The Sinocyclocheilus cavefish genome provides insights into cave adaptation

Abstract

BackgroundAn emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively.ResultsThe assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes.ConclusionAs the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users.

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

“…Among differentially expressed APA transcripts, 21 are found in the testes, 18 in the liver and 11 in the brain. Recently, it has been shown that APA regulation is important for RNA processing during spermatogenesis (93). We compared APA transcripts with published datasets derived from different testis cell types (87) and found that the Cd68 APA transcript has altered 3′UTR.…”

Selection of Reliable Reference Genes for Quantitative Real-Time PCR in Golden-Line Barbell (Sinocyclocheilus grahami) During Juvenile and Adult Stages

“…As far as we know, this is the first report about the reference gene selection in Sinocyclocheilus fishes. The species in this genus were served as an emerging cavefish model (Yang et al, 2016) that it can be expected more and more researches were conducting to this group of fishes in the future. As a natural group of tetraploid fishes, designing appropriate primers for distinguishing different copies was the very fundamental step before the qRT-PCR analyses.…”

“…It has now been categorized as a second-class, state protected animal due to a dramatic population decrease by human activities (Pan et al, 2009). In the recent decade, the artificial breeding of this fish had been succeeded (Yang et al, 2007) and many other following studies were also conducted, such as the aquaculture management and conservation (Pan et al, 2010;Pan et al, 2011), the wholegenome sequencing (Yang et al, 2016) and etc. But up to now, gene expression research on this fish is still blank.…”

Cavefish and the basis for eye loss

“…The genus Sinocyclocheilus (in the order of the Cypriniformes) contains at least 10 cavefish species. The availability of many closely related surface-dwelling species makes it a good model to study cave adaptation in an evolutionarily distant system from Astyanax mexicanus (which is found in the order of the Characiformes) [6,68]. Both orders share a common ancestor approx.…”

“…Worldwide, more than 150 species of obligate cavefish are described, endemic to all continents except Europe and Antarctica. The Northern cavefish Amblyopsis spelaea [3], the Somali cavefish Phreatichthys andruzzii [5], or the Chinese cavefish Sinocyclocheilus [6] are a few of the better-known species complementing work on Astyanax mexicanus. The cave forms of A. mexicanus are found in the Sierra del Abra of Northeastern Mexico in 29 known caves.…”