Chromosome-Level Genome Assembly of the Asian Red-Tail Catfish (Hemibagrus wyckioides)

Shao, Feng; Pan, Huamei; Li, Ping; Ni, Luyun; Xu, Yuan; Peng, Zhé

doi:10.3389/fgene.2021.747684

Cited by 15 publications

(16 citation statements)

References 45 publications

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“…2B ). According to previously reported studies, separation times were 41.73 Mya between H. wyckioides and P. fulvidraco , 38 and 26.2 Mya between L. longirostris and P. fulvidraco . 36 Therefore, among the four genera of the Bagridae family, Pseudobagrus and Pelteobagrus had the closet relationship.…”

Section: Discussionsupporting

confidence: 66%

“…Additionally, through annotations in five public databases, 22,039 (91.54%) of the predicted genes were annotated in at least one database ( Supplementary Table S4 ). The assembly and annotation data of P. ussuriensis were compared with those of some reported catfishes ( Table 4 ), including P. fulvidraco , 33 L. longirostris , 36 H. wyckioides , 38 G. maculatum , 101 B. yarrelli , 34 S. meridionalis , 35 Silurus asotus , 102 Silurus glanis , 103 Clarias batrachus , 104 I. punctatus , 105 and P. hypophthalmus . 37 …”

Section: Resultsmentioning

confidence: 99%

“…107 The size of the P. ussuriensis genome was similar to those of reported catfish species ( Table 4 ), and was closest to those of two Siluridae fishes: 738.90 Mb in S. meridionalis 35 and 744.12 Mb in S. asotus. 102 When compared with genome sizes of three reported Bagridae fishes, 33 , 36 , 38 the genome size of P. ussuriensis was closest to that of P. fulvidraco ( Table 4 ). The GC content in the genome of P. ussuriensis was similar to other catfishes ( Table 4 ).…”

Section: Discussionmentioning

confidence: 97%

“… 29–31 Chromosome-level genomes have also been reported in catfishes, such as channel catfish ( Ictalurus punctatus ), 32 yellow catfish ( Pelteobagrus fulvidraco ), 33 giant devil catfish ( Bagarius yarrelli ), 34 Southern catfish ( Silurus meridionalis ), 35 Chinese longsnout catfish ( Leiocassis longirostris ), 36 striped catfish ( Pangasianodon hypophthalmus ), 37 and redtail catfish ( Hemibagrus wyckioides ). 38 These chromosome-level assemblies have been widely used as reliable reference genomes for studies of many fields, including ecological adaptation, 35 , 39 , 40 genome evolution, 41–43 gene evolution, 44 , 45 immunology, 46–48 and identification of target-trait-related genes, 49 , 50 in aquatic animals. Moreover, chromosome-level genomes have also been used for studies on sex determination mechanisms, including identification of sex determination regions and genes, 51–53 sex reversal, 54 , 55 and sex chromosome evolutions.…”

Section: Introductionmentioning

confidence: 99%

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Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

et al. 2022

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Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related QTLs with a PVE value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 Mb to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.

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Section: Discussionsupporting

confidence: 66%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

et al. 2022

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“…Phylogenomic analysis of reference fish genomes in OrthoDB revealed that zebrafish was the closest outgroup species to catfish species, which is congruent with the known phylogeny of ray-finned fishes [ 120 ] and is also consistent with previous findings that the most closely related model fish species is zebrafish [ 121 ]. Many genomes are available in Siluriformes, including the Asian redtail catfish ( Hemibagrus wyckioides ) [ 122 ] and yellow catfish ( Tachysurus fulvidraco ) [ 123 ] in the family of Bagridae, giant devil catfish ( Bagarius yarrelli ) in Sisoridae [ 124 ], 12 Pangasiidae species [ 68–70 ], 3 Clariidae species [ 125–127 ], and channel catfish ( Ictalurus punctatus ) and black bullhead catfish ( Ameiurus melas , GCA_012411365) in the family of Ictaluridae. Our blue catfish genome will provide an invaluable resource to investigate molecular phylogeny and comparative analysis in Siluriformes.…”

Section: Discussionmentioning

confidence: 99%

Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

Wang

Butts

et al. 2022

GigaScience

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Background The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. Results The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. Conclusions We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish.

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Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures

Lemopoulos

Montoya‐Burgos

2022

Mol Genet Genomics

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The catfish Ancistrus triradiatus belongs to the species-rich family Loricariidae. Loricariids display remarkable traits such as herbivory, a benthic lifestyle, the absence of scales but the presence of dermal bony plates. They are exported as ornamental fish worldwide, with escaped fishes becoming a threat locally. Although genetic and phylogenetic studies are continuously increasing and developmental genetic investigations are underway, no genome assembly has been formally proposed for Loricariidae yet. We report a high-quality genome assembly of Ancistrus triradiatus using long and short reads, and a newly assembled transcriptome. The genome assembly is composed of 9530 scaffolds, including 85.6% of ray-finned fish BUSCOs, and 26,885 predicted protein-coding genes. The genomic GC content is higher than in other catfishes, reflecting the higher metabolism associated with herbivory. The examination of the SCPP gene family indicates that the genes presumably triggering scale loss when absent, are present in the scaleless A. triradiatus, questioning their explanatory role. The analysis of the opsin gene repertoire revealed that gene losses associated to the nocturnal lifestyle of catfishes were not entirely found in A. triradiatus, as the UV-sensitive opsin 5 is present. Finally, most gene family expansions were related to immunity except the gamma crystallin gene family which controls pupil shape and sub-aquatic vision. Thus, the genome of A. triradiatus reveals that fish herbivory may be related to the photic zone habitat, conditions metabolism, photoreception and visual functions. This genome is the first for the catfish suborder Loricarioidei and will serve as backbone for future genetic, developmental and conservation studies.

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Chromosome-Level Genome Assembly of the Asian Red-Tail Catfish (Hemibagrus wyckioides)

Cited by 15 publications

References 45 publications

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures

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