Plant Diversity最新文献

{"title":"Chromosome-level genome assembly of <i>Myristica yunnanensis</i> sheds light on genomic limitations underlying its critically endangered status in China.","authors":"Yongting Zhang, Zihe Li, Xue Liu, Peng Zeng, Chuan Peng, Botong Zhou, Yingmei Peng, Wenbo Zhu, Jian Huang, Jing Cai","doi":"10.1016/j.pld.2025.08.004","DOIUrl":"10.1016/j.pld.2025.08.004","url":null,"abstract":"<p><p>•The first chromosome-level assembly for the Myristicaceae family.•Myristicaceae represents the earliest diverging families within the Magnoliales•Genomic constraints and climatic fluctuations may have contributed to the endangered status of <i>Myristica</i> <i>yunnanensis</i>.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"843-847"},"PeriodicalIF":6.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analyses provide insights into the genetic basis of quality traits in <i>Amomum tsaoko</i>.","authors":"Yingmin Zhang, Congwei Yang, Jiahong Dong, Jinyu Zhang, Ticao Zhang, Guodong Li","doi":"10.1016/j.pld.2025.07.006","DOIUrl":"10.1016/j.pld.2025.07.006","url":null,"abstract":"<p><p>•A chromosome-level genome of <i>Amomum tsaoko</i> (1.967 Gb, 93.9% completeness) provides an improved genomic resource.•Expanded terpene synthase families likely enhance medicinal terpenoid accumulation.•Population genomics reveals low genetic differentiation linked to historical domestication.•GWAS identifies zinc finger and AP2/EREBP genes significantly associated with fruit length.•Integrated multi-omics analyses highlight plant hormone regulators influencing fruit morphology.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"839-842"},"PeriodicalIF":6.3,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome analyses provide insights into <i>Engelhardia</i>'s adaptation to East Asia summer monsoon.","authors":"Min Li, Jing-Jing Wu, Ren-Ping Su, Ou-Yan Fang, Xiang Cai, Pei-Han Huang, Xiao-Yang Gao, Xin-Xing Fu, Xiao-Hui Ma, Lin-Yue He, Yi-Gang Song, Guo-Xiong Hu, Shi-Shun Zhou, Yun-Hong Tan, Yves Van de Peer, Jie Li, Sheng-Dan Wu, Hong-Hu Meng","doi":"10.1016/j.pld.2025.07.003","DOIUrl":"10.1016/j.pld.2025.07.003","url":null,"abstract":"<p><p>Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon (EASM) and subtropical evergreen broad-leaved forests (EBLFs). However, how the genomic insights of EBLFs' species correspond to environmental shifts induced by the EASM remains limited. In this study, we investigated the adaptive mechanisms of evergreen <i>Engelhardia</i> species in response to the EASM through genome sequencing and comparative genomic analyses from the <i>de novo</i> genome assemblies of five closely related <i>Engelhardia</i> taxa and one <i>Rhoiptelea</i> species. Our findings revealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM. This genomic transition may have coincided with a significant expansion of the terpene synthase (TPS) gene family in <i>E. fenzelii</i>, driven by four distinct modes of gene duplication. This expansion enhances the biosynthesis of terpene volatiles, providing a defensive mechanism against potential herbivory in EASM affected environments. We also identified a shared whole-genome duplication (WGD) event across <i>Engelhardia</i>, along with substantial differences in transposable element (TE) composition and activity, which contributed to genome size variation between <i>E. fenzelii</i> and <i>E. roxburghiana</i>. In addition, demographic analyses revealed a continuous population decline over the past 10 million years, further exacerbated by recent human disturbance, underscoring the conservation urgency for these species. These results not only provide preliminary insights into the complex evolutionary dynamics within the <i>Engelhardia</i> genus from genomic insights (e.g., the intricate relationships between genomic variations, environmental changes, and adaptive responses driven by significant climatic events such as the EASM), but also provides valuable insights into the conservation significance of EBLFs.