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Genes 2018, 9(10), 464; https://doi.org/10.3390/genes9100464

B Chromosomes of the Asian Seabass (Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations

1
Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia
2
Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
3
School of Applied Science, Republic Polytechnic 9 Woodlands Avenue 9, Singapore 738964, Singapore
4
Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
5
Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
6
Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia
7
Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
8
Department of Animal Sciences, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Hungary
9
Center for Comparative Genomics, Murdoch University, 6150 Murdoch, Australia
*
Authors to whom correspondence should be addressed.
Received: 4 August 2018 / Revised: 6 September 2018 / Accepted: 12 September 2018 / Published: 20 September 2018
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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Abstract

The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing. View Full-Text
Keywords: teleost; population analysis; whole genome resequencing; DNA copy number variation; ribosomal DNA; B chromosomes teleost; population analysis; whole genome resequencing; DNA copy number variation; ribosomal DNA; B chromosomes
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Komissarov, A.; Vij, S.; Yurchenko, A.; Trifonov, V.; Thevasagayam, N.; Saju, J.; Sridatta, P.S.R.; Purushothaman, K.; Graphodatsky, A.; Orbán, L.; Kuznetsova, I. B Chromosomes of the Asian Seabass (Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations. Genes 2018, 9, 464.

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