Common Polymorphic and Unique Mtssrsmentioning

confidence: 99%

pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites

2022

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“…In the chloroplast genome, microsatellites or SSRs distributed in the genome with the length of almost 1 bp to 6 bp. Previously many studies reported SSRs at different positions in chloroplast genomes 55,56 . In the present study, SSRs distributed at different locations such as IR regions, LSC and SSC region were identified in the A. marina.…”

Section: Discussionmentioning

confidence: 99%

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Asaf

Khan

Numan

et al. 2021

Sci Rep

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Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

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In Silico Mining of Simple Sequence Repeats in Mitochondrial Genomes of Genus Orthotrichum

Kumar¹,

Kumari²,

Shanker³

2020

JSR

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In Silico Comparative Analysis of Simple Sequence Repeats in Chloroplast Genomes of Genus Nymphaea

Cited by 3 publications

References 27 publications

pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites

pSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

In Silico Mining of Simple Sequence Repeats in Mitochondrial Genomes of Genus Orthotrichum

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