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"718-732"},"PeriodicalIF":6.3,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversification rates in large-scale moss assemblages along latitudinal and climatic gradients across the world.","authors":"Hong Qian","doi":"10.1016/j.pld.2025.07.002","DOIUrl":"10.1016/j.pld.2025.07.002","url":null,"abstract":"<p><p>Species richness in any area results from the interplay of the processes of speciation, extinction, and dispersal. The relationships between species richness and climate should be considered as an outcome of the effects of climate on speciation, extinction, and dispersal. Diversification rate represents the balance of speciation and extinction rates over time. Here, I explore diversification rates in mosses across geographic and climatic gradients worldwide. Specifically, I investigate latitudinal patterns and climatic associations of the mean diversification rate of mosses at global, hemispheric, and smaller scales. I find that the mean diversification rate of mosses is positively correlated with species richness of mosses, increases with decreasing latitude and increasing mean annual temperature and annual precipitation, and is more strongly associated with mean annual temperature than with annual precipitation. These findings shed light on variation of species richness in mosses across the world. The negative relationship between species richness and latitude and the positive relationship between species richness and mean diversification rate in mosses suggest that higher moss species richness at lower latitudes might have resulted, at least to some degree, from higher moss diversification rates at lower latitudes.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"833-838"},"PeriodicalIF":6.3,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread <i>Oreocharis</i> species.","authors":"Nana Peng, Lihua Yang, Xizuo Shi, Hanghui Kong, Ming Kang","doi":"10.1016/j.pld.2025.06.006","DOIUrl":"10.1016/j.pld.2025.06.006","url":null,"abstract":"<p><p>Preserving genetic diversity is crucial for the long-term survival of wild plant species, yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation. Here, we present a comparative genomic study of the critically endangered <i>Oreocharis esquirolii</i> (Gesneriaceae) and its widespread congener <i>O. maximowiczii</i>. We assembled and annotated chromosome-level reference genomes for both species and generated whole-genome resequencing data from 28 <i>O. esquirolii</i> and 79 <i>O. maximowiczii</i> individuals. Our analyses reveal substantially lower genetic diversity and higher inbreeding in <i>O. esquirolii</i>, despite its overall reduced mutational burden. Notably, <i>O. esquirolii</i> exhibits an elevated proportion of strongly deleterious mutations relative to <i>O. maximowiczii</i>, suggesting that limited opportunities for purging have allowed these variants to accumulate. These contrasting genomic profiles likely reflect divergent demographic histories, with <i>O. esquirolii</i> having experienced severe bottlenecks and protracted population decline. Collectively, our findings highlight the critically endangered status of <i>O. esquirolii</i>, characterized by diminished genetic diversity, pronounced inbreeding, and reduced ability to eliminate deleterious alleles. This study provides valuable genomic resources for the Gesneriaceae family and underscores the urgent need for targeted conservation measures, including habitat protection and <i>ex situ</i> preservation efforts, to mitigate the extinction risk facing <i>O. esquirolii</i> and potentially other threatened congeners.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"746-758"},"PeriodicalIF":6.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biogeographic affinity partly shapes woody plant diversity along an elevational gradient in subtropical forests.","authors":"Zhaochen Zhang, Fang Wang, Xiaoran Wang, Mufan Sun, Pu Zheng, Jingchao Zhao, Junhong Chen, Min Guan, Pengcheng Liu, Xiaofan Shang, Yaoshun Lu, Qingpei Yang, Qingni Song, Lin Chen, Quying Zhong, Jian Zhang","doi":"10.1016/j.pld.2025.06.004","DOIUrl":"10.1016/j.pld.2025.06.004","url":null,"abstract":"<p><p>The ecological and evolutionary mechanisms underlying montane biodiversity patterns remain unresolved. To understand which factors determined community assembly rules in mountains, biogeographic affinity that represents the biogeographic and evolutionary history of species should incorporate with current environments. We aim to address two following questions: 1) How does plant taxonomic and phylogenetic diversity with disparate biogeographic affinities vary along the subtropical elevational gradient? 