Diversity in coding tandem repeats in related Neisseria spp.

Jordan, Philip W.; Snyder, Lori; Saunders, Nigel J.

doi:10.1186/1471-2180-3-23

Cited by 38 publications

(10 citation statements)

References 78 publications

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“…Evidences in support of such proposition are made available from studies in humans [32,33]. Jordan et al [34] also endorsed similar observations and conclusions on the basis of their cross-species comparisons in Neisseria spp., and suggested the significance of this phenomenon in providing adaptability to the host. This view later also got support from Verstrepen et al [35] and Levdansky et al [36] following their studies in yeast and Aspergillus fumigatus, respectively.…”

Section: Open Accesssupporting

confidence: 52%

Tandem repetitions in transcriptomes of some Solanaceae species

Grover¹,

Sharma²

2012

AJMB

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Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.

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Section: Open Accesssupporting

confidence: 52%

Tandem repetitions in transcriptomes of some Solanaceae species

Grover¹,

Sharma²

2012

AJMB

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“…We identified a greater percentage of genes (9%) containing VNTR polymorphisms in the P. falciparum genome than has been reported for any other species to date (Bowen et al 2005; Coil et al 2008; Jordan et al 2003; Levdansky et al 2007; O’Dushlaine et al 2005; Verstrepen et al 2005). These current findings are expected to be an underestimate due to several factors: (1) This analysis compared three genomes and we expect variation in the genomes of other parasite strains; (2) 1,111 or 20% of the predicted 3D7 P. falciparum transcript sequences could not be mapped to a homolog; (3) TRs were bioinformatically recognized in each individual parasite sequence and subsequently compared for copy number, causing us to miss examples of one or zero TR “copies” (i.e., a sequence present zero or one times is not recognized as a TR in the initial bioinformatic step); (4) The VNTR analysis was limited to repeat sizes that would be considered minisatellites (≥12 nt repeat unit) to monitor how variable larger repeats are.…”

Section: Discussionmentioning

confidence: 65%

“…(Jordan et al 2003), and humans (O’Dushlaine et al 2005). The reported percentage of ORFs with VNTRs varies in different species ranging from <0.01% in L. pneumophila to approximately 4.3% in S. cerevisiae .…”

Section: Introductionmentioning

confidence: 99%

Variable Numbers of Tandem Repeats in Plasmodium falciparum Genes

Tan

Checkley

et al. 2010

J Mol Evol

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Genome variation studies in Plasmodium falciparum have focused on SNPs and, more recently, large-scale copy number polymorphisms and ectopic rearrangements. Here, we examine another source of variation: variable number tandem repeats (VNTRs). Interspersed low complexity features, including the well-studied P. falciparum microsatellite sequences, are commonly classified as VNTRs; however, this study is focused on longer coding VNTR polymorphisms, a small class of copy number variations. Selection against frameshift mutation is a main constraint on tandem repeats (TRs) in coding regions, while limited propagation of TRs longer than 975 nt total length is a minor restriction in coding regions. Comparative analysis of three P. falciparum genomes reveals that more than 9% of all P. falciparum ORFs harbor VNTRs, much more than has been reported for any other species. Moreover, genotyping of VNTR loci in a drug-selected line, progeny of a genetic cross, and 334 field isolates demonstrates broad variability in these sequences. Functional enrichment analysis of ORFs harboring VNTRs identifies stress and DNA damage responses along with chromatin modification activities, suggesting an influence on genome mutability and functional variation. Analysis of the repeat units and their flanking regions in both P. falciparum and Plasmodium reichenowi sequences implicates a replication slippage mechanism in the generation of TRs from an initially unrepeated sequence. VNTRs can contribute to rapid adaptation by localized sequence duplication. They also can confound SNP-typing microarrays or mapping short-sequence reads and therefore must be accounted for in such analyses.

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“…gonorrhoeae strain FA1090 were analysed using ACEDB (R. Durbin, J.T. Thierry-Mieg, unpublished data, http://www.acedb.org) as described previously [37,55,63,64]. Perfect sequence repeats characteristic of phase variable genes were identified using ARRAYFINDER [65].…”

Section: Methodsmentioning

confidence: 99%

“…Repeats, the annotations from all four neisserial genome sequences, and other sequence features were displayed in their sequence context within ACEDB. Analysis of the potential for simple sequence repeats to generate transcriptional or translational phase variation was determined through analysis of the repeat in the sequence context, as has been done previously [37,55,63,64]. Unique genes were identified as those for which no homology was displayed, the display parameters within ACEDB being set to 1e−50 for DNA identity, and 1e−4 for amino acid similarity.…”

Section: Methodsmentioning

confidence: 99%

Meningococcal Genetic Variation Mechanisms Viewed through Comparative Analysis of Serogroup C Strain FAM18

et al. 2007

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The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.

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Diversity in coding tandem repeats in related Neisseria spp.

Cited by 38 publications

References 78 publications

Tandem repetitions in transcriptomes of some Solanaceae species

Tandem repetitions in transcriptomes of some Solanaceae species

Variable Numbers of Tandem Repeats in Plasmodium falciparum Genes

Meningococcal Genetic Variation Mechanisms Viewed through Comparative Analysis of Serogroup C Strain FAM18

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