Microsatellite analysis in organelle genomes of Chlorophyta

Kuntal, Himani; Sharma, Vinay; Daniell, Henry

doi:10.6026/97320630008255

Cited by 18 publications

(8 citation statements)

References 12 publications

(18 reference statements)

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“…For dinucleotide repeats, AT/TA motif was the most common dinucleotide repeat with a frequency of 83.9%. These results are in agreement with previous findings (Gandhi et al 2010;Rajendrakumar et al 2007;Kuntal et al 2012). The higher AT/TA frequencies in chloroplast genomes can be explained to be the conclusion of the high A/T content of the genomes.…”

Section: Distribution Of Cpssrssupporting

confidence: 93%

“…The higher AT/TA frequencies in chloroplast genomes can be explained to be the conclusion of the high A/T content of the genomes. Among the trinucleotide repeats, AAG/CTT motif was the most common (28.9%) followed by AAT/TTA (24.9%) and AAC/GTT (16%) and this finding was not consistent with earlier studies results (Rajendrakumar et al 2007;Melotto-passarin et al 2011;Kuntal et al 2012). In tetranucleotide SSR motifs, the maximum frequency of 47.1% was showed by AAAG/CTTT followed by AAAT/ATTT (29.4%).…”

Section: Distribution Of Cpssrscontrasting

confidence: 66%

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In Silico chloroplast SSRs mining of Olea species

Filiz

Koç

2012

Biodiversitas

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Filiz E, Koc E. 2012. In Silico chloroplast SSRs mining of Olea species. Biodiversitas 13: 114-117. Simple sequence repeat (SSR) markers are highly informative and have been widely applied as molecular markers in genetic studies. The purpose of present study is to analyze the occurrence and distribution of chloroplast SSRs in genic and intergenic regions from Olea species viz., Olea europaea, Olea europaea subsp. cuspidate, Olea europaea subsp. europaea, Olea europaea subsp. maroccana, Olea woodiana subsp. woodiana by using bioinformatics tools. We identified 1149 chloroplast SSRs (cpSSRs) in all genome and a total of 340 (29.6%) was located in genic regions. It was observed that the most abundant repeat types were found mononucleotide SSR (66.7 %) followed by trinucleotide SSR (28.3 %), dinucleotide (2.7%), tetranucleotide (1.5%) and pentanucleotide (0.8%). cpSSRs located in genic regions were identified only mono-and trinucleotide motifs, the most abundant of which was trinucleotide (16.2%) followed by mononucleotide (14.3%). All types of repeat motif (mono-, di-, tri-, tetra-and pentanucleotide) were detected except hexanucleotide motifs. According to SSRs analysis, the most abundant observed motifs were identified for mono-, di-, tri-, tetra-and pentanucleotide cpSSRs A/T, AT/TA, AAG/CTT, AAAG/AGTTT, and AATCC/ATTGG respectively. This study results provided scientific base for phylogenetics, evolutionary genetics and diversity studies on different Olea species in future.

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Section: Distribution Of Cpssrssupporting

confidence: 93%

Section: Distribution Of Cpssrscontrasting

confidence: 66%

In Silico chloroplast SSRs mining of Olea species

Filiz

Koç

2012

Biodiversitas

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“…Complete mitochondrial genome sequence of the Haberlea rhodopensis are composed primarily of AT/AT and the rest of SRRs have a high content of A/T. These observations confirm other studies that polyA and polyT repeats are found in the mt genomes (Kuntal et al, 2012).…”

Section: Srrssupporting

confidence: 89%

Analysis of the complete mitochondrial genome sequence of the resurrection plant Haberlea rhodopensis

et al. 2021

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Haberlea rhodopensis is a paleolithic tertiary relict species that belongs to the unique group of resurrection plants sharing remarkable tolerance to desiccation. When exposed to severe drought stress, this species shows an ability to maintain structural integrity of its deactivated photosynthetic apparatus, which easily reactivates upon rehydration. In addition to its homoiochlorophyllous nature, the resurrection capability of H. rhodopensis is of particular importance to the global climate change mitigation. In this study, we sequenced, assembled, and analyzed the mitochondrial (mt) genome of H. rhodopensis for the first time. The master circle has a typical circular structure of 484 138 bp in length with a 44.1% GC content in total. The mt genome of H. rhodopensis contains 59 genes in total, including 35 protein-coding, 21 tRNAs, and 3 rRNAs genes. 7 tandem repeats and 85 simple sequence repeats (SSRs) are distributed throughout the mt genome. The alignment of 20 plant mt genomes confirms the phylogenetic position of H. rhodopensis in the Lamiales order. Our comprehensive analysis of the complete mt genome of H. rhodopensis is a significant addition to the limited database of organelle genomes of resurrection species. Comparative and phylogenetic analysis provides valuable information for a better understanding of mitochondrial molecular evolution in plants.

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“…Moreover a specific poly (A) 12 mononucleotide genic sequence located in rps3 was found specifically in CCMP531 mt genome. SSRs offer potential advantage for strain discrimination as they are locus-specific, PCR-friendly and highly polymorphic [72]. Thus the three specific SSRs identified can be used to identify CCMP531 and IMET1.…”

Section: Resultsmentioning

confidence: 99%

Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae

Wei

Wang

et al. 2013

BMC Genomics

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BackgroundMicroalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes.ResultsUsing the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species.ConclusionThis first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy for intragenus phylotyping of microalgae was proposed which might be generally applicable to other microalgal genera and should serve as a valuable tool in the expanding algal biotechnology industry.

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Microsatellite analysis in organelle genomes of Chlorophyta

Cited by 18 publications

References 12 publications

In Silico chloroplast SSRs mining of Olea species

In Silico chloroplast SSRs mining of Olea species

Analysis of the complete mitochondrial genome sequence of the resurrection plant Haberlea rhodopensis

Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae

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