Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life

Abstract

Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448.52-Mb genome assembly with contig N50 length of 5.53 Mb by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin map. Demographic history reconstruction of the butterfly hillstream loach reveals that the population dynamics is correlated with the different stages of uplifting of the Tibetan Plateau. Comparative genomic analysis finds evidence of six keratin genes in butterfly hillstream loach evolving under positive selection. Within these genes, two keratin genes exhibit species-specific and divergent amino acid changes, suggesting a role in the formation of the unculi. Additionally, a series of positively selected genes, rapid evolving genes, specific variant genes and expanded gene families are found, including genes related to Hedgehog, Notch and BMP pathways, which may be involved in craniofacial development. These findings may have important implications for understanding the genetic basis of phenotypic adaptation to torrential mountain stream life.

Chromosome-level genome assembly of the primitive loach goby,Rhyacichthys aspro, reveals mechanisms underlying Gobioidei diversification

“…These loci may be associated with flattened heads and abdomens that characterize loach gobies, phenotypes that may underly adaptation to strong currents. Interestingly, we also found that the genome of a hill-stream loach Beaufortia kweichowensis from the Balitoridae (Cypriniformes) family that also has a flattened cranium (Deng et al, 2021) adaptive in fast mountain streams is also enriched in the GO: GO:0048702 category (Table S19a). The B. kweichowensis genome contains a paralog of Sec23A, Sec23B, that is also evolved in embryonic neurocranium morphogenesis (Lang, Lapierre, Frotscher, Goldenring, & Knapik, 2006).…”

The loach (Misgurnus anguillicaudatus) genome and the adaptation to a mud environment

“…In the loach genome, DNA transposons (39.39%), long terminal repeats (LTRs, 14.23%) and long interspersed nuclear elements (LINEs, 7.02%) were the most abundant (Fig S1a and Table S1-(4)). The content of repetitive sequences in the loach genome was much higher than that of some fish species: seen in Triplophysa tibetana (39.8%) (Yang et al 2019), Beaufortia kweichowensis (22.24%) (Deng et al 2021) and Ctenopharyngodon idellus (38%) (Wang et al 2015).…”

The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus)

“…The content of repetitive sequences in the loach genome was much higher than that of some fish species, including Triplophysa tibetana (39.80%) [ 19 ], Beaufortia kweichowensis (22.24%) [ 20 ], and Ctenopharyngodon idellus (38%) [ 21 ].…”