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Population genome of the newly discovered Jinchuan yak to understand its adaptive evolution in extreme environments and generation mechanism of the multirib trait

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Integrative Zoology 2021年第5期16卷 685-695页

作者： Daoliang LAN Wenhui JI Xianrong XIONG Qiqi LIANG Wenye YAO Tserang-Donko MIPAM Jincheng ZHONG Jian LI Ministry of Education of key laboratory of Qinghai-tibet plateau Animal Genetic Resource and Utilization Southwest Minzu UniversityChengduChina Institute of Qinghai-tibetan plateau Southwest Minzu UniversityChengduChina Novogene Bioinformatics Institute BeijingChina

The adaptation and diversity of animals to the extreme environments of the Qinghai–tibet plateau(QTP)are typical materials to study adaptive *** recently discovered Jinchuan yak population has many individuals with multiple ***,little is known about this yak’s origin,evolution,and the genetic mechanisms that formed its unique multirib ***,we report a valuable population genome resource of the Jinchuan yak by resequencing the whole genome of 150 *** genetic polymorphism and structure analysis reveal that Jinchuan yak can be differentiated as a unique and original yak population among the domestic *** with geological change,the Jinchuan yak’s evolutionary origin is speculated to be about 6290 years ago,which may be related to the unique geographical environment of the eastern edge of the QTP during this *** with other domestic yaks,this new population has 280 positively selected *** genes related to skeletal function hold a considerable and remarkable proportion,suggesting that the specific skeletal characteristics have been enhanced in the adaptive evolution of Jinchuan yak in the extreme plateau *** genome-wide association study has revealed that TUBA8 and TUBA4A,the genes that regulate the cytoskeleton,are potential genes associated with the multirib *** findings provide a basis to further understand the generation mechanism of the adaptive evolution of this new population in high-altitude extreme environments and the multivertebrate trait of domestic animals.

关键词： adaptive evolution genetic mechanism multirib trait Qinghai-tibet plateau yak

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Validation of the Satellite-Derived Rainfall Estimates over the tibet

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Acta meteorologica Sinica 2011年第6期25卷 734-741页

作者：除多普布顿珠罗布坚参 SAGAR Bajracharya MANDIRA Shrestha 郭建平 Institute of plateau Meteorology CMA tibet Institute of plateau Atmospheric and Environmental Sciences tibet Weather Observatory Tibet Meteorological Service International Centre for Integrated Mountain Development (ICIMOD) Chinese Academy of Meteorological Sciences CMA

Measuring rainfall from space appears to be the only cost effective and viable means in estimating regional precipitation over the tibet, and the satellite rainfall products are essential to hydrological and agricultural modeling. A long-standing problem in the meteorological and hydrological studies is that there is only a sparse raingauge network representing the spatial distribution of precipitation and its quantity on small scales over the tibet. Therefore, satellite derived quantitative precipitation estimates are extremely usefill for obtaining rainfall patterns that can be used by hydrological models to produce forecasts of river discharge and to delineate the flood hazard area. In this paper, validation of the US National Oceanic and Atmospheric Administration （NOAA） Climate Prediction Center （CPC） RFE （rainfall estimate） 2.0 data was made by using daily rainfall observations at 11 weather stations over different climate zones from southeast to northwest of the tibet during the rainy season from 1 June to 30 September 2005 and 2006. Analysis on the time series of daily rainfall of RFE-CPC and observed data in different climate zones reveals that the mean correlation coefficients between satellite estimated and observed rainfall is 0.74. Only at Pali and Nielamu stations located in the southern brink of the tibet along the Himalayan Mountains, are the correlation coefficients less than 0.62. In addition, continuous validations show that the RFE performed well in different climate zones, with considerably low mean error （ME） and root mean square error （RMSE） scores except at Nielamu station along the Himalayan range. Likewise, for the dichotomous validation, at most stations over the tibet, the probability of detection （POD） values is above 73% while the false alarm rate （FAR） is between 1% and 12%. Overall, NOAA CPC RFE 2.0 products performed well in the estimation and monitoring of rainfall over the tibet and can be used to analyze the precipitation pattern,

