scholarly journals De Novo Transcriptomic and Metabolomic Analyses Reveal the Ecological Adaptation of High-Altitude Bombus pyrosoma

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 631
Author(s):  
Yanjie Liu ◽  
Huiyue Zhao ◽  
Qihua Luo ◽  
Yadong Yang ◽  
Guangshuo Zhang ◽  
...  
Keyword(s):  
High Altitude ◽  
Signaling Pathways ◽  
De Novo ◽  
Tibet Plateau ◽  
Joint Analysis ◽  
Cold Temperatures ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Low Altitude ◽  
Upregulated Genes

Bombus pyrosoma is one of the most abundant bumblebee species in China, with a distribution range of very varied geomorphology and vegetation, which makes it an ideal pollinator species for research into high-altitude adaptation. Here, we sequenced and assembled transcriptomes of B. pyrosoma from the low-altitude North China Plain and the high-altitude Tibet Plateau. Subsequent comparative analysis of de novo transcriptomes from the high- and low-altitude groups identified 675 common upregulated genes (DEGs) in the high-altitude B. pyrosoma. These genes were enriched in metabolic pathways and corresponded to enzyme activities involved in energy metabolism. Furthermore, according to joint analysis with comparative metabolomics, we suggest that the metabolism of coenzyme A (CoA) and the metabolism and transport of energy resources contribute to the adaptation of high-altitude B. pyrosoma. Meanwhile, we found many common upregulated genes enriched in the Toll and immune deficiency (Imd)signaling pathways that act as important immune defenses in insects, and hypoxia and cold temperatures could induce the upregulation of immune genes in insects. Therefore, we suppose that the Toll and Imd signaling pathways also participated in the high-altitude adaptation of B. pyrosoma. Like other organisms, we suggest that the high-altitude adaptation of B. pyrosoma is controlled by diverse mechanisms.

scholarly journals Miocene Diversification and High-Altitude Adaptation of Parnassius Butterflies (Lepidoptera: Papilionidae) in Qinghai–Tibet Plateau Revealed by Large-Scale Transcriptomic Data

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 754
Author(s):  
Chengyong Su ◽  
Tingting Xie ◽  
Yunliang Wang ◽  
Chengcai Si ◽  
Luyan Li ◽  
...  
Keyword(s):  
High Altitude ◽  
Large Scale ◽  
Molecular Dating ◽  
Tibet Plateau ◽  
Butterfly Species ◽  
Evolutionary Pattern ◽  
High Altitude Adaptation ◽  
Time Calibration ◽  
Altitude Adaptation ◽  
Qinghai Tibet Plateau

The early evolutionary pattern and molecular adaptation mechanism of alpine Parnassius butterflies to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now, due to difficulties in sampling, limited sequence data, and time calibration issues. Here, we present large-scale transcriptomic datasets of eight representative Parnassius species to reveal the phylogenetic timescale and potential genetic basis for high-altitude adaptation with multiple analytic strategies using 476 orthologous genes. Our phylogenetic results strongly supported that the subgenus Parnassius formed a well-resolved basal clade, and the subgenera Tadumia and Kailasius were closely related in the phylogenetic trees. In addition, molecular dating analyses showed that the Parnassius began to diverge at about 13.0 to 14.3 million years ago (middle Miocene), correlated with their hostplant’s spatiotemporal distributions, as well as geological and palaeoenvironmental changes of the Qinghai–Tibet Plateau. Moreover, the accelerated evolutionary rate, candidate positively selected genes and their potentially functional changes were detected, probably contributed to the high-altitude adaptation of Parnassius species. Overall, our study provided some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, which will help to address evolution, biodiversity, and conservation questions concerning Parnassius and other butterfly species.

scholarly journals Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1715
Author(s):  
Xu Zhang ◽  
Yanxia Sun ◽  
Jacob B. Landis ◽  
Jun Shen ◽  
Huajie Zhang ◽  
...  
Keyword(s):  
High Altitude ◽  
High Throughput Sequencing ◽  
Extreme Environments ◽  
Tibet Plateau ◽  
Reference Level ◽  
High Altitude Adaptation ◽  
Genomic Resources ◽  
Ideal System ◽  
Alpine Species ◽  
Altitude Adaptation

