Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics

Kadota, Mitsutaka; Tatsumi, Kaori; Yamaguchi, Kazuaki; Uno, Yoshinobu; Kuraku, Shigehiro

doi:10.1101/2023.02.23.529029

Cited by 5 publications

(17 citation statements)

References 51 publications

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“…The extracted genomic DNA was used for the estimation of nuclear DNA content with the method using quantitative PCR (qPCR). 19 Three protein-coding genes included in Table 1 were selected from those contained in the transcript contigs (see Materials and methods) and detected as single-copy genes. We designed specific primers for these genes and prepared standard molecules for each of them by PCR.…”

Section: Resultsmentioning

confidence: 99%

“…The genome size was quantified with the qPCR-based protocol sQuantGenome 19 ( https://github.com/Squalomix/c-value ) with the same DNA sample used for whole genome sequencing. Three protein-coding genes, ACAT1 , DLD , and RFC3 from the single-copy orthologous gene set CVG 20 (Core Vertebrate Genes), whose transcript sequences ( Supplementary Table S1 ) were identified in the transcriptome sequence assembly (see below).…”

Section: Methodsmentioning

confidence: 99%

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Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

Sato,

Fukuda,

Kadota

et al. 2024

DNA Research

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Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asia. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to ~30-folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards ‘telomere-to-telomere’ sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions were predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

Sato,

Fukuda,

Kadota

et al. 2024

DNA Research

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show abstract

“…The extracted genomic DNA was used for the estimation of nuclear DNA content with the method using quantitative PCR (qPCR) 19 . Three protein-coding genes included in Table 1 were selected from those contained in the transcript contigs (see Materials and Methods) and detected as single copy genes.…”

Section: Resultsmentioning

confidence: 99%

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

Sato,

Fukuda,

Kadota

et al. 2023

Preprint

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Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asian. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to approximately 30 folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards telomere-to-telomere sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions was predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.

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“…We focused on the zebra shark (or leopard shark) Stegostoma tigrinum (formerly, S. fasciatum ) with the haploid nuclear DNA content of 3.79 pg (3.71 Gb; Kadota et al 2023 ) and the karyotype of 2n = 102 ( Uno et al 2020 ). Using genomic DNA extracted from blood cells of a female adult, the whole genome was sequenced and assembled with short reads.…”

Section: Resultsmentioning

confidence: 99%

Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization

Yamaguchi,

Uno,

Kadota

et al. 2023

Genome Res.

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Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra sharkStegostoma tigrinum, an endangered species that has a relatively small genome among sharks (3.71 Gb), as well as for the whale sharkRhincodon typus. Our analysis employing a male-female comparison identified an X Chromosome, the first genomically characterized shark sex chromosome. The X Chromosome harbors the Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes exhibit a gradualism of chromosome length with remarkable length-dependent characteristics—shorter chromosomes tend to have higher GC-content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed repeat content. We challenge the traditional binary classification of karyotypes as with and without so-called microchromosomes. Even without microchromosomes, the length-dependent characteristics persist widely in some other vertebrate lineages. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout. It also paves the way to dissecting more genomes with variable sizes to be sequenced on high quality.

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Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics

Cited by 5 publications

References 51 publications

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization

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