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Green revolution gene drives adaptation of Arabidopsis to the extremely high altitude

Science China(Life Sciences) 2025年第3期68卷 859-870页

作者： Xing-Hui Hou Yong-Chao Xu Tianshu Sun Yan-Bo Gong Xin-Tong Li Guang-Teng Jin Yu-Tao Bian Yi-Ni Liu Juan Jiang Xiao-Min Niu Hongya Gu Ya-Long Guo State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China China National Botanical Garden Beijing 100093China State Key Laboratory for Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

To elucidate the process of adaptation,particularly the traits subject to natural selection and the molecular mechanisms underlying their natural variation,is one of the primary objectives of evolutionary *** uplifted landscape offers an excellent framework for understanding how organisms adapt to dramatic climatic *** investigate the genetic basis of plant adaptation to the extremely high altitude,we first compared the genomic and phenotypic variations of two closely related Arabidopsis thaliana accessions from high altitude(Xizang,also known as“Tibet”)and low altitude(Yunnan),*** Xizang population represents a relict group characterized by a small effective population ***,the Xizang genome has more transposable elements(TEs)and more gene loss-offunction(LoF)*** expressed genes were enriched in biological processes of cellular response to oxygen-containing compound,regulation of defense response,and response to light ***,the phenotypic selection analysis revealed that silique density was under natural ***,we genetically mapped and validated that the LoF mutation of GA20ox1,the homologous gene of green revolution in rice,resulted in a higher silique density in Xizang *** that GA20ox1 is linked to Arabidopsis adaptation to the Alps Mountains,its parallel evolution plays an important role in the adaptation to Alpine ***,our results highlight that identifying adaptive traits and elucidating the molecular mechanisms underlying natural variation of these traits is crucial for unraveling the mystery of adaptive evolution and has significant implications for crop breeding.

关键词： adaptation adaptive trait Arabidopsis thaliana high altitude molecular mechanism natural variation parallel evolution

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Assembly-free reads accurate identification(AFRAID)approach outperforms other methods of DNA barcoding in the walnut family(Juglandaceae)

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Plant Diversity 2025年第1期47卷 115-126页

作者： Yanlei Liu Kai Chen Lihu Wang Xinqiang Yu Chao Xu Zhili Suo Shiliang Zhou Shuo Shi Wenpan Dong School of Landscape and Ecological Engineering Hebei University of EngineeringHandan 056038China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China College of Life Science Hebei Normal UniversityShijiazhuang 050024China School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China

DNA barcoding has been extensively used for species ***,species identification of mixed samples or degraded DNA is limited by current DNA barcoding *** this study,we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification(AFRAID)method of species identification,a novel approach for precise species identification in ***,we determined(1)the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae,(2)the minimum size of chloroplast dataset for species discrimination,and(3)minimum amount of next generation sequencing(NGS)data required for species *** found that species identification rates were highest when whole chloroplast genomes were used,followed by taxon-specific DNA barcodes,and then universal DNA *** identification of 100%was achieved when chloroplast genome sequence coverage reached 20%and the original sequencing data reached 500,000 *** accurately identified species for all samples tested after 500,000 clean reads,with far less computing time than common *** results provide a new approach to accurately identify species,overcoming limitations of traditional DNA *** method,which uses next generation sequencing to generate partial chloroplast genomes,reveals that DNA barcode regions are not necessarily fixed,accelerating the process of species identification.

关键词： DNA barcode Species identification Random DNA barcode Juglandaceae Assembly-free

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The chromosome-scale genome of black wolfberry(Lycium ruthenicum)provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

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Plant Diversity 2025年第2期47卷 201-213页

作者： Gulbar Yisilam Enting Zheng Chuanning Li Zhiyong Zhang Ying Su Zhenzhou Chu Pan Li Xinmin Tian Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection(Ministry of Education)&Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Guangxi Normal UniversityGuilin 541006China Xinjiang Key Laboratory of Biological Resources and Genetic Engineering College of Life Science and TechnologyXinjiang UniversityUrumqi 830046China Laboratory of Systematic&Evolutionary Botany and Biodiversity College of Life SciencesZhejiang UniversityHangzhou 310058China Guangxi University Enginering Research Center of Bioinformation and Genetic Improvement of Speciaty Crops Guangxi Normal UniversityGuilin 541006China

The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic *** fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional ***,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary *** this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of ***(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C *** assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally *** 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium *** species-specific genes of *** were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid *** on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of ***,most of which were highly expressed at a later stage in fruit ***,154 potential disease resistance-related nucleotidebinding genes have been identified in the *** *** whole-genome and proximal,dispersed,and tandem duplication genes in the *** genome enriched the number of genes involved in anthocyanin synthesis and resistance-related *** results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.