2) How do biogeographic affinity and environmental drivers regulate the community assembly? We collected woody plant survey data of 32 forest plots in a subtropical mountain of Mt. Guanshan with typical transitional characteristics, including 250 woody plant species belonging to 56 families and 118 genera. We estimated the effects of biogeographic affinity, climate and soil properties on taxonomic and phylogenetic diversity of plant communities employing linear regression and structural equation models. We found that the richness of temperate-affiliated species increased with elevations, but the evenness decreased, while tropical-affiliated species had no significant patterns. Winter temperature directly or indirectly via biogeographic affinity shaped the assemblage of woody plant communities along elevations. Biogeographic affinity affected what kind of species could colonize higher elevations while local environment determined their fitness to adapt. These results suggest that biogeographic affinity and local environment jointly lead to the dominance of temperate-affiliated species at higher elevations and shape the diversity of woody plant communities along elevational gradients. Our findings highlight the legacy effect of biogeographic affinity on the composition and structure of subtropical montane forests.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"784-792"},"PeriodicalIF":6.3,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the relative importance of phylogeny and predictors in phylogenetic generalized linear models using the <i>phylolm.hp</i> R package.","authors":"Jiangshan Lai, Yan He, Mi Hou, Aiying Zhang, Gang Wang, Lingfeng Mao","doi":"10.1016/j.pld.2025.06.003","DOIUrl":"10.1016/j.pld.2025.06.003","url":null,"abstract":"<p><p>Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry (phylogeny) from those of ecological or trait-based predictors on species traits. Phylogenetic Generalized Linear Models (PGLMs) address this issue by integrating phylogenetic relationships into statistical models. However, accurately partitioning explained variance among correlated predictors remains challenging. The <i>phylolm.hp</i> R package tackles this problem by extending the concept of \"average shared variance\" to PGLMs, enabling nuanced quantification of the relative importance of phylogeny and other predictors. The package calculates individual likelihood-based R² contributions of phylogeny and each predictor, accounting for both unique and shared explained variance. This approach overcomes limitations of traditional partial R² methods, which often fail to sum the total R² due to multicollinearity. We demonstrate the functionality of <i>phylolm.hp</i> through two case studies: one involving continuous trait data (maximum tree height in Californian species) and another focusing on binary trait data (species invasiveness in North American forests). The <i>phylolm.hp</i> package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"709-717"},"PeriodicalIF":6.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic insights into <i>Adenophora</i> and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics.","authors":"Xiao-Hua Lin, Si-Yu Xie, Dai-Kun Ma, Shuai Liao, Bin-Jie Ge, Shi-Liang Zhou, Liang Zhao, Chao Xu, De-Yuan Hong, Bin-Bin Liu","doi":"10.1016/j.pld.2025.05.010","DOIUrl":"10.1016/j.pld.2025.05.010","url":null,"abstract":"<p><p>Hybridization and introgression have long obscured relationships within <i>Adenophora</i> and its relatives, complicating generic delimitation. Leveraging deep genome skimming (DGS) data, we generated a large dataset, including thousands of single-copy nuclear (SCN) genes and plastomes, to untangle this reticulate history. Specifically, 9.89 terabytes (TB) of DGS data from 165 samples-representing 48 species and 13 subspecies of <i>Adenophora</i> (out of <i>ca.</i> 72 species) plus 24 outgroup species-yielded 1506 SCN genes and 77 plastid coding sequences. Tree-like phylogenies inferred with both coalescent- and concatenation-based methods revealed pronounced gene tree heterogeneity. Subsequent analysis showed that incomplete lineage sorting contributed minimally to this discordance; instead, hybridization and introgression were the primary drivers of early diversification. Integrating phylogenomic, morphological, and geographic evidence, we propose a revised generic framework for this group. <i>Adenophora</i> is expanded to include <i>Campanula delavayi</i> and the Korean Peninsula endemic genus <i>Hanabusaya</i>. We also recommend reinstating <i>Hyssaria</i> as a distinct Central Asian genus and introducing two new genera, <i>Boreoasia</i> and <i>Rosomala</i>.