Polyploidy is a major factor in the evolution of plants, yet we know little about the origin and evolution of polyploidy in intertidal species. This study aimed to identify the evolutionary transitions in three true-mangrove species of the genus Acanthus distributed in the Indo-West Pacific region. For this purpose, we took an integrative approach that combined data on morphology, cytology, climatic niche, phylogeny, and biogeography of 493 samples from 42 geographic sites. Our results show that the Acanthus ilicifolius lineage distributed east of the Thai-Malay Peninsula possesses a tetraploid karyotype, which is morphologically distinct from that of the lineage on the west side. The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes, one each from A. ilicifolius and A.ebracteatus, the paternal and maternal parents, respectively. Population structure analysis also supports the hybrid speciation history of the new tetraploid species. The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene. Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids, but also expanded into novel environments. Our findings suggest that A. ilicifolius species distributed on the east side of the Thai-Malay Peninsula should be regarded as a new species, A. tetraploideus, which originated from hybridization between A. ilicifolius and A. ebracteatus, followed by chromosome doubling. This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction, which explains the long-term adaptive potential of the species.
多倍体是植物进化的一个重要因素,但我们对潮间带物种多倍体的起源和进化知之甚少。本研究旨在确定分布在印度-西太平洋地区的三个真红树属物种的进化转变。为此,我们采用了一种综合方法,结合了来自 42 个地理位置的 493 个样本的形态学、细胞学、气候生态位、系统发育和生物地理学数据。结果表明,分布在泰国-马来半岛以东的Acanthus ilicifolius品系具有四倍体核型,在形态上与西侧的品系截然不同。叶绿体基因组和八个核基因的单倍型网络和系统发生树显示,该四倍体物种有两个亚基因组,分别来自父本 A. ilicifolius 和母本 A. ebracteatus。种群结构分析也支持四倍体新物种的杂交分化历史。四倍体物种的两个亚基因组是在更新世期间从它们的二倍体祖先分化而来的。环境生态位模型显示,四倍体物种不仅占据了二倍体近乎完整的生态位空间,而且还扩展到了新的环境中。我们的研究结果表明,分布在泰国-马来半岛东侧的A. ilicifolius物种应被视为一个新物种,即A. tetraploideus,它起源于A. ilicifolius和A. ebracteatus的杂交,随后染色体加倍。这是首次报道能进行有性繁殖和克隆繁殖的真红树异源多倍体物种,这解释了该物种的长期适应潜力。
{"title":"Origin and evolution of a new tetraploid mangrove species in an intertidal zone.","authors":"Hui Feng, Achyut Kumar Banerjee, Wuxia Guo, Yang Yuan, Fuyuan Duan, Wei Lun Ng, Xuming Zhao, Yuting Liu, Chunmei Li, Ying Liu, Linfeng Li, Yelin Huang","doi":"10.1016/j.pld.2024.04.007","DOIUrl":"https://doi.org/10.1016/j.pld.2024.04.007","url":null,"abstract":"<p><p>Polyploidy is a major factor in the evolution of plants, yet we know little about the origin and evolution of polyploidy in intertidal species. This study aimed to identify the evolutionary transitions in three true-mangrove species of the genus <i>Acanthus</i> distributed in the Indo-West Pacific region. For this purpose, we took an integrative approach that combined data on morphology, cytology, climatic niche, phylogeny, and biogeography of 493 samples from 42 geographic sites. Our results show that the <i>Acanthus ilicifolius</i> lineage distributed east of the Thai-Malay Peninsula possesses a tetraploid karyotype, which is morphologically distinct from that of the lineage on the west side. The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes, one each from <i>A. ilicifolius</i> and <i>A</i> <i>.</i> <i>ebracteatus</i>, the paternal and maternal parents, respectively. Population structure analysis also supports the hybrid speciation history of the new tetraploid species. The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene. Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids, but also expanded into novel environments. Our findings suggest that <i>A. ilicifolius</i> species distributed on the east side of the Thai-Malay Peninsula should be regarded as a new species, <i>A</i>. <i>tetraploideus</i>, which originated from hybridization between <i>A. ilicifolius</i> and <i>A. ebracteatus</i>, followed by chromosome doubling. This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction, which explains the long-term adaptive potential of the species.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"46 4","pages":"476-490"},"PeriodicalIF":4.6,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11390703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293611","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}
China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere. Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations. One of these relict lineages is Dipteronia, an oligotypic tree genus with a fossil record extending to the Paleocene. Here, we investigated the genetic variability, demographic dynamics and diversification patterns of the two currently recognized Dipteronia species (Dipteroniasinensis and D.dyeriana). Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions, two single copy nuclear genes and 15 simple sequence repeat loci. The genetic study was combined with niche comparison analyses on the environmental space, ecological niche modeling, and landscape connectivity analysis. We found that the two Dipteronia species have highly diverged both in genetic and ecological terms. Despite the incipient speciation processes that can be observed in D. sinensis, the occurrence of long-term stable refugia and, particularly, a dispersal corridor along Daba Shan-west Qinling, likely ensured its genetic and ecological integrity to date. Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic, but also provide insight into how Arcto-Tertiary relict plants in East Asia survived, evolved, and diversified.
