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. 2022 Nov;297(6):1627-1642.
doi: 10.1007/s00438-022-01947-6. Epub 2022 Aug 25.

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

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

Alexandre Lemopoulos et al. Mol Genet Genomics. 2022 Nov.

Abstract

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.

Keywords: Freshwater; Genomics; Herbivory; Loricariidae; Loricarioidei; Vision.

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Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Pictures of the male voucher specimen of Ancistrus triradiatus Eigenmann, 1918 used for the whole genome sequencing (voucher number MHNG2786065 belonging to the collection of the Museum of Natural History of Geneva, Switzerland). Lateral (top), ventral (middle) and dorsal (bottom) views. This specimen is 74.21 mm in Standard Length (SL)
Fig. 2
Fig. 2
Synteny analysis between the reported genome of Ancitrus triradiatus and the genome of Ictalurus punctatus (Liu et al. 2016). Only scaffolds > 250 KB are considered for the A. triraditus genome assembly (small numbered bars on the left and bottom part of the external circle) while full chromosomes were considered for the Ictalurus punctatus genome assembly (numbered grey boxes on the right side of the external circle)
Fig. 3
Fig. 3
Gene family expansion and contraction in seven actinopterygian species related to Ancistrus triradiatus. The number of expanded gene families is shown in green (upper part of the circle), while the number of contracted gene families is shown in purple (lower part of the circle). Gene family expansion/contraction analysis was performed with CAFE5 (Mendes et al. 2020), and using previously published genomes (see “Matherials and methods”). The phylogenetic tree was extracted from the actinopterygian phylogeny of Rabosky et al. (2018)

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