Chromosome-Level Genome Assembly of the Burbot (Lota lota) Using Nanopore and Hi-C Technologies

Song, Dan; Qian, Yuting; Meng, Minghui; Dong, Xiaoli; Lv, Wenqi; Huo, Tangbin

doi:10.3389/fgene.2021.747552

Cited by 5 publications

(3 citation statements)

References 42 publications

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“…The chromosome-level genome assemblies generated, corresponded to the numbers of chromosomes reported from cytogenetic studies (see Table S1), except for burbot where we obtained a total of n=23 haploid chromosomes vs. n=24 haploid chromosomes reported by two different cytogenetic studies [40,41]. We cannot rule out resulting in n=24 chromosomes [52]. Combined, these results suggest that there are chromosomal differences between different lineages of burbot.…”

Section: Chromosome Number Variability In Codfishesmentioning

confidence: 70%

“…Moreover, two different chromosome-level burbot assemblies have previously been constructed, which resulted in different numbers of chromosomes, one by Han et al 2021 of a specimen sampled in Heilong River (Raohe county) in the northeastern part of China resulting in n=22 chromosomes[51], and another by Song et al 2021 resulting in n=24 chromosomes[52]. Combined, these results suggest that there are chromosomal differences between different lineages of burbot.…”

Section: Discussionmentioning

confidence: 99%

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Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

Hoff,

Maurstad,

Tørresen

et al. 2024

Preprint

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The evolutionary impact of structural variants, such as chromosomal inversions, is well documented, especially for their role in local adaptation in high gene flow systems. However, the role of other genomic rearrangements like chromosomal fusions, fissions, and translocations is still relatively unexplored. Here we present six chromosome-level Gadid reference genomes for the non-migratory Atlantic cod (Gadus morhua) i.e., Norwegian coastal cod (NCC), Atlantic haddock(Melanogrammus aeglefinus),burbot (Lota lota), European hake (Merluccius merluccius) as well as two keystone Arctic codfishes: the polar cod (Boreogadus saida) and Arctic cod (Arctogadus glacialis). Within a comparative genomics framework, we uncovered several lineage-specific chromosomal fusions, resulting in a reduced number of chromosomes compared to the ancestral state in the two cold-water adapted codfishes. The identified fusions were not homologous, i.e., indicating that they originate from independent evolutionary events. Additionally, a high number of partly overlapping chromosomal inversions between the two species were detected. Using a smaller population dataset, we uncovered a high degree of conservation for some of the overlapping inversions (including some breakpoint regions), suggesting that these regions are under selection, and potentially of evolutionary importance. With the use of chromosome-level genome assemblies, we demonstrate how large genomic reorganizations are likely to play important roles in speciation processes and thus, in particular to adaptation to freezing environmental conditions. Moreover, we observe that such massive rearrangement events can take place across relatively short evolutionary time scales.

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Section: Chromosome Number Variability In Codfishesmentioning

confidence: 70%

Section: Discussionmentioning

confidence: 99%

Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

Hoff,

Maurstad,

Tørresen

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Three years later, also using the PacBio long-read and NGS data, the reference of the Indian rhesus macaque (Mmul_10) was improved significantly (∼120-fold) in sequence contiguity (46Mb of contig N50) relative to rheMac8 [19]. In recent years, another big step forward for de novo genome assembly comes from the development of the Nanopore long-read sequencing with its cost-effective advantage [36, 37], which improved the genome references for multiple species, such as humans [38-41], mammals [42-44], birds [45, 46], plants [47-49], fishes [50, 51], fruit flies [52], etc. However, there is still no nanopore derived reference assembly and related analyses (such as methylation, recombination rate, etc.)…”

Section: Introductionmentioning

confidence: 99%

The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations

Chen

Zhong

et al. 2022

Preprint

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Rhesus macaques (Macaca mulatta) are the most extensively studied nonhuman primate species for human biomedical modeling. However, little is known about the biological pattern of genome-wide structural variations (SVs) and the evolutionary forces underlying SVs. Here, we conducted genomic sequencing and analyses based on Nanopore long reads and Illumina short reads technology. We called SVs between the two subspecies (China vs. India), using three methods of assembly-based and long-reads-based algorithms. Interestingly, we found significantly more SVs in X-chromosome than in autosomes, consistent with the expectation of the faster-X divergence at the subspecies level. With the fine-scale methylation frequencies and recombination rates, we found duplications with significantly lower methylation frequencies while higher recombination rates than other types of SVs, suggesting a higher level of transcriptional and evolutionary potential for duplications than for other SVs types. A genome-wide scan of selective sweep revealed that over 3% of SVs are under positive selection. Moreover, X chromosome showed significantly higher number of positively selected SVs than do autosomes, suggesting the “faster-X effect” of SVs. Our study revealed a different evolutionary importance for duplications compared with other SVs forms. We also revealed the “faster-X effect” of SVs, which could provide raw material upon which positive selection can further play.

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An improved genetic marker panel for conservation monitoring of upper Kootenay River burbot

Harris,

Coykendall,

Lamson

et al. 2024

Conservation Genet Resour

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Chromosome-Level Genome Assembly of the Burbot (Lota lota) Using Nanopore and Hi-C Technologies

Cited by 5 publications

References 42 publications

Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations

An improved genetic marker panel for conservation monitoring of upper Kootenay River burbot

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