Chromosome-Scale Genome Assembly and Transcriptome Assembly of Kawakawa Euthynnus affinis; A Tuna-Like Species

Havelka, Miloš; Sawayama, Eitaro; Saito, Taiju; Yoshitake, Kazutoshi; Saka, Daiki; Ineno, Toshinao; Asakawa, Shuichi; Takagi, Motohiro; Goto, Ryoji; Matsubara, Takahiro

doi:10.3389/fgene.2021.739781

Cited by 4 publications

(1 citation statement)

References 65 publications

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“…Whole genome sequencing and de novo assembly of kawakawa was recently done in the South Ehime Fisheries Research Center (SEFRC), Ehime University [46]. The full length kawakawa slc24a5 (ka-slc24a5) gene sequence was extracted from the draft of the whole genome sequence (can be found below; doi:https://www.ddbj.nig.ac.jp/, 3 December 2021, BPLY01000001-BPLY01010237, ICRR01000001-ICRR01049510, DRA012118, DRA012140, DRA012141) to determine its genome location.…”

Section: Genome Sequence and Talen Design For Kawakawa Slc24a5mentioning

confidence: 99%

TALEN-Mediated Gene Editing of slc24a5 (Solute Carrier Family 24, Member 5) in Kawakawa, Euthynnus affinis

Pandey

Matsubara

Saito

et al. 2021

JMSE

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Transcription activator-like effector (TALE) nucleases (TALENs) mediated gene editing methods are becoming popular and have revealed the staggering complexity of genome control during development. Here, we present a simple and efficient gene knockout using TALENs in kawakawa, Euthynnus affinis, using slc24a5. We examined slc24a5 gene expression and functional differences between two TALENs that hold the TALE scaffolds, +153/+47 and +136/+63 and target slc24a5. Developmental changes in slc24a5 transcripts were seen in early-stage embryos by real-time PCR; slc24a5 expression was first detected 48 h post fertilization (hpf), which increased dramatically at 72 hpf. Four TALENs, 47- and 63-type of two different target loci (A and B), respectively, were constructed using Platinum TALEN and evaluated in vitro by a single-strand annealing (SSA) assay. TALEN activities were further evaluated in vivo by injecting TALEN mRNAs in the two-cell stage of the zygote. Most of the TALEN-induced mutants showed mosaic patterns in the retinal pigment epithelium (RPE) and fewer melanin pigments on the body at 72 hpf and later when compared to the control, implying the gene’s association with melanin pigment formation. A heteroduplex mobility assay (HMA) and the genome sequence further confirmed the TALEN-induced mutations of substitution, insertion, and deletion at an endogenous locus.

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Section: Genome Sequence and Talen Design For Kawakawa Slc24a5mentioning

confidence: 99%

TALEN-Mediated Gene Editing of slc24a5 (Solute Carrier Family 24, Member 5) in Kawakawa, Euthynnus affinis

Pandey

Matsubara

Saito

et al. 2021

JMSE

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Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts

Wu,

Gao,

et al. 2023

Sci. China Life Sci.

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Chromosome-level genome assembly of Indo-Pacific king mackerel (Scomberomorus guttatus)

Gao,

Liu,

Gutang

et al. 2024

Sci Data

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The Indo-Pacific king mackerel, scientifically known as Scomberomorus guttatus , is a valued marine species that holds significant commercial importance in the Indo-Pacific region. However, the lack of genomic resources has hindered a comprehensive understanding of this species. In this study, we constructed a genome of Indo-Pacific king mackerel at the chromosome level using a combination of PacBio HiFi reads and a chromosome contact map (Hi-C). The resulting genome had high contig and scaffold N50 values of 8.84 Mb and 32.9 Mb, respectively. In the genome assembly, which is 797.66 Mb in size and consists of 24 chromosomes, we also identified 35.89% repetitive elements and predicted 25,886 protein-coding genes. Our study not only benefits to reveal the possible mechanism of adaptive evolution in this fish, but also offers insight for the future sustainable management of these valuable biological resources.

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Chromosome-Scale Genome Assembly and Transcriptome Assembly of Kawakawa Euthynnus affinis; A Tuna-Like Species

Cited by 4 publications

References 65 publications

TALEN-Mediated Gene Editing of slc24a5 (Solute Carrier Family 24, Member 5) in Kawakawa, Euthynnus affinis

TALEN-Mediated Gene Editing of slc24a5 (Solute Carrier Family 24, Member 5) in Kawakawa, Euthynnus affinis

Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts

Chromosome-level genome assembly of Indo-Pacific king mackerel (Scomberomorus guttatus)

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