关键词： Lycium ruthenicum Genome Anthocyanin biosynthesis Gene duplication Comparative genomics

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Phylogenetic regionalization of the Pan-Himalayan vascular flora

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Journal of systematics and Evolution 2025年第1期63卷 12-24页

作者： Liu, Yun Saqib, Saddam Lu, Limin Lai, Yangjun Hu, Haihua Peng, Danxiao Zaman, Wajid Zhao, Lina Liu, Bing Wang, Qiang Lu, Anming Hong, Deyuan Ye, Jianfei Chen, Zhiduan State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China China National Botanical Garden Beijing 100093 China College of Life Sciences Capital Normal University Beijing 100048 China State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems College of Ecology Lanzhou University Lanzhou 730000 China Department of Life Sciences Yeungnam University Gyeongbuk Gyeongsan 38541 South Korea Sino-Africa Joint Research Center Chinese Academy of Sciences Wuhan 430074 China State Key Laboratory of Biocontrol School of Ecology Shenzhen Campus Sun Yat-sen University Shenzhen 518107 China

Pan-Himalaya, including Himalaya and its neighboring areas, hosts a rich and unique flora that is crucial for understanding the evolutionary history of mountainous biodiversity. Phylogenetic regionalization can provide novel insights into biodiversity distribution patterns and their formation mechanisms. In this study, based on comprehensive species distribution data and a species-level phylogenetic tree, we propose a phylogenetic regionalization scheme of the Pan-Himalayan vascular flora comprising 15 zones, which can be grouped into five floristic subregions and three floristic regions (i.e., the West Himalayan [WH], the Southeast Himalayan [SEH], and the Northeast Himalayan [NEH] regions). Our results reveal that the SEH and NEH regions are closely clustered, which are then grouped with the WH region. The floras of these three regions exhibit distinct evolutionary histories and phylogenetic structures. The WH region presents a phylogenetically clustered flora with Euro-Mediterranean affinities and the highest evolutionary uniqueness. The NEH region has the highest species richness and phylogenetic diversity, with most of its areas, especially at higher elevations, displaying phylogenetic clustering. In contrast, the SEH region exhibits a phylogenetically overdispersed flora, characterized by harboring species-rich families with tropical, temperate, and alpine distributions, as well as relict plant lineages. This study provides valuable insights into the evolutionary history of the Pan-Himalayan flora and informs the development of effective conservation strategies. © 2025 Institute of botany, Chinese Academy of Sciences.

关键词： beta diversity bioregionalization evolutionary history Pan-Himalaya phylogenetic diversity phylogenetic structure

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Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae

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Journal of Genetics and Genomics 2025年

作者： Yan, Xueqing Yu, Runxian Wang, Jinpeng Jiao, Yuannian State Key Laboratory of Plant Diversity and Specialty Crops Institute of Botany The Chinese Academy of Sciences Beijing 100093 China State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China University of Chinese Academy of Sciences Beijing 100049 China School of Life Sciences and Center for Genomics and Computational Biology North China University of Science and Technology Hebei Tangshan 063210 China

Chromosomal rearrangements (CRs) often cause phenotypic variations. Although several major rearrangements have been identified in Triticeae, a comprehensive study of the order, timing, and breakpoints of CRs has not been conducted. Here, we reconstruct high-quality ancestral genomes for the most recent common ancestor (MRCA) of the Triticeae, and the MRCA of the wheat lineage (Triticum and Aegilops). The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060, respectively, which were arranged in their ancestral order. By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes, we revisit the rye chromosome structural evolution and propose alternative evolutionary routes. The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu are found to have occurred independently and are unlikely the result of chromosomal introgression following distant hybridization. We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event. Lastly, we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution, representing potential CR hotspots. This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae. © 2025 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China

关键词： Ancestral genome reconstruction Chromosome rearrangement Evolution Structure variations Translocation Triticeae

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Pollen Morphology of the Platycodonoid Group (Campanulaceae ***.) and Its systematic Implications

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Journal of Integrative Plant Biology 2012年第10期54卷 773-789页

作者： HONG De-Yuan PAN Kai-Yu State Key Laboratory of Systematic&Evolutionary Botany Institute of BotanyThe Chinese Academy of SciencesChina

In this study, we examined the pollen morphology of the platycodonoid group in Campanulaceae s. str. using a scanning electronic microscope. We used pollen grains of 25 accessions representing 24 species of the Codonopsis complex （including Campanumoea, Cyclocodon, Leptocodon, and all three subgenera of Codonopsis）, which is extremely controversial among authors for taxonomic treatment. Pollen morphology of all the other genera in the group observed by previous authors is taken into account in our discussion. A total of nine pollen types with two subtypes in the group were recognized and named for the first time. Molecular and morphological data imply that each pollen type corresponds to a natural group at generic level, and thus the mergence of Leptocodon with Codonopsis and the restoration of Cyclocodon as a separate genus are justifiable, and Codonopsis subg. Pseudocodonopsis, subg. Obconicicapsula, and two species of Codonopsis subg. Codonopsis （C. purpurea and C. chimiliensis） may be better classified as three independent genera separate from the core Codonopsis.

关键词： Campanulaceae s. str. platycodonoid group Codonopsis complex pollen morphology pollen type taxonomy systematics.

