De novo sequencing and chromosomal‐scale genome assembly of leopard coral grouper, Plectropomus leopardus

Abstract

The leopard coral grouper, Plectropomus leopardus, belonging to the family Epinephelinae, is a carnivorous coral reef fish widely distributed in tropical and subtropical waters of the Indo‐Pacific. Due to its appealing body appearance and delicious taste, P. leopardus has become a popular commercial fish for aquaculture in many countries. However, the lack of genomic and molecular resources for P. leopardus has hindered study of its biology and genomic breeding programmes. Here we report the de novo sequencing and assembly of the P. leopardus genome using a combination of 10 × Genomics, high‐throughput chromosome conformation capture (Hi‐C) and PacBio long‐read sequencing technologies. The genome assembly has a total length of 881.55 Mb with a scaffold N50 of 34.15 Mb, consisting of 24 pseudochromosome scaffolds. busco analysis showed that 97.2% of the conserved single‐copy genes were retrieved, indicating the assembly was almost entire. We predicted 25,248 protein‐coding genes, among which 96.5% were functionally annotated. Comparative genomic analyses revealed that gene family expansions in P. leopardus were associated with immune‐related pathways. In addition, we identified 5,178,453 single nucleotide polymorphisms based on genome resequencing of 54 individuals. The P. leopardus genome and genomic variation data provide valuable genomic resources for studies of its genetics, evolution and biology. In particular, it is expected to benefit the development of genomic breeding programmes in the farming industry.

Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae

“…In our present study, a total of 29,509 genes were annotated from the spiny head croaker genome, which are more than those from a previous study ( Cai et al, 2019 ). The number is higher than that of large yellow croaker (23,172 genes; Chen et al, 2019 ), miiuy croaker (21,960 genes; Xu et al, 2016a ), and leopard coral grouper (25,248 genes; Zhou et al, 2020 ), whereas it is similar to Nile tilapia (29,249 genes; Conte et al, 2017 ). Moreover, our current work investigated gene families in spiny head croaker based on an integration of PacBio long-read sequencing and Hi-C technology.…”

Chromosome-Level Genome Assembly and Transcriptome Comparison Analysis of Cephalopholis sonnerati and Its Related Grouper Species

“…Similar results have also been reported in previ-ous research, i.e., Triplophysa tibetana [ 57 ], E. akaara [ 14 ], and Spotted Scat ( Scatophagus argus ) [ 58 ]. Moreover, the genome size of the C. sonnerati was shorter than the genomes of the red-spotted grouper (1135 Mb) [ 14 ] and the giant grouper (1086 Mb) [ 13 ], but longer than the genome of the leopard coral grouper (881.55 Mb) [ 15 ]. In addition, the heterozygosity of C. sonnerati (0.84%) was higher than that in E. akaara (0.375%) [ 14 ], P. leopardus (0.635%) [ 15 ], M. peelii (0.113%) [ 59 ], S. lucioperca (0.14%) [ 60 ], and T. tibetana (0.1%) [ 57 ], suggesting high population genetic diversity for the C. sonnerati grouper and non-selective breeding in aquaculture.…”

“…Moreover, the genome size of the C. sonnerati was shorter than the genomes of the red-spotted grouper (1135 Mb) [ 14 ] and the giant grouper (1086 Mb) [ 13 ], but longer than the genome of the leopard coral grouper (881.55 Mb) [ 15 ]. In addition, the heterozygosity of C. sonnerati (0.84%) was higher than that in E. akaara (0.375%) [ 14 ], P. leopardus (0.635%) [ 15 ], M. peelii (0.113%) [ 59 ], S. lucioperca (0.14%) [ 60 ], and T. tibetana (0.1%) [ 57 ], suggesting high population genetic diversity for the C. sonnerati grouper and non-selective breeding in aquaculture. Repeat content was approximately 42.99% in C. sonnerati , higher than that in P. leopardus (34.6%) [ 15 ] and E. lanceolatus (41.01%) [ 13 ], but lower than that in E. akaara (43.02%) [ 14 ].…”

Vasa Is a Potential Germ Cell Marker in Leopard Coral Grouper (Plectropomus leopardus)

“…The splicing sites of exons and introns, together with their positions and sizes in the genome, were identified according to the sequencing results of vasa mRNA and the full genome of leopard coral groupers [ 39 ]. The SMART website ( , accessed on 27 August 2021) was used for the identification and annotation of protein domains and the analysis of protein domain architectures [ 40 ].…”