• Discovery of a high-altitude ecotype and ancient lineage of Arabidopsis thaliana from Tibet

      Zeng, Liyan; Gu, Zhuoya; Xu, Min; Zhao, Ning; Zhu, Weidong; Yonezawa, Takahiro; Liu, Tianmeng; Qiong, Lha; Tersing, Tashi; Xu, Lingli; et al. (Elsevier, 2017-12-29)
      Arabidopsis thaliana (A. thaliana) has long been a model species for dicotyledon study, and was the first flowering plant to get its genome completed sequenced [1]. Although most wild A. thaliana are collected in Europe, several studies have found a rapid A. thaliana west-east expansion from Central Asia [2]. The Qinghai-Tibet Plateau (QTP) is close to Central Asia and known for its high altitude, unique environments and biodiversity [3]. However, no wild-type A. thaliana had been either discovered or sequenced from QTP. Studies on the A. thaliana populations collected under 2000 m asl have shown that the adaptive variations associated with climate and altitudinal gradients [4]. Hence a high-altitude A. thaliana provides a precious natural material to investigate the evolution and adaptation process. Here, we present the genome of a new ecotype of A. thaliana collected in the Gongga County, Tibet (4200 m asl) (Fig. 1a), to demonstrate its evolutionary history and adaptation to highaltitude regions.
    • The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

      Qiao, Qin; Huang, Yanyan; Qi, Ji.; Qu, Mingzhi; Jiang, Chen; Lin, Pengcheng; Li, Renhui; Song, Lirong; Yonezawa, Takahiro; Hasegawa, Masami; et al. (NATURE PUBLISHING GROUP, 2016-07-06)
      The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP.
    • Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

      Geng, Yu-peng; Guan, Yabin; Qiong, La; Lu, Shugang; An, Miao; Crabbe, M. James C.; Qi, Ji.; Zhao, Fangqing; Qiao, Qin; Zhang, Ti-Cao; et al. (Springer Nature, 2021-07-22)
      Background: Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results: We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two highand two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions: Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.
    • Identification of new antibacterial targets in RNA polymerase of Mycobacterium tuberculosis by detecting positive selection sites

      Wang, QingBiao; Xu, Yiqin; Gu, Zhuoya; Liu, Nian; Jin, Ke; Li, Yao; Crabbe, M. James C.; Zhong, Yang; Fudan University; Oxford University; et al. (Elsevier, 2017-11-21)
      Bacterial RNA polymerase (RNAP) is an effective target for antibacterial treatment. In order to search new potential targets in RNAP of Mycobacterium, we detected adaptive selections of RNAP related genes in 13 strains of Mycobacterium by phylogenetic analysis. We first collected sequences of 17 genes including rpoA, rpoB, rpoC, rpoZ, and sigma factor A-M. Then maximum likelihood trees were constructed, followed by positive selection detection. We found that sigG shows positive selection along the clade (M. tuberculosis, M. bovis), suggesting its important evolutionary role and its potential to be a new antibacterial target. Moreover, the regions near 933Cys and 935His on the rpoB subunit of M. tuberculosis showed significant positive selection, which could also be a new attractive target for anti-tuberculosis drugs.
    • Single enrichment systems possibly underestimate both exposures and biological effects of organic pollutants from drinking water

      Yang, Lan; Zhou, Ying; Chen, Li; Chen, Hanyi; Liu, Wenhao; Zheng, Weiwei; Andersen, Melvin E.; Zhang, Yubing; Hu, Yi; Crabbe, M. James C.; et al. (Elsevier, 2022-01-03)
      Comprehensive enrichment of contaminants in drinking water is an essential step for accurately determining exposure levels of contaminants and testing their biological effects. Traditional methods using a single absorbent for enriching contaminants in water might not be adequate for complicated matrices with different physical-chemical profiles . To examine this hypothesis, we used an integrated enrichment system that had three sequential stages-XAD-2 resin, poly (styrene–divinylbenzene) and activated charcoal to capture organic pollutants and disinfection by-products (DBPs) from drinking water in Shanghai. Un-adsorbed Organic Compounds in Eluates (UOCEs) named UOCEs-A, -B, and-C following each adsorption stage were determined by gas chromatography-mass spectromet ry to evaluate adsorption efficiency of the enrichment system . Meanwhile, biological effects such as cytotoxicity, effects on reactive oxygen species (ROS) generation and glutathione (GSH) depletion were determined in human LO2 cells to identify potential adverse effects on exposure to low dose contaminants. We found that poly-styrene–divinylbenzene (PS-DVB) and activated charcoal (AC) could still partly collect UOCEs-A and-B that the upper adsorption column incompletely captured, and that potential carcinogens like 2- naphthamine were present in all eluates. UOCEs-A at (1-4000), UOCEs-B at (1000-4000), and UOCEs-C at (2400-4000) folds of the actual concentrations had significant cytotoxicity to LO2 cells. Additionally, ROS and GSH change in cells treated with UOCEs indicated the potential for long-term effects of exposure to some mixtures of contaminants such as DBPs at low doses . These results suggested that an enriching system with a single adsorbent would underestimate the exposure level of pollutants and the biological effects of organic pollutants from drinking water. Effective methods for pollutants’ enrichment and capture of drinking water should be given priority in future studies on accurate evaluation of biological effects exposed to mixed pollutants via drinking water.