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

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.

The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses

“…Apart from the presence of transposons and pseudogenes/fragments of genes on Bs, the latest research studies [25,44,56,75,77,78,79] have also found protein coding intact genes that we call “B essential genes” (see definitions in Box 1) which might be critical for the survival and transmission of Bs during their earlier stages of evolution (see details in next topic section). To create a reference of B-linked genes, we have organized a database that contain a list of genes detected in different species (Supplementary Dataset S1).…”

“…The integrative Illumina and Pacbio sequencing data analysis of several cichlids species from Lake Malawi identified many gene fragments and genes located on Bs, some of which could possibly function in the regulation of Bs establishment [44]. The sequences of microdissected Bs in a fish species, Asian Seabass, were assembled and their annotations recorded a total of 75 genes out of which 10 genes, including ASTN2, BRE, DPF3, FBXO33, FKBP, GABRB2, MYT1L, RAB14, RXRAB, and PACRG, were known to be involved with particular expression in the brain and gonads [79].…”

“…More recent analysis of 0B and 1B transcriptomes in E. plorans has shown the presence of Bs causes differential expression of 46 genes associated with different functions such as cell death, histone-methyltransferase activity, protein modification, regulation of genes, stress response and chemical defense [107]. Apart from the listed genes in Table 1, we gathered an extensive list of genes and gene fragments (a total of 17,139) that have been reported on the Bs of different species [25,44,50,79,107]. This list is given as Supplementary Dataset S1 and can be used as a reference database for further investigation of B-linked genes.…”

Transcriptomic Analysis of Gill and Kidney from Asian Seabass (Lates calcarifer) Acclimated to Different Salinities Reveals Pathways Involved with Euryhalinity

“…Due to their ability to adapt to varying salinities, euryhaline fishes provide an excellent model to understand the genetic basis of salt acclimation in the aquatic environment [ 30 , 31 , 32 , 33 ]. Asian seabass ( L. calcarifer ; Bloch, 1790), also known as barramundi or giant perch, is an euryhaline, carnivorous teleost, popular as a food fish in southeast Asia, Australia, and most of the Indian subcontinent [ 34 , 35 , 36 , 37 , 38 , 39 ]. Asian seabass is catadromous (fish that spend most of their life in freshwater, but spawn in seawater), although Asian seabass do not necessarily always migrate [ 39 ].…”

Evolution, Composition and Regulation of Supernumerary B Chromosomes

“…Milani et al Another interesting animal group for B studies is represented by fish species. Komissarov et al [4] investigate Bs of the Asian Seabass (Lates calcarifer), and give support to the view that Bs contribute to the variations in the genome among individuals and populations of the species. Among fish, cichlids have appeared as an interesting model for B studies.…”