scholarly journals Genomic signature of ongoing alkaline adaptation in a Schizothoracine fish (Cyprinidae) inhabiting soda lake on the Tibetan Plateau

2019 ◽  
Author(s):  
Chao Tong ◽  
Miao Li ◽  
Yongtao Tang ◽  
Kai Zhao
Keyword(s):  
Molecular Evolution ◽  
Comparative Genomics ◽  
Tibetan Plateau ◽  
Ion Transport ◽  
Fish Species ◽  
Soda Lake ◽  
Genomic Signature ◽  
The Tibetan Plateau ◽  
Rate Of Molecular Evolution ◽  
Schizothoracine Fish

AbstractComparative genomics has elucidate the molecular footprints of adaptations to extreme environments at high altitude including hypoxia, but insight into the genomic basis of saline and alkaline adaptation in highland fish has rarely been provided. The increasing of water salinization is a growing threat to Tibetan endemic fish species. Here we performed one of the first comparative genomics studies and began to characterize genomic signature of alkaline adaptation in a Schizothoracine fish inhabiting soda lake on the Tibetan Plateau. We found that expansions of lineage-specific genes associated with ion transport and transmembrane functions, genome-wide elevated rate of molecular evolution in Schizothoracine fishes relative to other lowland teleost fish species. In addition, we found specific changes in the rate of molecular evolution between G. p. kelukehuensis and other teleost fishes for ion transport-related genes. Furthermore, we identified a set of genes associated with ion transport and energy metabolism underwent positive selection. Using tissue-transcriptomics, we found that most REGs and PSGs in G. p. kelukehuensis were broadly expressed across three tissues and significantly enriched for ion transport functions. Finally, we identified a set of ion transport-related genes with evidences for both selection and co-expressed which contributed to alkaline tolerance in G. p. kelukehuensis. Altogether, our study identified putative genomic signature and potential candidate genes contributed to ongoing alkaline adaptation in Schizothoracine fish.

scholarly journals Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish

2019 ◽  
Author(s):  
Chao Tong ◽  
Miao Li
Keyword(s):  
Comparative Genomics ◽  
Tibetan Plateau ◽  
Ion Transport ◽  
High Salinity ◽  
Adaptation To Hypoxia ◽  
Biological Macromolecules ◽  
The Tibetan Plateau ◽  
Accelerated Evolution ◽  
Genome Wide ◽  
Schizothoracine Fish

AbstractTibetan Plateau imposes extremely inhospitable environment on most wildlife. Besides the harsh aquatic environment including hypoxia and chronic cold, high salinity and alkalinity is an increasing threat to Tibetan endemic fishes. Previous genome-wide studies identified key genes contributed to highland fish adaptation to hypoxia and long-term cold, while our understanding of saline and alkaline adaptation in Tibetan fish remains limited. In this study, we performed a comparative genomics analysis in a saline lake-dwelling highland fish Gymnocypris przewalskii, aimed to identify candidate genes that contributed to saline and alkaline adaptation. We found elevated genome-wide rate of molecular evolution in G. przewalskii relative to lowland teleost fish species. In addition, we found nine genes encoding biological macromolecules associated with ion transport functions underwent accelerated evolution in G. przewalskii, which broadly expressed across kidney, gill, liver, spleen, brain and muscle tissues. Moreover, we found putative evidence of ion transport under selection were interacted by co-expression in G. przewalskii adaptation to high salinity and alkalinity environment of Lake Qinghai. Taken together, our comparative genomics study identified a set of rapidly evolving ion transport genes and transcriptomic signatures in Schizothoracine fish adaptation to saline and alkaline environment on the Tibetan Plateau.

scholarly journals Adaptive Evolution of the Eda Gene and Scales Loss in Schizothoracine Fishes in Response to Uplift of the Tibetan Plateau

2018 ◽  
Vol 19 (10) ◽  
pp. 2953 ◽  
Author(s):  
Cunfang Zhang ◽  
Chao Tong ◽  
Arne Ludwig ◽  
Yongtao Tang ◽  
Sijia Liu ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Major Gene ◽  
Phylogenetic Analyses ◽  
The Tibetan Plateau ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Structure Changes ◽  
Pharyngeal Teeth ◽  
Eda Gene ◽  
Schizothoracine Fish

Schizothoracine is the predominant wild fish subfamily of the Tibetan plateau (TP). Their scales, pharyngeal teeth and barbels have gradually regressed with increasing altitude. Schizothoracine have been divided into three groups: primitive, specialized and highly specialized. Ectodysplasin-A (Eda) has been considered as a major gene that contributes to the development of skin appendages. The present study cloned the Eda genes of 51 Schizothoracine fish species which represent the three groups and five Barbinae species. Phylogenetic analyses indicated that Eda may have acted as the genetic trigger for scale loss in the Schizothoracine. Furthermore, 14 single nucleotide polymorphisms (SNPs) and two deletions (18 bp and 6 bp in size), were also detected in the Eda coding sequence of the highly specialized group compared to the primitive group. The same SNPs and two indels result in four non-synonymous and two G-X-Y and 1 XY motif indels, which possibly contribute to significant structure changes in the Eda gene. The domain including (G-X-Y)n motif in the Eda gene is relatively conserved amongst teleosts. Based on the above results, we hypothesize that the evolution of Eda gene might be associated with the scale loss in Schizothoracine fishes in response to the phased uplift of the TP.

scholarly journals Genomic signature of shifts in selection and alkaline adaptation in highland fish

2020 ◽  
Author(s):  
Chao Tong ◽  
Miao Li ◽  
Yongtao Tang ◽  
Kai Zhao
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
High Altitude ◽  
Fish Species ◽  
Comparative Studies ◽  
Genomic Signature ◽  
Adaptive Molecular Evolution ◽  
Tolerant Species ◽  
Genomic Basis ◽  
Alkaline Tolerant

AbstractUnderstanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed mainly related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species and four alkaline intolerant relatives. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of core shared genes associated with ion transport, apoptosis, immune response and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.Significance StatementLittle is known about how wild fish responds to extreme alkaline stress besides hypoxia at high altitude. Comparative genomics has begun to elucidate the genomic basis of alkaline adaptation in lowland fish, such as killifish, but insight from highland fish has lagged behind. The common role of adaptive molecular evolution during alkaline adaptation in highland and lowland fish has rarely been discussed. We address this question by comparing 15 fish omics data. We find numbers of shared orthologs exhibited consistent patterns of molecular evolution in alkaline tolerant species relative to intolerant species. We further identify remarkably consistent signatures of rapidly evolving and positive selection in a substantial shared core of genes in both highland and lowland alkaline tolerant species.

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