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

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

“…Common, polymorphic, and unique mtSSRs identified in this study were not equally distributed among each genus of Metazoa and Viridiplantae. The findings are also in harmony with the length variation of microsatellites detected between each pair of species in the genus Triticum (Kapil et al, 2014), genus Arabidopsis (Kumar & Shanker, 2018a), Order Hypnales (Anand et al, 2019), and genus Orthotrichum (Kumar et al, 2020).…”

“…In this study, microsatellites were identified in mitochondrial genomes of Metazoa and Viridiplantae and further categorized based on their genus as common, polymorphic, and unique. 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).…”

“…These repeats are found in coding, non-coding, and coding-non-coding regions of both eukaryotic and prokaryotic genomes (Shanker et al, 2007a(Shanker et al, , 2007bKapil et al, 2014;Kabra et al, 2016;Kumar & Shanker, 2018a). Moreover, these repeats have also been reported in organellar genome including mitochondria (Kumar et al, 2014(Kumar et al, , 2020Kumar & Shanker, 2020a).…”

“…Length variation between mined mtSSRs was detected using inhouse-developed Perl scripts. A reciprocal similarity search was performed using the Basic Local Alignment Search Tool (Altschul et al, 1997) to establish homologous relationship between sequences containing mtSSR and, 200 base pairs of flanking sequences from both upstream and downstream of microsatellites or all nucleotides if <200 (Kabra et al, 2016;Kumar & Shanker, 2018a;Kumar et al, 2020). Microsatellites having identical repeating units with equal length and showing significant sequence similarity were categorized as common mtSSRs (found in more than one organism), whereas identical repeating units with unequal length and showing significant sequence similarity were categorized as polymorphic mtSSRs (showing length variation between organisms of a genus).…”

“…Consequently, microsatellites were applied for a variety of purposes including genetic, evolutionary, molecular breeding, and phylogenetic studies (Agarwal et al, 2008;Stolle et al, 2013;Deng et al, 2016;Fu et al, 2016). Earlier, studies were conducted to identify microsatellites in mitochondrial genomes of the order Hypnales (Anand et al, 2019), Aneura pinguis (Kumar & Shanker, 2020a), and Orthotrichum (Kumar et al, 2020).…”