Centromere evolution and CpG methylation during vertebrate speciation

Ichikawa, Kazuki; Tomioka, Shingo; Suzuki, Yuta; Nakamura, Ryohei; Doi, Kouki; Yoshimura, Junichi; Kumagai, Masahiko; Inoue, Yusuke; Uchida, Yui; Irie, Naoki; Takeda, Hiroyuki; Morishita, Shinichi

doi:10.1038/s41467-017-01982-7

Cited by 83 publications

(88 citation statements)

References 69 publications

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“…The contig and scaffold N50 length of the final assembly reached 2.9 and 24.9 Mb, respectively, which provided the first chromosomal genome assembly for T. tibetana (Table ). Continuity at the contig and scaffold level was comparable to other model teleosts, such as medaka (Ichikawa et al, ) and tilapia (Conte, Gammerdinger, Bartie, Penman, & Kocher, ). There were still 280 unanchored contigs after the Hi‐C‐based chromosome construction with an N50 length of 40.4 kb, which was significantly smaller than that of the anchored contigs.…”

Section: Resultssupporting

confidence: 69%

“…and 80.47% of all of the contigs at the base and sequence number level, respectively. The contig and scaffold N50 length of the final assembly reached 2.9 and 24.9 Mb, respectively, which provided the first chromosomal genome assembly for T. tibetana ( other model teleosts, such as medaka (Ichikawa et al, 2017) and tilapia (Conte, Gammerdinger, Bartie, Penman, & Kocher, 2017).…”

Section: Chromosome Sequence Assemblymentioning

confidence: 99%

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Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Yang

et al. 2019

Molecular Ecology Resources

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Triplophysa is an endemic fish genus of the Tibetan Plateau in China. Triplophysa tibetana, which lives at a recorded altitude of ~4,000 m and plays an important role in the highland aquatic ecosystem, serves as an excellent model for investigating high‐altitude environmental adaptation. However, evolutionary and conservation studies of T. tibetana have been limited by scarce genomic resources for the genus Triplophysa. In the present study, we applied PacBio sequencing and the Hi‐C technique to assemble the T. tibetana genome. A 652‐Mb genome with 1,325 contigs with an N50 length of 3.1 Mb was obtained. The 1,137 contigs were further assembled into 25 chromosomes, representing 98.7% and 80.47% of all contigs at the base and sequence number level, respectively. Approximately 260 Mb of sequence, accounting for ~39.8% of the genome, was identified as repetitive elements. DNA transposons (16.3%), long interspersed nuclear elements (12.4%) and long terminal repeats (11.0%) were the most repetitive types. In total, 24,372 protein‐coding genes were predicted in the genome, and ~95% of the genes were functionally annotated via a search in public databases. Using whole genome sequence information, we found that T. tibetana diverged from its common ancestor with Danio rerio ~121.4 million years ago. The high‐quality genome assembled in this work not only provides a valuable genomic resource for future population and conservation studies of T. tibetana, but it also lays a solid foundation for further investigation into the mechanisms of environmental adaptation of endemic fishes in the Tibetan Plateau.

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Section: Resultssupporting

confidence: 69%

Section: Chromosome Sequence Assemblymentioning

confidence: 99%

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Yang

et al. 2019

Molecular Ecology Resources

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“…Importantly, our demographic inferences suggesting a relatively recent (20–33 KYA) evolutionary establishment of Newfoundland Canada lynx supports DNA methylation as a marker to examine rapid evolutionary change. Evolutionary theory in model organisms has predicted that epimutations and methylome evolution often precede genomic changes (Smith, Martin, Nguyen, & Mendelson, ; Vidalis et al, ), which has been further substantiated with empirical evidence examining epigenetic changes over structural genomic variants in the absence of (Ichikawa et al, ) and phenotypic responses in the absence of standing genetic variation (Sentis et al, ).…”

Section: Discussionmentioning

confidence: 96%

Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

2019

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Determining the molecular signatures of adaptive differentiation is a fundamental component of evolutionary biology. A key challenge is to identify such signatures in wild organisms, particularly between populations of highly mobile species that undergo substantial gene flow. The Canada lynx (Lynx canadensis) is one species where mainland populations appear largely undifferentiated at traditional genetic markers, despite inhabiting diverse environments and displaying phenotypic variation. Here, we used high‐throughput sequencing to investigate both neutral genetic structure and epigenetic differentiation across the distributional range of Canada lynx. Newfoundland lynx were identified as the most differentiated population at neutral genetic markers, with demographic modelling suggesting that divergence from the mainland occurred at the end of the last glaciation (20–33 KYA). In contrast, epigenetic structure revealed hidden levels of differentiation across the range coincident with environmental determinants including winter conditions, particularly in the peripheral Newfoundland and Alaskan populations. Several biological pathways related to morphology were differentially methylated between populations, suggesting that epigenetic modifications might explain morphological differences seen between geographically peripheral populations. Our results indicate that epigenetic modifications, specifically DNA methylation, are powerful markers to investigate population differentiation in wild and non‐model systems.