关键词： precipitation validation satellite rainfall estimation tibetan plateau

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Expression of HIF-1α and Its Target Genes in the Nanorana parkeri Heart：Implications for High Altitude Adaptation

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Asian Herpetological Research 2016年第1期7卷 12-20页

作者： Qiong ZHANG Xingzhi HAN Yinzi YE Robert H.S.KRAUS Liqing FAN Le YANG Yi TAO key laboratory of Animal ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China College of Life Sciences Harbin Normal University Harbin 150025 Heilongjiang China College of Life Sciences Hangzhou Normal University Hangzhou 311121 Zhejiang China Department of Biology University of Konstanz Konstanz 78457 Germany Max Planck Institute for Ornithology Department of Migration and Immuno-Ecology Am Obstberg 1 Radoljzell 78315 Germany College of Agricultural and Animal Husbandry Tibet University Tibet 860000 China tibet plateau Institute of Biology Tibet 850001 China

Hypoxia-inducible factor 1 alpha（HIF-1α） and its target genes vascular endothelial growth factor（VEGF） and transferrins（TF） play an important role in native endothermic animals＇ adaptation to the high altitude environments. For ectothermic animals – especially frogs – it remains undetermined whether HIF-1α and its target genes（VEGF and TF） play an important role in high altitude adaptation, too. In this study, we compared the gene sequences and expression of HIF-1α and its target genes（VEGF and TF） between three Nanorana parkeri populations from different altitudes（3008 m a.s.l., 3440 m a.s.l. and 4312 m a.s.l.）. We observed that the c DNA sequences of HIF-1A exhibited high sequence similarity（99.38%） among the three altitudinally separated populations; but with increasing altitude, the expression of HIF-1A and its target genes（VEGF and TF） increased significantly. These results indicate that HIF-1α plays an important role in N. parkeri adaptation to the high altitude, similar to its role in endothermic animals.

关键词： Hypoxia cold-temperature ectothermic animals Nanorana parkeri high altitude vascular endothelial growth factor transferrins anura amphibia

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Phylogenetic patterns of shrub communities along the longitudinal and latitudinal gradients on the northeastern Qinghai–tibetan plateau

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Journal of Mountain Science 2020年第5期17卷 1106-1114页

作者： XIAO Yuan-ming YANG Lu-cun NIE Xiu-qing LI Chang-bin XIONG Feng ZHOU Guo-ying Northwest Institute of plateau Biology Chinese Academy of SciencesXining 810008China key laboratory of tibetan Medicine Research Chinese Academy of SciencesXining 810008China Qinghai key laboratory of Qinghai-tibet plateau Biological Resources Xining 810008China University of Chinese Academy of Sciences Beijing 100049China

Biodiversity distribution patterns are a basic and long-standing but crucial aspect of ecology *** patterns form the primary source of data used to develop biodiversity protection practices,especially in mountain *** comprise one of the main types of vegetation on the Qinghai–tibetan plateau,where they serve vital ecological *** this study,we used a community phylogenetic approach to examine the distribution patterns of shrub communities along the longitudinal and latitudinal gradients on the northeastern Qinghai–tibetan *** observed significant latitudinal trends in both the phylogenetic diversity(PD)and net relatedness index(NRI)values of shrub communities,such that the former decreased and the latter increased with increasing ***,no significant PD,NRI and nearest taxon index(NTI)distribution patterns were observed along a longitudinal gradient.A further analysis revealed that the combination of temperature-related and precipitation-related climate variables most strongly affected the PD,NRI and NTI values of shrub communities,indicating that the latitudinal patterns in the PD,NRI and NTI of a shrub community may be determined mainly by interactions with these climate factors.

