Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes

Kabra, Ritika; Kapil, Aditi; Attarwala, Kherunnisa; Kant, Piyush; Shanker, Asheesh

doi:10.1007/s11274-016-2061-0

Cited by 12 publications

(15 citation statements)

References 30 publications

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“…Computational approaches have become a relatively less time consuming and inexpensive to develop SSRs. Previously, using computational approaches SSRs were mined in large amount of sequence data retrieved from National Centre for Biotechnology Information (NCBI) and online databases were developed for obtained information (Kapil et al, 2014;Kumar et al, 2014;Kabra et al, 2016). The availability of nucleotide/genome sequence of various organisms in biological databases proved to be a fast and inexpensive way for computational mining of SSRs (Shanker, 2013(Shanker, , 2014Shanker, 2016;Kumar & Shanker, 2018c).…”

Section: Introductionmentioning

confidence: 99%

“…Earlier, SSRs were identified in various plants including Citrus sinensis (Shanker et al, 2007), Gracilaria tenuistipitata (Song et al, 2014), Cocos nucifera (Srivastava & Shanker, 2015), Glycine species (Ozyigit et al, 2015), Magnoliids (Srivastava & Shanker, 2016), Euphorbia esula (Sen et al, 2017), Arabidopsis (Kumar & Shanker, 2018), and Triticum (Kapil et al, 2018). However, the trend to detect common, polymorphic, and unique cpSSRs is relatively new (Kabra et al, 2016;Kapil et al, 2018) and no such information is available for genus Nymphaea. Therefore, the present analysis was conducted to mine SSRs in chloroplast genomes of genus Nymphaea and detect common, polymorphic, and unique cpSSRs in them.…”

Section: Introductionmentioning

confidence: 99%

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

Kumar¹,

Shanker²

2020

JSR

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Simple sequence repeats (SSRs) also known as microsatellites, found in almost all organisms, are one of the widely used genetic markers. Despite the availability of a number of chloroplast genome of genus Nymphaea the information about its chloroplast SSR (cpSSR) is not well understood. In the present study, a total of 96 cpSSRs were mined in 6 chloroplast genome of genus Nymphaea (N. alba, N. ampla, N. capensis, N. jamesoniana, N. lotus, and N. mexicana). Mononucleotides (33, 34.38%) were most abundant followed by tri-nucleotides (24, 25%), tetra-nucleotides (19, 19.79%), di-nucleotides (14, 14.58%), whereas penta-and hexanucleotides (3, 3.13%) were found with equal frequency among chloroplast genomes of genus Nymphaea. Moreover, common, polymorphic, and unique SSRs were also searched between each chloroplast genomes. The identified common, polymorphic, and unique cpSSRs may play an important role in analysis of genetic diversity of genus Nymphaea.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Kumar¹,

Shanker²

2020

JSR

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“…Microsatellites, which is also acknowledged as Simple Sequence Repeats (SSRs) are short repeat sequences of 1-6 nucleotides present in both prokaryotic and eukaryotic organism (1,2). These repetitions are omnipresent and play a key role in the development of molecular markers.…”

Section: Introductionmentioning

confidence: 99%

“…Computational microsatellites mining is easier, inexpensive and helps in repeat identification in whole genome sequences. Therefore, microsatellites specific biological databases were developed (1,5,6).…”

Section: Introductionmentioning

confidence: 99%

Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)

et al. 2019

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Microsatellites or SSRs are the markers of selection due to their reproducibility, degree of polymorphism, distribution throughout the genome and co-dominant nature. Microsatellites are used primarily to study the genetic variability in various species and marker aided selection. Since microsatellites can be readily amplified by PCR, they have been utilized most extensively. To reduce time and cost to a great extent, the computational approach for identifying and developing microsatellite markers by mining nucleotide sequences is preferred over the conventional methods. In present analysis an in-silico method was used to detect microsatellites effectively in mitochondrial genomes of Anomodon rugelii (Müll. Hal.) Keissl., Anomodon attenuates (Hedw.) Hueb., Climacium americanum (Renauld & Cardot) Kindberg, and Hypnum imponens Hedw. (Bryopsida; Hypnales). A total of 101 perfect microsatellites were mined with an average density of 1 microsatellite/4.21 kb. The hexa-nucleotide repeats were not detected in mitochondrial genomes of studied taxa. Di-nucleotides were seen to be the most frequent repeats followed by tetra-nucleotides. The identified microsatellites were also checked for variability in length between species. The mined microsatellites will be used for gene tagging, species identification and population genetic studies.

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“…CyanoBase is a popular cyanobacterial genome database that covers the sequence of 39 strains of cyanobacteria and related species . In addition to CyanoBase, more than 281 cyanobacterial genome sequences are currently available, and this number continues to grow.…”

Section: Genetic Engineering Improvements To Cyanobacteria For Industmentioning

confidence: 99%

Molecular genetic improvements of cyanobacteria to enhance the industrial potential of the microbe: A review

Johnson

Gibbons

et al. 2016

Biotechnology Progress

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The rapid increase in worldwide population coupled with the increasing demand for fossil fuels has led to an increased urgency to develop sustainable sources of energy and chemicals from renewable resources. Using microorganisms to produce high-value chemicals and next-generation biofuels is one sustainable option and is the focus of much current research. Cyanobacteria are ideal platform organisms for chemical and biofuel production because they can be genetically engineered to produce a broad range of products directly from CO , H O, and sunlight, and require minimal nutrient inputs. The purpose of this review is to provide an overview on advances that have been or could be made to improve strains of cyanobacteria for industrial purposes. First, the benefits of using cyanobacteria as a platform for chemical and biofuel production are discussed. Next, an overview of cyanobacterial strain improvements by genetic engineering is provided. Finally, mutagenesis techniques to improve the industrial potential of cyanobacteria are described. Along with providing an overview on various areas of research that are currently being investigated to improve the industrial potential of cyanobacteria, this review aims to elucidate potential targets for future research involving cyanobacteria as an industrial microorganism. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1357-1371, 2016.

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Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes

Cited by 12 publications

References 30 publications

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

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

Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)

Molecular genetic improvements of cyanobacteria to enhance the industrial potential of the microbe: A review

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