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Genome assembly of the snow lotus species Saussurea involucrata provides insights into acacetin and rutin biosynthesis and tolerance to an alpine environment

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Horticulture Research 2023年第10期10卷 8-11页

作者： Yanxia Sun Aidi Zhang Jacob BLandis Wei Shi Xiujun Zhang Hang Sun Hengchang Wang CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhan 430074HubeiChina Center of Conservation Biology Core Botanical GardensChinese Academy of SciencesWuhan 430074HubeiChina Center of Economic Botany Core Botanical GardensChinese Academy of SciencesWuhan 430074HubeiChina BTI Computational Biology Center Boyce Thompson InstituteIthacaNY 14853USA School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNY 14853USA Xinjiang Institute of Ecology and Geography Chinese Academy of SciencesUrumchi 830011XinjiangChina Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina

Dear Editor,Understanding the evolution and survival mechanisms of endangered wild medicinal herbs is crucial for their cultivation,utilization,and conservation.The snow lotus species Saussurea involucrata(Kar.&Kir.)Sch.Bip.(2n=32)(i.***.the well-known Tianshan snow lotus)which belongs to the eudicot family Asteraceae,is a famous traditional Chinese medicinal herb having anti-inflammatory.

关键词： Tianshan belongs involucrata

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The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit

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Horticulture Research 2023年第4期10卷 147-160页

作者： Xu Zhang Rui Guo Ruinan Shen Jacob BLandis Quan Jiang Fang Liu Hengchang Wang Xiaohong Yao CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Gardenthe Chinese Academy of SciencesWuhan 430074HubeiChina College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNY 14853 USA BTI Computational Biology Center Boyce Thompson InstituteIthacaNY 14853USA

A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates.Actinidia eriantha is a shade-tolerant species,widely distributed in the southern tropical region of China,occurring in spatially heterogeneous environments.In the present study we combined population genomic,epigenomic,and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient,and to assess genomic offset to climatic change for A.eriantha.The population structure is strongly shaped by geography and influenced by restricted gene f low resulting from isolation by distance due to habitat fragmentation.In total,we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation,which were enriched in functional categories related to development processes and stress response;both temperature and precipitation are important factors driving adaptive variation.In addition to single-nucleotide polymorphisms(SNPs),a total of 27 single-methylation variants(SMVs)had significant correlation with at least one of four climatic variables and 16 SMVswere located in or adjacent to genes,several of whichwere predicted to be involved in plant response to abiotic or biotic stress.Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change.Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation.Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.

关键词： local adaptation shaped

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An updated classification for the hyper-diverse genus Corydalis(Papaveraceae: Fumarioideae)based on phylogenomic and morphological evidence

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植物学报:英文版 2023年第9期65卷 2138-2156页

作者： Jun‐Tong Chen Magnus Lidén Xian‐Han Huang Liang Zhang Xin‐Jian Zhang Tian‐Hui Kuang Jacob BLandis Dong Wang Tao Deng Hang Sun CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China University of Chinese Academy of Sciences Beijing 100049China Evolutionary Biology Centre Systematic BiologyUppsala UniversityUppsala 75236Sweden School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNew York 14853USA BTI Computational Biology Center Boyce Thompson InstituteIthacaNew York 14853USA School of Life Sciences Central China Normal UniversityWuhan 430079China

The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses,based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa,using 65 shared protein-coding plastid genes from313 accessions(including 280 samples of ca. 226species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions(including 271samples of Corydalis) covering all 42 previously recognized sections and five independent “series”.Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include:(i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data;the third,subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus;(ii) among all 42 sections and five“series”, 25 sections and one “series” are resolved as monophyletic in both data sets;(iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes;(iv) we provide a new classification of Corydalis with four subgenera(of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly imp

关键词： character evolution Corydalis genome skimming Papaveraceae phylogeny

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Genomic convergence underlying high-altitude adaptation in alpine plants

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Journal of Integrative Plant Biology 2023年第7期65卷 1620-1635页

作者： Xu Zhang Tianhui Kuang Wenlin Dong Zhihao Qian Huajie Zhang Jacob BLandis Tao Feng Lijuan Li Yanxia Sun Jinling Huang Tao Deng Hengchang Wang Hang Sun CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture The Chinese Academy of SciencesWuhan Botanical GardenWuhan 430074China Center of Conservation Biology Core Botanical GardensThe Chinese Academy of SciencesWuhan 430074China Yunnan International Joint Laboratory for Biodiversity of Central Asia Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyThe Chinese Academy of SciencesKunming 650201China University of Chinese Academy of Sciences Beijing 100049China School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNew York 14850USA BTI Computational Biology Center Boyce Thompson InstituteIthacaNew York 14853USA State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Department of Biology East Carolina UniversityGreenvilleNorth Carolina 27858USA

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection.However, genomic evidence for convergent adaptation to extreme environments remains scarce.Here, we assembled reference genomes of two alpine plants, Saussurea obvallata(Asteraceae)and Rheum alexandrae(Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes,we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of diseaseresistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present.We identified signatures of positive selection on a set of genes involved in reproduction and respiration(e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification,DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level,aiding in a deep understanding of genetic adaptation to complex environments.

关键词： adaptation alpine plants evolutionary rates genomic convergence “greenhouse”morphology high altitude

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