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Analysis of plastid and nuclear DNA data in plant phylogenetics——evaluation and improvement

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Science China(Life Sciences) 2014年第3期57卷 280-286页

作者： WANG Wei LI HongLei CHEN ZhiDuan State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of Sciences

Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical *** accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA *** first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal systematic botany between 2005 and *** studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data *** reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating *** attention is given to explanation of the cause of *** hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.

关键词： combined analysis plastid DNA incongruence nuclear DNA phylogenetics

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Phylogenetic analyses reveal three new genera of the Campanulaceae

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植物分类学报 2014年第5期52卷 541-550页

作者： Qiang WANG Xin-Tang MA De-Yuan HONG State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China

The genus Codonopsis has been controversial in its circumscription. In the strict sense, the genus consists of three subgenera, Codonopsis , Pseudocodonopsis , and Obconicicapsula . Recent molecular and palynological analyses suggest that the latter two subgenera and Cod. purpurea Wall. are separated from rest Codonopsis . In the present study, extensive observations were carried out in wild populations and on more than 800 specimens of subg. Pseudocodonopsis , subg. Obconicicapsula , and Cod. purpurea . Their chromosome numbers were counted for the first time. Recent palynological and molecular data were also analyzed and reevaluated. Our integrated phylogenetic analyses revealed that the three groups are distinct from the rest of Codonopsis . Furthermore, they are also distinct from each other, and cannot be circumscribed in a single genus. Therefore, three new genera are here proposed based on molecular phylogenetics, palynology, cytology, and external morphology. New combinations are made in the present article.

关键词： chromosome number external morphology Himalacodon molecular phylogeny Pankycodon pollen morphology Pseudocodon

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Revisiting the phylogeny of Ranunculeae: Implications for divergence time estimation and historical biogeography

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植物分类学报 2014年第5期52卷 551-565页

作者： Wei WANG Hong-Lei LI Xiao-Guo XIANG Zhi-Duan CHEN State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China

Previous studies based on different molecular datasets have generated conflicting topologies for Ranunculeae. Here, we revisit the phylogeny of Ranunculeae by analyzing the individual matK/trnK, psbJ-petA, and internal transcribed spacer (ITS) data, the combined matK/trnK, psbJ-petA, and ITS dataset, and the combined rbcL, trnL-F, matK/trnK, psbJ-petA, and ITS dataset. Based on the tree-based comparisons, BLAST searches against NCBI of the sequences, and close examination of the alignment, we found that 10 psbJ-petA sequences previously used were questionable (erroneous or problematic) and responsible for previous conflicting topologies. After omitting these questionable sequences, we provide a new phylogeny for Ranunculeae, in which Beckwithia-Cyrtorhyncha, Kumlienia, and Peltocalathos were replaced. These new replacements are supported by corresponding morphological characters. Moreover, three previously proposed intercontinental disjunct distributions within Ranunculus were also refuted. In our framework, our divergence time and biogeographic analyses indicate that divergence time estimates and the ancestral areas reconstructed for 10 of the 15 nodes in the genus-level phylogeny were influenced by elimination of the questionable sequences. The most recent common ancestor of Ranunculeae was inferred to be present in Europe and North America during the late Eocene. Clades I and II began to diversify in Europe and North America, respectively, and subsequently migrated to other continents. This study shows that it is necessary to analyze individual chloroplast DNA region datasets separately to detect questionable sequences early in the study. The combined dataset including the questionable sequences resulted in an erroneous phylogenetic tree, and the use of this tree subsequently affected age estimates and biogeographic analyses.

关键词： biogeography combined analysis divergence-time estimates phylogeny Ranunculeae

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Variations of 18S rDNA Loci Among Six Populations of Paeonia obovata Maxim. （Paeoniaceae） Revealed by Fluorescence In Situ Hybridization

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Journal of Integrative Plant Biology 2006年第5期48卷 497-502页

作者： Rui Luo Chao Wang Daming Zhang State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany the Chinese Academy of Sciences Beijing 100093 China

The localization of 18S ribosomal RNA genes （rDNA） by fluorescence in situ hybridization （FISH） had been performed for some species of Paeonla. However, the pattern of 18S rDNA loci among populations Is Indistinct. In the present study, we localized 18S rDNA loci on meiotic or mitotic chromosomes of six populations of Paeonla obovata Maxim. （Paeonlaceae）. Different numbers of rDNA loci were found with different diploid （2n=10） populations, namely eight （Lushl and Mt. JIuhua populations）, 10 （Mt. Talbal population）, and seven （Mt. Guandl population）, whereas tetraplold （2n=20） populations were all found with 16 loci. Aii rDNA loci were mapped near teiomeres of mitotic chromosomes and there was no chromosome with two loci. The present results show that molecular cytological polymorphlsm exists among P. obovata diploid populations, Indicating that structural variations occurred frequently during the evolutionary history of this species, accompanied with differentiation among populations.

关键词： cytotype fluorescence in situ hybridization (FISH) Paeonia obovata 18S rDNA tetraploid.

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