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B chromosomes of the asian seabass (Lates calcarifer) contribute to genome variations at the level of individuals and populations. / Komissarov, Aleksey; Vij, Shubha; Yurchenko, Andrey et al.
In: Genes, Vol. 9, No. 10, 464, 20.09.2018, p. 1.-15.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - B chromosomes of the asian seabass (Lates calcarifer) contribute to genome variations at the level of individuals and populations
AU - Komissarov, Aleksey
AU - Vij, Shubha
AU - Yurchenko, Andrey
AU - Trifonov, Vladimir
AU - Thevasagayam, Natascha
AU - Saju, Jolly
AU - Sridatta, Prakki Sai Rama
AU - Purushothaman, Kathiresan
AU - Graphodatsky, Alexander
AU - Orbán, László
AU - Kuznetsova, Inna
N1 - Publisher Copyright: © 2018, MDPI AG. All rights reserved.
PY - 2018/9/20
Y1 - 2018/9/20
N2 - 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.
AB - 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.
KW - B chromosomes
KW - Dna copy number variation
KW - Population analysis
KW - Ribosomal dna
KW - Teleost
KW - Whole genome resequencing
KW - LOCALIZATION
KW - ribosomal DNA
KW - EARLY LIFE-HISTORY
KW - SIZE
KW - TRANSCRIPTION
KW - ELIMINATION
KW - teleost
KW - DNA copy number variation
KW - FISH ASTATOTILAPIA-LATIFASCIATA
KW - whole genome resequencing
KW - DNA-CONTENT
KW - BARRAMUNDI
KW - TELEOSTEI
KW - DIFFERENTIATION
KW - population analysis
UR - http://www.scopus.com/inward/record.url?scp=85054793349&partnerID=8YFLogxK
U2 - 10.3390/genes9100464
DO - 10.3390/genes9100464
M3 - Article
C2 - 30241368
AN - SCOPUS:85054793349
VL - 9
SP - 1.-15
JO - Genes
JF - Genes
SN - 2073-4425
IS - 10
M1 - 464
ER -
ID: 17116902