Genome-wide investigation and analysis of microsatellites and compound microsatellites in Leptolyngbya species, Cyanobacteria

Abstract Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in 36 genomes of Leptolyngbya. The results disclosed diversified patterns of distribution, abundance, density and diversity of SSRs and CSSRs in Leptolyngbya genomes. The numbers of SSRs and CSSRs were extremely uneven distributed among genomes, ranging from 11,086 to 27,292 and from 286 to 1,102, respectively. Mononucleotide SSRs were the most abundant category in 14 genomes, while the other 22 genomes followed the pattern: di- > mono- > trinucleotide SSRs. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly correlated with genome size (P < 0.01) and but not closely correlated with GC content (P > 0.05). Moreover, the motif (A/T)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 33 genomes. This study provides the first insight into SSRs and CSSRs in Leptolyngbya genomes and will be useful to contribute to future use as molecular markers in closely-related species.

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Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria

Life ◽

10.3390/life11111258 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1258

Author(s):

Dan Yao ◽

Lei Cheng ◽

Lianming Du ◽

Meijin Li ◽

Maurycy Daroch ◽

...

Keyword(s):

Environmental Changes ◽

Gc Content ◽

Phylogenetic Groups ◽

Coding Regions ◽

Genome Wide ◽

Evolutionary Advantage ◽

Fast Adaptation ◽

Almost All ◽

Insight Into ◽

Simple Sequence

Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in genomes of Leptolyngbya-like strains. The results disclosed diversified patterns of distribution, abundance, density, and diversity of SSRs and CSSRs in genomes, indicating that they may be subject to rapid evolutionary change. The numbers of SSRs and CSSRs were extremely unevenly distributed among genomes, ranging from 11,086 to 24,000 and from 580 to 1865, respectively. Dinucleotide SSRs were the most abundant category in 31 genomes, while the other 15 genomes followed the pattern: mono- > di- > trinucleotide SSRs. The patterns related to SSRs and CSSRs showed differences among phylogenetic groups. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly positively correlated with genome size (p < 0.01) and negatively correlated with GC content (p < 0.05). Moreover, the motif (A/C)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 39 genomes. This study provides the first insight into SSRs and CSSRs in genomes of Leptolyngbya-like strains and will be useful to understanding their distribution, predicting their function, and tracking their evolution. Additionally, the identified SSRs may provide an evolutionary advantage of fast adaptation to environmental changes and may play an important role in the cosmopolitan distribution of Leptolyngbya strains to globally diverse niches.

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The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”

Scientific Reports ◽

10.1038/srep12441 ◽

2015 ◽

Vol 5 (1) ◽

Author(s):

Geng Zou ◽

Bernardo Bello-Orti ◽

Virginia Aragon ◽

Alexander W. Tucker ◽

Rui Luo ◽

...

Keyword(s):

Amino Acids ◽

Simple Sequence Repeats ◽

Potential Role ◽

Gc Content ◽

Nucleotide Metabolism ◽

Coding Regions ◽

Purine Nucleotide Metabolism ◽

Go Terms ◽

Simple Sequence

Abstract Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like “vampire pathogens” (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3 and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.

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Genetic diversity and molecular markers of five snapper species

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236207001210 ◽

2007 ◽

Vol 4 (1) ◽

pp. 39-46 ◽

Cited By ~ 2

Author(s):

