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 -