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. 2018 Nov 1;7(11):giy114.
doi: 10.1093/gigascience/giy114.

Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus

Changwei Shao  1   2 , Chang Li  3   4   5 , Na Wang  1   2 , Yating Qin  4   5 , Wenteng Xu  1 , Qun Liu  4 , Qian Zhou  1   2 , Yong Zhao  4 , Xihong Li  1 , Shanshan Liu  4   5 , Xiaowu Chen  6 , Shahid Mahboob  7   8 , Xin Liu  4   5 , Songlin Chen  1   2
Affiliations

Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus

Changwei Shao et al. Gigascience. .

Abstract

Background: The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking.

Findings: Here, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly, and annotation. The genome scale was 0.67 Gb with contig and scaffold N50 length of 31 Kb and 1,040 Kb, respectively. Hi-C scaffolding of the genome resulted in 24 pseudochromosomes containing 77.68% of the total assembled sequences. A total of 132.38 Mb repeat sequences were detected, accounting for 20.73% of the assembled genome. A total of 22, 015 protein-coding genes were predicted, of which 96.52% were homologous to proteins in various databases. In addition, we constructed a phylogenetic tree using 1,586 single-copy gene families and identified 125 unique gene families in the spotted sea bass genome.

Conclusions: We assembled a spotted sea bass genome that will be a valuable genomic resource to understanding the biology of the spotted sea bass and will also lead to the development of molecular breeding techniques to generate spotted sea bass with better economic traits.

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Figures

Figure 1.
Figure 1.
Example of a spotted sea bass (L. maculatus) (Image from Jilun Hou)
Figure 2.
Figure 2.
Collinear blocks between the spotted sea bass (L. maculatus) and European sea bass (D. labrax) genomes. Each colored arc represents a best match between the two species. Lma_HiC1–24 represents pseudochromosomes 1–24 of the spotted sea bass genome and Dla_LG1–24 represents chromosomes 1–24 of the European sea bass genome.
Figure 3.
Figure 3.
Phylogenetic tree constructed with orthologous genes. Phylogenetic tree was constructed using 1,586 single-copy orthologous gene families from nine teleost species. Divergence times from human—D. rerio (438∼455 Mya), D. rerio—O. latipes (258∼307 Mya), O. latipes—O. niloticus (87∼151 Mya), and T. nigroviridis—T. rubripes (42∼59 Mya) from the TimeTree database were used as the calibration times. The blue numbers on the branches indicate the estimated diverge times in millions of years ago (Mya), and red circles indicate the calibration time.
Figure 4.
Figure 4.
Venn diagram of orthologous gene families. Nine teleost species (D. rerio, D. labrax, G. aculeatus, L. calcarifer, L. maculatus, O. niloticus, O. latipes, T. nigroviridisand, and T. rubripes) were used to generate the Venn diagram based on the gene family cluster analysis.
See this image and copyright information in PMC

References

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