关键词： Phylogenetic diversity Phylogenetic community structure Shrub communities Qinghai–tibetan plateau Net Relatedness Index Nearest Taxon Index

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Large-scale characteristics of thermokarst lakes across the source area of the Yellow River on the Qinghai-tibetan plateau

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Journal of Mountain Science 2023年第6期20卷 1589-1604页

作者： LIU Wen-hui ZHOU Guang-hao LIU Hai-rui LI Qing-peng XIE Chang-wei LI Qing ZHAO Jian-yun ZHANG Qi State key laboratory of plateau ecology and Agriculture Qinghai UniversityXining 810016China Department of Geological Engineering Qinghai UniversityXining 810016China College of Eco-Environmental Engineering Qinghai UniversityXining 810016China Cryosphere Research Station on the Qinghai-tibet plateau State Key Laboratory of Cryosphere SciencesNorthwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhou 73ooooChina

As significant evidence of permafrost degradation,thermokarst lakes play an important role in the permafrost regions by regulating hydrology,ecology,and *** the Sources area of the Yellow River(SAYR),permafrost degradation has accelerated since the 1980s,and numerous thermokarst lakes have been *** this paper,we use Sentinel-2 images to extract thermokarst lake boundaries and perform a regional-scale study on their geometry across the permafrost region in the *** also explored the spatiotemporal variations and potential drivers from the perspectives of the permafrost,climate,terrain and vegetation *** results showed that there were 47,518 thermokarst lakes in 2021 with a total area of 190.22×106 m^(2),with an average size of 4,003.3 m^(2).The 44,928 ponds(≤10,000 m^(2))predominated the whole lake number(94.1%)but contributed to a small portion of the total lake area(28.8%).With 2,590 features(5.9%),small-sized(10,000 to 100,000 m^(2))and large-sized lakes(>100,000 m^(2))constituted up to 71.2%of the total lake *** lakes developed more significantly in warm permafrost regions than in cold permafrost areas;74.1%of lakes with a total area of 119.6×106 m^(2)(62.9%),were distributed in warm permafrost *** thermokarst lakes were likely to develop within the elevation range of 4,500~4,800 m,on flat terrain(slopearea of 58.63×106 m^(2)(49.0%).This shrinkage of the thermokarst lake area was attributable mainly to the intensified degradation of rich-ice permafrost thawing arising from continued climate warming,despite the wetting climatic trend.

关键词： Thermokarst lake Spatial characteristic Influencing factor Source area of the Yellow River

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Evolutionary history of a desert perennial Arnebia szechenyi(Boraginaceae):Intraspecific divergence,regional expansion and asymmetric gene flow

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Plant Diversity 2021年第6期43卷 462-471页

作者： Meng-Jiao Fu Hai-Yang Wu Dong-Rui Jia Bin Tian key laboratory for forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of EducationSouthwest Forestry UniversityKunming 650224China School of ecology and Environmental Science&Yunnan key laboratory for plateau Mountain ecology and Restoration of Degraded Environments Yunnan UniversityKunming 650091China CAS key laboratory for Plant Diversity and Biogeography Kunming Institute of BotanyChinese Academy of SciencesKunming 650204China

The complex interactions of historical,geological and climatic events on plant evolution have been an important research focus for many ***,the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well *** the present study,we investigated the phylogeography of Arnebia szechenyi,a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest *** measured genetic diversity of populations using three maternally inherited chloroplast DNA(cpDNA)fragments and seven bi-paternally inherited nuclear DNA(nDNA)loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the *** data indicated a considerably high level of genetic variation within *** and noteworthy asymmetry in historical migration from the east to the ***,two nuclear genetic groups of populations were revealed,corresponding to the two geographic regions separated by the Tengger ***,analysis of cpDNA data did not show significant geographic *** most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that *** populations experienced long periods of geographic isolation followed by range expansion,which would have promoted generalized recombination of the nuclear *** findings further highlight the important role that the Tengger Desert,together with the Helan Mountains,has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.