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 4","pages":"576-592"},"PeriodicalIF":6.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144744381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RBOHD, GLR3.3, and GLR3.6 cooperatively control wounding hypocotyl-induced systemic Ca²⁺ signals, jasmonic acid, and glucosinolates in Arabidopsis leaves.","authors":"Che Zhan, Na Xue, Zhongxiang Su, Tianyin Zheng, Jianqiang Wu","doi":"10.1016/j.pld.2025.05.004","DOIUrl":"10.1016/j.pld.2025.05.004","url":null,"abstract":"<p><p>Ca²⁺ signaling plays crucial roles in plant stress responses, including defense against insects. To counteract insect feeding, different parts of a plant deploy systemic signaling to communicate and coordinate defense responses, but little is known about the underlying mechanisms. In this study, micrografting, in vivo imaging of Ca²⁺ and reactive oxygen species (ROS), quantification of jasmonic acid (JA) and defensive metabolites, and bioassay were used to study how Arabidopsis seedlings regulate systemic responses in leaves after hypocotyls are wounded. We show that wounding hypocotyls rapidly activated both Ca²⁺ and ROS signals in leaves. RBOHD, which functions to produce ROS, along with two glutamate receptors GLR3.3 and GLR3.6, but not individually RBOHD or GLR3.3 and GLR3.6, in hypocotyls regulate the dynamics of systemic Ca²⁺ signals in leaves. In line with the systemic Ca²⁺ signals, after wounding hypocotyl, RBOHD, GLR3.3, and GLR3.6 in hypocotyl also cooperatively regulate the transcriptome, hormone jasmonic acid, and defensive secondary metabolites in leaves of Arabidopsis seedlings, thus controlling the systemic resistance to insects. Unlike leaf-to-leaf systemic signaling, this study reveals the unique regulation of wounding-induced hypocotyl-to-leaf systemic signaling and sheds new light on how different plant organs use complex signaling pathways to modulate defense responses.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 4","pages":"690-701"},"PeriodicalIF":6.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144744383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into the evolutionary history and conservation of the living fossil <i>Tetracentron sinense</i>.","authors":"Zhao-Yang Jing, Ren-Gang Zhang, Yang Liu, Ke-Guang Cheng, De-Tuan Liu, Heng Shu, Jiali Kong, Zhong-Hua Liu, Yong-Peng Ma, Ping-Li Liu","doi":"10.1016/j.pld.2025.05.008","DOIUrl":"10.1016/j.pld.2025.05.008","url":null,"abstract":"<p><p><i>Tetracentron sinense</i> is a 'living fossil' tree in East Asia. Understanding how this 'living fossil' responds to climate change and adapts to local environments is critical for its conservation. Here, we used re-sequenced genomes to clarify the evolutionary history and adaptive potential of <i>T</i>. <i>sinense</i>. We identified six divergent lineages in <i>T. sinense</i>: three lineages from southwestern China (Yunnan Province) and three lineages from the central subtropical region of China. Additionally, we detected hybridization events between some adjacent lineages. Demographic analysis revealed that over the past 10,000 years the effective population size (<i>Ne</i>) of three <i>T. sinense</i> lineages (i.e., NORTH, SWEST, and YNWEST) increased after their last bottleneck and then remained stable, whereas that of the remaining three lineages (i.e., YSEAST, YC, and EAST) declined steadily. The decline in effective population size in the Yunnan lineages aligned well with the decrease in genome-wide diversity and a significant increase in the frequency of runs of homozygosity. Deleterious variants and positively selected sites were involved in the evolution of different lineages. Further, genotype-environment association (GEA) analyses indicated adaptation to temperature- and precipitation-related factors. Genomic offset analyses found the most vulnerable populations, while SC and SC-yad were predicted to better handle extreme changes. Our findings provide insights into the evolutionary history and conservation of <i>T. sinense</i> and enhance our understanding of the evolution of living fossil species.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"759-771"},"PeriodicalIF":6.3,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}