Understanding how species adapt to extreme environments is an extension of the main goals of evolutionary biology. While alpine plants are an ideal system for investigating the genetic basis of high-altitude adaptation, genomic resources in these species are still limited. In the present study, we generated reference-level transcriptomic data of five Saussurea species through high-throughput sequencing and de novo assembly. Three of them are located in the highland of the Qinghai-Tibet Plateau (QTP), and the other two are close relatives distributed in the lowland. A series of comparative and evolutionary genomics analyses were conducted to explore the genetic signatures of adaptive evolution to high-altitude environments. Estimation of divergence time using single-copy orthologs revealed that Saussurea species diversified during the Miocene, a period with extensive tectonic movement and climatic fluctuation on the QTP. We characterized gene families specific to the alpine species, including genes involved in oxidoreductase activity, pectin catabolic process, lipid transport, and polysaccharide metabolic process, which may play important roles in defense of hypoxia and freezing temperatures of the QTP. Furthermore, in a phylogenetic context with the branch model, we identified hundreds of genes with signatures of positive selection. These genes are involved in DNA repair, membrane transport, response to UV-B and hypoxia, and reproductive processes, as well as some metabolic processes associated with nutrient intake, potentially responsible for Saussurea adaptation to the harsh environments of high altitude. Overall, our study provides valuable genomic resources for alpine species and gained helpful insights into the genomic basis of plants adapting to extreme environments.

scholarly journals Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation

2020 ◽  
Author(s):  
Ke Cao ◽  
Zhen Peng ◽  
Xing Zhao ◽  
Yong Li ◽  
Kuozhan Liu ◽  
...  
Keyword(s):  
High Altitude ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Genomic Analysis ◽  
Gene Families ◽  
Wild Relatives ◽  
Comparative Genomic ◽  
High Altitude Adaptation ◽  
Pan Genome ◽  
Altitude Adaptation

AbstractAs a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica. Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.

scholarly journals Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cheng Quan ◽  
Yuanfeng Li ◽  
Xinyi Liu ◽  
Yahui Wang ◽  
Jie Ping ◽  
...  
Keyword(s):  
High Altitude ◽  
Structural Variation ◽  
Tibet Plateau ◽  
Base Pairs ◽  
Adaptation Studies ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
And Function ◽  
Genomic Regions

Abstract Background Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far. Results Here, we generate a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% are sequence-resolved for the first time. We systematically assess the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 276 genomes, we identify 69 Tibetan-Han stratified SVs and 80 candidate adaptive genes. We also discover a few adaptive introgressed SV candidates and provide evidence for a deletion of 335 base pairs at 1p36.32. Conclusions Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans’ adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future high-altitude adaptation studies.

scholarly journals Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Keren Long ◽  
Siyuan Feng ◽  
Jideng Ma ◽  
Jinwei Zhang ◽  
Long Jin ◽  
...  
Keyword(s):  
High Altitude ◽  
Hemoglobin Concentration ◽  
High Energy ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
High Altitude Adaptation ◽  
Non Coding Rna ◽  
Altitude Adaptation ◽  
Low Altitude ◽  
Multiple Species

Abstract Animals that lived at high altitudes have evolved distinctive physiological traits that allow them to tolerate extreme high-altitude environment, including higher hemoglobin concentration, increased oxygen saturation of blood and a high energy metabolism. Although previous investigations performed plenty of comparison between high- and low-altitude mammals at the level of morphology, physiology and genomics, mechanism underlying high-altitude adaptation remains largely unknown. Few studies provided comparative analyses in high-altitude adaptation, such as parallel analysis in multiple species. In this study, we generated high-quality small RNA sequencing data for six tissues (heart, liver, spleen, lung, kidney and muscle) from low- and high-altitude populations of four typical livestock animals, and identified comparable numbers of miRNAs in each species. This dataset will provide valuable information for understanding the molecular mechanism of high-altitude adaptation in vertebrates.

scholarly journals Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and Introgression

2020 ◽  
Author(s):  
Cheng Quan ◽  
Yuanfeng Li ◽  
Yahui Wang ◽  
Jie Ping ◽  
Yiming Lu ◽  
...  
Keyword(s):  
High Altitude ◽  
Structural Variation ◽  
Tibet Plateau ◽  
Base Pairs ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
And Function ◽  
Genomic Regions ◽  
Qinghai Tibet Plateau

AbstractStructural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. To investigate the role of SVs in high-altitude adaptation (HAA), we here generated a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using the nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% were sequence-resolved for the first time. We systemically assessed the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 189 genomes, we identified 90 Tibetan-Han stratified SVs and 124 candidate adaptive genes. Besides, we discovered 15 adaptive introgressed SV candidates and provided evidence for a deletion of 335 base pairs at 1p36.32. Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans’ adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future HAA studies.

scholarly journals Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

2021 ◽  
Author(s):  
Pamela Wiener ◽  
Christelle Robert ◽  
Abulgasim Ahbara ◽  
Mazdak Salavati ◽  
Ayele Abebe ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Variables ◽  
Large Scale ◽  
Sequence Data ◽  
Strong Association ◽  
Environmental Adaptation ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

Mitochondrial nt3010G-nt3970C haplotype is implicated in high-altitude adaptation of Tibetans

2011 ◽  
Vol 22 (5-6) ◽  
pp. 181-190 ◽  
Author(s):  
Yongjun Luo ◽  
Wenxiang Gao ◽  
Fuyu Liu ◽  
Yuqi Gao
Keyword(s):  
High Altitude ◽  
High Altitude Adaptation ◽  
Altitude Adaptation
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