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“…Recently, the advent of long-read sequencing technologies has paved the way for direct, comprehensive observation of sequence variations among various human populations [29][30][31][32][33] . While long-read sequencing was capable of yielding contiguous reference sequences of centromeres for several species 34,35 , reconstruction of whole centromeric sequences for human genomes is still challenging due to their idiosyncratic repeat structures. To date, it has been achieved only for the X and Y chromosomes, which both exist in a haploid state 36,37 .…”

Section: Mainmentioning

confidence: 99%

“…One of the major driving forces leading to such centromeric variation has been thought to be structural alterations such as unequal crossovers and/or gene conversions 26,27 .Previous studies have investigated centromeric sequence variations via traditional approaches such as restriction enzymes sensitive to alpha-satellite monomers, Southern blotting, or analysis of k-mers unique to centromeres in short reads obtained in the 1000 Genomes Project 28 , but their observations have remained indirect and were confined to specific types of variations due to technological limitations.Recently, the advent of long-read sequencing technologies has paved the way for direct, comprehensive observation of sequence variations among various human populations [29][30][31][32][33] . While long-read sequencing was capable of yielding contiguous reference sequences of centromeres for several species 34,35 , reconstruction of whole centromeric sequences for human genomes is still challenging due to their idiosyncratic repeat structures. To date, it has been achieved only for the X and Y chromosomes, which both exist in a haploid state 36,37 .…”

mentioning

confidence: 99%

Long-read Data Revealed Structural Diversity in Human Centromere Sequences

Suzuki

Myers

Morishita

2019

Preprint

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Centromeres invariably serve as the loci of kinetochore assembly in all eukaryotic cells, but their underlying DNA sequences evolve rapidly. Human centromeres are characterized by their extremely repetitive structures, i.e., higher-order repeats, rendering the region one of the most difficult parts of the genome to assess. Consequently, our understanding of centromere sequence variations across human populations is limited. Here, we analyzed chromosomes 11, 17, and X using long sequencing reads of two European and two Asian genomes, and our results show that human centromere sequences exhibit substantial structural diversity, harboring many novel variant higher-order repeats specific to individuals, while frequent single-nucleotide variants are largely conserved. Our findings add another dimension to our knowledge of centromeres, challenging the notion of stable human centromeres. The discovery of such diversity prompts further deep sequencing of human populations to understand the true nature of sequence evolution in human centromeres. MainCentromeres have been one of the most mysterious parts of the human genome since they were characterized, in the 1970s, as large tracts of 171 bp strings called alpha-satellite monomers 1, 2 . With a growing body of evidence suggesting their relevance to human diseases as sources of genomic instability or as repositories of haplotypes containing causative mutations 3-8 , it has become more important to investigate the underlying sequence variations in centromeres 9, 10 .Human centromeres have nested repeat structures. Namely, a series of distinctively divergent alpha-satellite monomers compose a larger unit called higher-order repeat (HOR) unit, and copies of an HOR unit are tandemly arranged thousands of times to form large, homogeneous HOR arrays. While HOR units are chromosome-specific and consist of two to 34 alphasatellite monomers, copies of an HOR unit are almost identical (95 ∼ 100%) within a chromosome (Figure 1a) [11][12][13][14][15][16][17] . The total HOR array length in each chromosome is known to differ dramatically among individuals 7, 18 or across human populations 19,20 . In addition to array length, other types of variation are known to exist within an HOR array, such as structurally variant HORs that consist of different numbers and/or types of alpha-satellite monomers 20-23 and also single-nucleotide variations (SNVs) between the HOR units 20, 24, 25 . One of the major driving forces leading to such centromeric variation has been thought to be structural alterations such as unequal crossovers and/or gene conversions 26,27 .Previous studies have investigated centromeric sequence variations via traditional approaches such as restriction enzymes sensitive to alpha-satellite monomers, Southern blotting, or analysis of k-mers unique to centromeres in short reads obtained in the 1000 Genomes Project 28 , but their observations have remained indirect and were confined to specific types of variations due to technological limitations.Recently, the advent of long-rea...

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Centromere evolution and CpG methylation during vertebrate speciation

Cited by 83 publications

References 69 publications

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

Long-read Data Revealed Structural Diversity in Human Centromere Sequences

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