Jennifer 39;s Body Indo Sub

[Analisa Wack]

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Mackerels are a group of migratory, schooling, marine, coastal-pelagic fish in the family Scombridae1,2. Pacific chub mackerels (e.g. Scomber japonicus Houttuyun, 1782) are the primary and most widespread species of the mackerel group3, composing 43% of Scombridae landings4. They are classified as a distinct species from Atlantic chub mackerel (Scomber colias) based on differences in morphology and molecular data5. Chub mackerels have an elongated body2,6, which is dorsally pale green with faint steel blue wavy lines and laterally silvery yellow with round blotches that develop over time7,8 (Fig. 1a). They are characterized by two separated dorsal fins, a pectoral fin on each side, an anal fin and a caudal fin2. Ecologically, they inhabit temperate to subtropical waters of Pacific, Atlantic and Indian Oceans, displaying antitropical distributions9 (Fig. 1b). They are prey for larger pelagic fish and marine mammals10, playing a crucial role in the marine food chain. Commercially, this marine fish is captured and consumed worldwide11 and serves as significant sources of omega-3 fatty acids, which are in high demand and predominantly derived from fish oil4. Additionally, their population is dispersed across discrete and disjunct geographical areas9, making them suitable for comparative genetic studies. Despite their ecological and commercial value, the population size of chub mackerel has recently declined11 due to climate change affecting optimal habitat conditions and temperature-dependent hatching rates12, placing the genetic resources of chub mackerel at stake.

Integrated information of every recorded occurrence of chub mackerel was retrieved from Ocean Biodiversity Information System (OBIS) database25. Citations for subsets of every dataset are provided in Supplementary table S1. The geographic distribution map (Fig. 1b,c) was visualized using rnaturalearth package26 for R27 by plotting coordinate information of OBIS data for mackerel occurrences on the world map.

All repetitive regions of the fScoJap1 genome were located, soft-masked and incorporated in the assembly with WindowMasker41. Specific repetitive elements and their numbers were identified with RepeatMasker v4.1.542 using Dfam v3.743 library for zebrafish (Danio rerio).

A total of 19,994 genes contain various duplications classified into 13,158 dispersed, 1,092 proximal, 2,873 tandem and 2,871 WGD/segmental duplications, respectively (Table 6). Visual inspection of the circus plot suggested an overall tendency for genic duplications to be less in regions of the genome where transposons were located (Fig. 3a). To quantify this, we calculated the total length of transposons in duplicated genic regions of the genome compared to other regions. Whole genic regions had lower proportion overlapped with transposon elements (2.03%) than did whole intergenic regions (2.56%). Within the genic regions, the percentage of duplicated genic regions covered by transposon elements (1.30%) were almost twice as less than the percentage of singleton genic regions covered by transposons (2.37%; Table 7), suggesting a disposition of transposons to overlap less with duplicated genes. This finding is intriguing, as it is counterintuitive to the fact that transposons are in part responsible for forming new gene duplications50.

We deeply appreciate the fishery farm, Se-Bo Su-San (세보수산), for providing the chub mackerel samples. The authors are grateful to the Vertebrate Genomes Project (VGP), especially for efforts of the VGP assembly working group to optimize the genome assembly pipelines, and to Michael Paulini and Ying Sims for contributing to the assembly curation. This study was supported by the Marine Biotechnology Program of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Ocean and Fisheries (MOF) (No. 20180430), Republic of Korea to HK and CL and by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (No. NRF-2021R1A2C2094111) to HK and YHL. This study was supported by HHMI to EDJ, USA. Curation was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194, ).

Chul Lee, Bohye Nam, Eun Soo No, Hye-Ran Kim, Erich D. Jarvis and Heebal Kim conceived the study; Chul Lee and Jin-Koo Kim collected the sample; Jin-Koo Kim contributed species and sex identification and anatomical sampling of tissues; Chul Lee and Young Wook Kim exported the isolated samples for sequencing and genome assembly at Vertebrates Genomes Laboratory, Rockefeller university; Olivier Fedrigo and Jennifer Balacco extracted Genomic DNA and performed sequencing; Linelle Abueg and Giulio Formenti assembled the genome; Kerstin Howe, Alan Tracey, and Jo Wood performed manual curations of assembled primary sequences; Franoise Thibaud-Nissen performed the RefSeq annotation; Young Ho Lee and Linelle Abueg assessed the assembly quality; Young Ho Lee, Chul Lee, Erich D. Jarvis, and Heebal Kim wrote the manuscript. Also, all authors read, edited, and approved the final manuscript.

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