Komissarov, A. et al. (2018) B Chromosomes of the Asian seabass (Lates calcarifer) contribute to genome variations at the level of individuals and populations. Genes, 9(10), 464. (doi: 10.3390/genes9100464) (PMID:30241368) (PMCID:PMC6211105)
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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.
| Item Type: | Articles |
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| Additional Information: | This research was supported by the National Research Foundation, Prime Minister’s Office, Singapore under its Competitive Research Program (CRP Award No. NRF-CRP7-2010-01); interdisciplinary grant of the SB RAS No. 137; supported by RFBR grants 17-00-00144 and 17-00-00146 as part of 17-00-00148; VAT was supported by RSF (No. 18-44-04007). |
| Keywords: | B chromosomes, DNA copy number variation, population analysis, ribosomal DNA, teleost, whole genome resequencing. |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Yurchenko, Dr Andrey |
| Authors: | Komissarov, A., Vij, S., Yurchenko, A., Trifonov, V., Thevasagayam, N., Saju, J., Sridatta, P. S. R., Purushothaman, K., Graphodatsky, A., Orbán, L., and Kuznetsova, I. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine |
| Journal Name: | Genes |
| Publisher: | MDPI |
| ISSN: | 2073-4425 |
| ISSN (Online): | 2073-4425 |
| Published Online: | 20 September 2018 |
| Copyright Holders: | Copyright © 2018 The Authors |
| First Published: | First published in Genes 9(10): 464 |
| Publisher Policy: | Reproduced under a Creative Commons License |
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