关键词： Asymmetric gene flow Cytonuclear discordance Desert growth Intraspecific divergence

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High-quality assembly and methylome of a tibetan wild tree peony genome(Paeonia ludlowii)reveal the evolution of giant genome architecture

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Horticulture Research 2023年第12期10卷 248-263页

作者： Pei-Xuan Xiao Yuanrong Li Jin Lu Hao Zuo Gesang Pingcuo Hong Ying Fan Zhao Qiang Xu Xiuli Zeng Wen-Biao Jiao National key laboratory for Germplasm Innovation&Utilization of Horticultural Crops Huazhong Agricultural UniversityWuhan 430070China Hubei Hongshan laboratory Wuhan 430070China Qinghai-tibet plateau Fruit Trees Scientific Observation Test Station(Ministry of Agriculture and Rural Affairs) LhasaTibet 850032China Institute of Vegetables Tibet Academy of Agricultural and Animal Husbandry SciencesLhasaTibet 850002China

Tree peony belongs to one of the Saxifragales families,*** is one of the most famous ornamental plants,and is also a promising woody oil *** two Paeoniaceae genomes have been released,their assembly qualities are still to be ***,more genomes from wild peonies are needed to accelerate genomic-assisted *** we assemble a high-quality and chromosome-scale 10.3-Gb genome of a wild tibetan tree peony,Paeonia ludlowii,which features substantial sequence divergence,including around 75%specific sequences and gene-level differentials compared with other peony *** phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa and,together with rosids,they are the sister taxon to *** *** genome is characterized by frequent chromosome reductions,centromere rearrangements,broadly distributed heterochromatin,and recent continuous bursts of transposable element(TE)movement in peony,although it lacks recent whole-genome *** recent TE bursts appeared during the uplift and glacial period of the Qinghai-tibet plateau,perhaps contributing to adaptation to rapid climate *** integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation,TE removal,and DNA methylation *** interactions also impact numerous recently duplicated genes,particularly those related to oil biosynthesis and flower *** genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study of the evolution of huge genome structures as well as their protein-coding genes.

关键词： tibetan evolution breeding

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Dynamic changes in lakes in the Hoh Xil region before and after the 2011 outburst of Zonag Lake

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Journal of Mountain Science 2019年第5期16卷 1098-1110页

作者： LIU Wen-hui XIE Chang-wei ZHAO Lin WU Tong-hua WANG Wu ZHANG Yu-xin YANG Gui-qian ZHU Xiao-fan YUE Guang-yang Cryosphere Research Station on the Qinghai-tibet plateau State Key Laboratory of Cryosphere Sciences Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences University of Chinese Academy of Sciences

Zonag, Kusai, Hedin Noel and Yanhu Lakes are independent inland lakes in the Hoh Xil region on the Qinghai-tibet plateau. In September2011, Zonag Lake burst after the water level had increased for many years. Floods flowed through Kusai and Hedin Noel Lakes into Yanhu Lake; since then, the four small endorheic catchments merged into one larger catchment. This hydrological process caused the rapid shrinkage of Zonag Lake and continuous expansion of Yanhu Lake. In this study,based on satellite images, meteorological data and field investigations, we examined the dynamic changes in the four lakes and analyzed the influencing factors. The results showed that before 2011, the trends in the four lake areas were similar and displayed several stages. The change in the area of Zonag Lake corresponded well to the change in annual precipitation(AP), but the magnitude of the change was less than that of a non-glacier-fed lake. Although increased precipitation was the dominant factor that caused Zonag Lake to expand, increased glacier melting and permafrost thawing due to climate warming also had significant effects. After the 2011 outburst of Zonag Lake, due to the increasing AP and accelerating glacier melting, the increases in water volume of the three lakes were absorbed by Yanhu Lake, and Yanhu Lake expanded considerably. According to the rapid growth rates in water level and lake area, Yanhu Lake is likely to burst in 1-2 years.