Liu Li ◽

Liu Chu-Wu

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Simple Sequence Repeats ◽

Microsatellite Loci ◽

Random Amplified Polymorphic Dna ◽

Genetic Distances ◽

The Other ◽

Information Contents ◽

The Mean ◽

Simple Sequence

AbstractIn order to protect and develop valuable snappers (Lutjanus spp.), genetic diversity and molecular markers of five species (Lutjanus vitta, L. fulvus, L. fulviflamma, L. sebae and L. stellatus) were detected and analysed using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) techniques. The polymorphic loci ratio (P) (86.00–92.11%), the mean intraspecies genetic distances (D) (0.1775–0.3431) and the intraspecies genetic diversity indexes (Hi) (0.1022–0.1634) were calculated using the RAPD technique. The genetic diversities of L. fulviflamma and L. vitta were richest in terms of P, and D and Hi, respectively. The results of SSR showed that low effective numbers of alleles (1.7893–3.6591), medium average heterozygosities (0.332–0.676) and medium polymorphism information contents (PIC) (0.302–0.641) occurred in five species of snappers, indicating comparatively rich genetic diversity among these fish. Nine molecular markers in the products amplified by primers OPA8 and OPP10, and six molecular markers in 11 microsatellite loci were found to be useful as specific markers to identify five species of snappers. Two neighbour-joining (NJ) dendrograms based on the results of RAPD and SSR suggested that L. stellatus and L. sebae are closely related and clustered in one branch, with L. vitta, L. fulviflamma and L. fulvus in the other.

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Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd ( Benincasa hispida )

Plant Breeding ◽

10.1111/pbr.12990 ◽

2022 ◽

Author(s):

Qianmei Hu ◽

Haiping Wang ◽

Biao Jiang ◽

Huayu Zhu ◽

Xiaoming He ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Genome Wide ◽

Benincasa Hispida ◽

Wax Gourd ◽

Simple Sequence

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Transcriptome analysis of two contrasting genotypes of pearl millet to gain insight into heat stress responses

10.21203/rs.3.rs-23605/v1 ◽

2020 ◽

Author(s):

Albert Maibam ◽

Sunil Nigombam ◽

Harinder Vishwakarma ◽

Showkat Ahmad Lone ◽

Kishor Gaikwad ◽

...

Keyword(s):

Heat Stress ◽

Pearl Millet ◽

Stress Responses ◽

Simple Sequence Repeats ◽

Pennisetum Glaucum ◽

Average Length ◽

Gc Content ◽

Functional Markers ◽

Sequencing Data ◽

Simple Sequence

Abstract Background Pennisetum glaucum (L.) R. Br. is mainly grown in arid and semi-arid regions. Being naturally tolerant to various adverse condtitions, it is a good biological resource for deciphering the molecular basis of abiotic stresses such as heat stress in plants but limited studies have been carried out till date to this effect. Here, we performed RNA-sequencing from the leaf of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42 °C for 6 h). Results Over 274 million high quality reads with an average length of 150 nt were generated. Assembly was carried out using trinity, obtaining 47,310 unigenes having an average length of 1254 nucleotides, N50 length of 1853 nucleotides and GC content of 53.11%. Blastx resulted in annotation of 35,628 unigenes and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms, 13,786 unigenes allocated to 23 Clusters of Orthologous Groups and 4,255 unigenes distributed into 132 functional KEGG pathways. 12,976 simple sequence repeats were identified from 10,294 unigenes for the development of functional markers. A total of 3,05,759 SNPs were observed in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidates genes were selected based on log2 fold change and adjusted p-value parameters for their differential gene expression by qRT-PCR. Conclusions The dynamic expression changes in two genotypes of P. glaucum reflect transcriptome regulation of signaling pathways in heat stress response. In order to develop genetic markers, 12,976 simple sequence repeats (SSRs) were identified. The sequencing data generated in this study shall serve as an important resource for further research in the area of crop biotechnology.

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SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

International Journal of Molecular Sciences ◽

10.3390/ijms21249421 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9421

Author(s):

Lidia Skuza ◽

Ewa Filip ◽

Izabela Szućko ◽

Jan Bocianowski

Keyword(s):

Mitochondrial Dna ◽

Molecular Markers ◽

Related Species ◽

Economic Importance ◽

Closely Related Species ◽

Coding Sequences ◽

Coding Regions ◽

Genomic Regions ◽

Tribe Triticeae

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

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Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics

Microorganisms ◽

10.3390/microorganisms8050662 ◽

2020 ◽

Vol 8 (5) ◽

pp. 662 ◽

Cited By ~ 1

Author(s):

Yuan Li ◽

Xiao Chen ◽

Kun Wu ◽

Jiao Pan ◽

Hongan Long ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Evolutionary History ◽

Rapid Evolution ◽

Genome Diversity ◽

Unicellular Eukaryotes ◽

Genome Wide ◽

Species Analysis ◽

Simple Sequence ◽

High Diversity

Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1–100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.

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