{"title":"Genetically- and environmentally-dependent processes drive interspecific and intraspecific divergence in the Chinese relict endemic genus <i>Dipteronia</i>.","authors":"Tao Zhou, Xiaodan Chen, Jordi López-Pujol, Guoqing Bai, Sonia Herrando-Moraira, Neus Nualart, Xiao Zhang, Yuemei Zhao, Guifang Zhao","doi":"10.1016/j.pld.2024.04.008","DOIUrl":"https://doi.org/10.1016/j.pld.2024.04.008","url":null,"abstract":"<p><p>China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere. Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations. One of these relict lineages is <i>Dipteronia</i>, an oligotypic tree genus with a fossil record extending to the Paleocene. Here, we investigated the genetic variability, demographic dynamics and diversification patterns of the two currently recognized <i>Dipteronia</i> species (<i>D</i> <i>ipteronia</i> <i>sinensis</i> and <i>D</i> <i>.</i> <i>dyeriana</i>). Molecular data were obtained from 45 populations of <i>Dipteronia</i> by genotyping three cpDNA regions, two single copy nuclear genes and 15 simple sequence repeat loci. The genetic study was combined with niche comparison analyses on the environmental space, ecological niche modeling, and landscape connectivity analysis. We found that the two <i>Dipteronia</i> species have highly diverged both in genetic and ecological terms. Despite the incipient speciation processes that can be observed in <i>D. sinensis</i>, the occurrence of long-term stable refugia and, particularly, a dispersal corridor along Daba Shan-west Qinling, likely ensured its genetic and ecological integrity to date. Our study will not only help us to understand how populations of <i>Dipteronia</i> species responded to the tectonic and climatic changes of the Cenozoic, but also provide insight into how Arcto-Tertiary relict plants in East Asia survived, evolved, and diversified.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"46 5","pages":"585-599"},"PeriodicalIF":4.6,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11403150/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293623","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}
•Phylogenomic analysis uncovers widespread discordance in the extended Picea likiangensis complex.•Introgression (54.99%) and incomplete lineage sorting (ILS; 33.12%) are key drivers of this incongruity.•Recombination rates shape ILS and introgression, with high rates correlating with elevated levels.•Genes linked to abiotic stress responses exhibit significant introgression and ILS, suggesting adaptive evolution.•Lower recombination rates improve accuracy in species relationships.
-基因与非生物应激反应相关,表现出显著的内向性和内向性,表明适应性进化。
{"title":"Comparative analysis shows high level of lineage sorting in genomic regions with low recombination in the extended <i>Picea likiangensis</i> species complex.","authors":"Hui Zhu, Weixiao Lei, Qing Lai, Yongshuai Sun, Dafu Ru","doi":"10.1016/j.pld.2024.04.004","DOIUrl":"https://doi.org/10.1016/j.pld.2024.04.004","url":null,"abstract":"<p><p>•Phylogenomic analysis uncovers widespread discordance in the extended <i>Picea likiangensis</i> complex.•Introgression (54.99%) and incomplete lineage sorting (ILS; 33.12%) are key drivers of this incongruity.•Recombination rates shape ILS and introgression, with high rates correlating with elevated levels.•Genes linked to abiotic stress responses exhibit significant introgression and ILS, suggesting adaptive evolution.•Lower recombination rates improve accuracy in species relationships.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"46 4","pages":"547-550"},"PeriodicalIF":4.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11390601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293609","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}
Vernalization is necessary for winter wheat to flower. However, it is unclear whether vernalization is also required for spring wheat, which is frequently sown in fall, and what molecular mechanisms underlie the vernalization response in wheat varieties. In this study, we examined the molecular mechanisms that regulate vernalization response in winter and spring wheat varieties. For this purpose, we determined how major vernalization genes (VRN1, VRN2, and VRN3) respond to vernalization in these varieties and whether modifications to histones play a role in changes in gene expression. We also identified genes that are differentially regulated in response to vernalization in winter and spring wheat varieties. We found that in winter wheat, but not in spring wheat, VRN1 expression decreases when returned to warm temperature following vernalization. This finding may be associated with differences between spring and winter wheat in the levels of tri-methylation of lysine 27 on histone H3 (H3K27me3) and tri-methylation of lysine 4 on histone H3 (H3K4me3) at the VRN1 gene. Analysis of winter wheat transcriptomes before and after vernalization revealed that vernalization influences the expression of several genes, including those involved in leucine catabolism, cysteine biosynthesis, and flavonoid biosynthesis. These findings provide new candidates for further study on the mechanism of vernalization regulation in wheat.