关键词： Dynamic change Lake areas Influencing factors Glacier change Permafrost thawing Zonag Lake

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Phenotypic Diversity of Different Populations of Paeonia ludlowii in Nyingchi of tibet

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Medicinal Plant 2019年第4期10卷 62-65页

作者： Qingsong GE Yi GAO Hang WANG Jiangping FANG Res. Institute of tibet plateau ecology Tibet Agriculture & Animal Husbandry University Nyingchi 860000 China tibet key laboratory of forest ecology in plateau area Ministry of Education Nyingchi 860000 China National key Station of Field Scientific Observation & Experiment Nyingchi 860000 China key laboratory of forest ecology in plateau area Tibet Autonomous Region Nyingchi 860000 China United key Laboratories of Ecological Security Tibet Autonomous Region Nyingchi 860000 China Resources & Environment College Tibet Agriculture & Animal Husbandry University Nyingchi 860000 China Food Science College Tibet Agriculture & Animal Husbandry University Nyingchi 860000 China

[Objectives] To study the differences in fruit traits of different populations of Paeonia ludlowii , and to provide basic data for the identification, protection and utilization of germplasm resources of P. ludlowii .[Methods] Nine fruit traits of three different populations of P. ludlowii in tibet were tested and analyzed.[Results] The mean values of 9 fruit traits of P. ludlowii were different in different populations;the coefficients of variation of different traits of different populations were also different;there were morphological differences of different sizes among individuals in each population;there were significant differences in 8 traits (pod length, pod width, pod thickness, pod weight, seeds per pod, seed length, seed width, and seed weight) among different populations. Among the 9 traits of the three P. ludlowii populations, the variability of the five traits was higher in the fruit pods, the variation degree of five traits including pod weight, pod thickness, seeds per pod, and seed weight was higher. It is of great significance for the screening and preservation of the germplasm resources of P. ludlowii . According to the principal component analysis (PCA), the seed weight, seed width, and seed length, i.e. the seed traits, were the main factors causing differences in fruit traits among populations. There was a certain correlation between different traits of P. ludlowii . Among the 36 Pearson- related combinations of 9 fruit traits, 11 combinations had extremely significant correlations, and 8 combinations had significant correlations, indicating that there was a certain correlation between fruit traits in the growth and development. Through cluster analysis, three populations of P. ludlowii can be divided into two categories. The BV population was a category, which is characterized by long pods, long seeds, wide seeds, thick seeds and large seed weight. Therefore, the BV population is suitable material for breeding excellent varieties.[Conclusions

关键词： Paeonia ludlowii Different populations Fruit traits Diversity

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BrrTCP4b interacts with BrrTTG1 to suppress the development of trichomes in Brassica rapa var. rapa

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Plant Diversity 2024年第3期46卷 416-420页

作者： Cheng Li Li Zhang Hefan Li Yuanwen Duan Xuemei Wen Yongping Yang Xudong Sun The Germplasm Bank of Wild Species Yunnan Key Laboratory of Crop Wild Relatives OmicsInstitute of Tibetan Plateau Research at KunmingKunming Institute of BotanyChinese Academy of SciencesKunming 650201China University of Chinese Academy of Sciences BeijingChina tibet plateau Institute of Biology Lhasa 850001TibetChina

The number of trichomes significantly increased in CRISPR/Cas9-edited BrrTCP4b turnip(Brassica rapa ***)***,the underlying molecular mechanism remains to be *** this study,we performed the Y2H screen using BrrTCP4b as the bait,which unveiled an interaction between BrrTCP4b and BrrTTG1,a pivotal WD40-repeat protein transcription factor in the MYB-bHLH-WD40(MBW)*** physical interaction was further validated through bimolecular luciferase complementation and ***,it was found that the interaction between BrrTCP4b and BrrTTG1 could inhibit the activity of MBW complex,resulting in decreased expression of BrrGL2,a positive regulator of trichomes *** contrast,AtTCP4 is known to regulate trichomes development by interacting with AtGL3 in Arabidopsis ***,this study revealed that BrrTCP4b is involved in trichome development by interacting with BrrTTG1 in turnip,indicating a divergence from the mechanisms observed in model plant *** findings contribute to our understanding of the regulatory mechanisms governing trichome development in the non-model plants turnip.

关键词： TCP transcription factor MBW complex Trichome development Turnip

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