Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element

Koga, Akihiko

doi:10.1139/g11-088

Cited by 7 publications

(4 citation statements)

References 18 publications

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“…It is worth noting that the relationship between total coverage of a genome and the size of the discrepancy was weakly negative but marginally non-significant (r ¼ 20.117, p ¼ 0.088, n ¼ 212 contrasts), suggesting that at least some of the information that may be missing from many sequence datasets is indeed difficult to obtain. As an example, Koga [24] showed that harder to assemble internal regions of the Tol2 DNA transposon in the Oryzias latipes genome were missing from the assembly but were nonetheless quantifiable using a Southern blot analysis of genomic DNA. Perhaps more important is the disparity in the sizes of genomes that have been examined using sequencing versus traditional methods.…”

Section: Discussion (A) Sequence and Sizementioning

confidence: 99%

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Elliott

Gregory

2015

Phil. Trans. R. Soc. B

233

221

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One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content Tyler A. Elliott and T. Ryan Gregory Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of 'complete' genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.

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Section: Discussion (A) Sequence and Sizementioning

confidence: 99%

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Elliott

Gregory

2015

Phil. Trans. R. Soc. B

233

221

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“…CENP-B boxes are embedded in centromeric repetitive DNA. In genome sequence databases constructed through next-generation sequencing, repetitive DNA is generally underrepresented and susceptible to artificial alterations because of the difficulty in assembling contigs [17,18]. The centromere regions are still left as large gaps even in the human sequence databases.…”

Section: Discussionmentioning

confidence: 99%

CENP-B box, a nucleotide motif involved in centromere formation, occurs in a New World monkey

et al. 2016

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Centromere protein B (CENP-B) is one of the major proteins involved in centromere formation, binding to centromeric repetitive DNA by recognizing a 17 bp motif called the CENP-B box. Hominids (humans and great apes) carry large numbers of CENP-B boxes in alpha satellite DNA (AS, the major centromeric repetitive DNA of simian primates). Only negative results have been reported regarding the presence of the CENP-B box in other primate taxa. Consequently, it is widely believed that the CENP-B box is confined, within primates, to the hominids. We report here that the common marmoset, a New World monkey, contains an abundance of CENP-B boxes in its AS. First, in a long contig sequence we constructed and analysed, we identified the motif in 17 of the 38 alpha satellite repeat units. We then sequenced terminal regions of additional clones and found the motif in many of them. Immunostaining of marmoset cells demonstrated that CENP-B binds to DNA in the centromeric regions of chromosomes. Therefore, functional CENP-B boxes are not confined to hominids. Our results indicate that the efficiency of identification of the CENP-B box may depend largely on the sequencing methods used, and that the CENP-B box in centromeric repetitive DNA may be more common than researchers previously thought.

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“…In this previous study, however, our BLAST search of the tammar wallaby genome database resulted in the detection of only one sequence that was aligned to the LTR portion of walb . This is not a contradiction, considering that repetitive sequences tend to be underrepresented or even missing in genome databases constructed through the assembly of short sequence reads (Koga, 2012; Weissensteiner et al, 2017). In the present study, as an approach with a lower risk of representation bias, we performed NCBI BLAST searches of the Illumina short‐read data collections of two tammar wallaby individuals (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Marsupial genome analysis suggests that satellite DNA formation from walb endogenous retrovirus is an event specific to the red‐necked wallaby

Koga

Hashimoto²,

Honda

et al. 2022

Genes to Cells

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We recently identified walbRep, a satellite DNA residing in the genome of the red-necked wallaby Notamacropus rufogriseus. It originates from the walb endogenous retrovirus and is organized in a manner in which the provirus structure is retained. The walbRep repeat units feature an average pairwise nucleotide identity as high as 99.5%, raising the possibility of a recent origin. The tammar wallaby N. eugenii is a species estimated to have diverged from the red-necked wallaby 2-3 million years ago. In PCR analyses of these two and other related species, walbRep-specific fragment amplification was observed only in the red-necked wallaby. Sequence database searches for the tammar wallaby resulted in sequence alignment lists that were sufficiently powerful to exclude the possibility of walbRep existence. These results suggested that the walbRep formation occurred in the red-necked wallaby lineage after its divergence from the tammar wallaby lineage, thus in a time span of maximum 3 million years.

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Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element

Cited by 7 publications

References 18 publications

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

CENP-B box, a nucleotide motif involved in centromere formation, occurs in a New World monkey

Marsupial genome analysis suggests that satellite DNA formation from walb endogenous retrovirus is an event specific to the red‐necked wallaby

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