{"title":"Epigenetic control on transcription of vernalization genes and whole-genome gene expression profile induced by vernalization in common wheat.","authors":"Yunzhen Li, Liujie Jin, Xinyu Liu, Chao He, Siteng Bi, Sulaiman Saeed, Wenhao Yan","doi":"10.1016/j.pld.2024.02.005","DOIUrl":"10.1016/j.pld.2024.02.005","url":null,"abstract":"<p><p>Vernalization is necessary for winter wheat to flower. However, it is unclear whether vernalization is also required for spring wheat, which is frequently sown in fall, and what molecular mechanisms underlie the vernalization response in wheat varieties. In this study, we examined the molecular mechanisms that regulate vernalization response in winter and spring wheat varieties. For this purpose, we determined how major vernalization genes (<i>VRN1</i>, <i>VRN2</i>, and <i>VRN3</i>) respond to vernalization in these varieties and whether modifications to histones play a role in changes in gene expression. We also identified genes that are differentially regulated in response to vernalization in winter and spring wheat varieties. We found that in winter wheat, but not in spring wheat, <i>VRN1</i> expression decreases when returned to warm temperature following vernalization. This finding may be associated with differences between spring and winter wheat in the levels of tri-methylation of lysine 27 on histone H3 (H3K27me3) and tri-methylation of lysine 4 on histone H3 (H3K4me3) at the <i>VRN1</i> gene. Analysis of winter wheat transcriptomes before and after vernalization revealed that vernalization influences the expression of several genes, including those involved in leucine catabolism, cysteine biosynthesis, and flavonoid biosynthesis. These findings provide new candidates for further study on the mechanism of vernalization regulation in wheat.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"46 3","pages":"386-394"},"PeriodicalIF":4.6,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11119517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155706","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}
Pub Date : 2024-02-08eCollection Date: 2024-05-01DOI: 10.1016/j.pld.2024.02.003
Ya-Dong Qie, Qi-Wei Zhang, Scott A M McAdam, Kun-Fang Cao
Stomatal regulation is critical for mangroves to survive in the hyper-saline intertidal zone where water stress is severe and water availability is highly fluctuant. However, very little is known about the stomatal sensitivity to vapour pressure deficit (VPD) in mangroves, and its co-ordination with stomatal morphology and leaf hydraulic traits. We measured the stomatal response to a step increase in VPD in situ, stomatal anatomy, leaf hydraulic vulnerability and pressure-volume traits in nine true mangrove species of five families and collected the data of genome size. We aimed to answer two questions: (1) Does stomatal morphology influence stomatal dynamics in response to a high VPD in mangroves? with a consideration of possible influence of genome size on stomatal morphology; and (2) do leaf hydraulic traits influence stomatal sensitivity to VPD in mangroves? We found that the stomata of mangrove plants were highly sensitive to a step rise in VPD and the stomatal responses were directly affected by stomatal anatomy and hydraulic traits. Smaller, denser stomata was correlated with faster stomatal closure at high VPD across the species of Rhizophoraceae, and stomata size negatively and vein density positively correlated with genome size. Less negative leaf osmotic pressure at the full turgor (πo) was related to higher operating steady-state stomatal conductance (gs); and a higher leaf capacitance (Cleaf) and more embolism resistant leaf xylem were associated with slower stomatal responses to an increase in VPD. In addition, stomatal responsiveness to VPD was indirectly affected by leaf morphological traits, which were affected by site salinity and consequently leaf water status. Our results demonstrate that mangroves display a unique relationship between genome size, stomatal size and vein packing, and that stomatal responsiveness to VPD is regulated by leaf hydraulic traits and stomatal morphology. Our work provides a quantitative framework to better understand of stomatal regulation in mangroves in an environment with high salinity and dynamic water availability.
{"title":"Stomatal dynamics are regulated by leaf hydraulic traits and guard cell anatomy in nine true mangrove species.","authors":"Ya-Dong Qie, Qi-Wei Zhang, Scott A M McAdam, Kun-Fang Cao","doi":"10.1016/j.pld.2024.02.003","DOIUrl":"10.1016/j.pld.2024.02.003","url":null,"abstract":"<p><p>Stomatal regulation is critical for mangroves to survive in the hyper-saline intertidal zone where water stress is severe and water availability is highly fluctuant. However, very little is known about the stomatal sensitivity to vapour pressure deficit (VPD) in mangroves, and its co-ordination with stomatal morphology and leaf hydraulic traits. We measured the stomatal response to a step increase in VPD <i>in situ</i>, stomatal anatomy, leaf hydraulic vulnerability and pressure-volume traits in nine true mangrove species of five families and collected the data of genome size. We aimed to answer two questions: (1) Does stomatal morphology influence stomatal dynamics in response to a high VPD in mangroves? with a consideration of possible influence of genome size on stomatal morphology; and (2) do leaf hydraulic traits influence stomatal sensitivity to VPD in mangroves? We found that the stomata of mangrove plants were highly sensitive to a step rise in VPD and the stomatal responses were directly affected by stomatal anatomy and hydraulic traits. Smaller, denser stomata was correlated with faster stomatal closure at high VPD across the species of Rhizophoraceae, and stomata size negatively and vein density positively correlated with genome size. Less negative leaf osmotic pressure at the full turgor (π<sub>o</sub>) was related to higher operating steady-state stomatal conductance (<i>g</i><sub>s</sub>); and a higher leaf capacitance (<i>C</i><sub>leaf</sub>) and more embolism resistant leaf xylem were associated with slower stomatal responses to an increase in VPD. In addition, stomatal responsiveness to VPD was indirectly affected by leaf morphological traits, which were affected by site salinity and consequently leaf water status. Our results demonstrate that mangroves display a unique relationship between genome size, stomatal size and vein packing, and that stomatal responsiveness to VPD is regulated by leaf hydraulic traits and stomatal morphology. Our work provides a quantitative framework to better understand of stomatal regulation in mangroves in an environment with high salinity and dynamic water availability.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"46 3","pages":"395-405"},"PeriodicalIF":4.8,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11119510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155708","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}
Pub Date : 2023-12-01DOI: 10.1016/j.pld.2023.12.001
Bailong Zhao
{"title":"pyIFPNI: A package for querying and downloading plant fossil data from the IFPNI","authors":"Bailong Zhao","doi":"10.1016/j.pld.2023.12.001","DOIUrl":"https://doi.org/10.1016/j.pld.2023.12.001","url":null,"abstract":"","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"102 s406","pages":""},"PeriodicalIF":4.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138622542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-01DOI: 10.1016/j.pld.2023.12.002
Xing-jin He
{"title":"Integrating high-volume molecular and morphological data into the evolutionary studies of Allium","authors":"Xing-jin He","doi":"10.1016/j.pld.2023.12.002","DOIUrl":"https://doi.org/10.1016/j.pld.2023.12.002","url":null,"abstract":"","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"310 2","pages":""},"PeriodicalIF":4.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139021958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-01DOI: 10.1016/j.pld.2023.11.004
Hong Qian, Brent D. Mishler, Jian Zhang, Shenhua Qian
{"title":"Global patterns and ecological drivers of taxonomic and phylogenetic endemism in angiosperm genera","authors":"Hong Qian, Brent D. Mishler, Jian Zhang, Shenhua Qian","doi":"10.1016/j.pld.2023.11.004","DOIUrl":"https://doi.org/10.1016/j.pld.2023.11.004","url":null,"abstract":"","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":" 47","pages":""},"PeriodicalIF":4.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138611307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}