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Past, present, and future of mountain and island systems 山区和岛屿系统的过去、现在和未来
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-04-09 DOI: 10.1111/jse.13073
Alexandra N. Muellner‐Riehl, Fabien Anthelme, Thomas Ibanez
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引用次数: 0
Dense infraspecific sampling reveals cryptic differentiation in the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae) 密集的种下取样揭示了神秘的半寄生爱情藤 Cassytha filiformis(月桂科)的隐秘分化
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-04-01 DOI: 10.1111/jse.13069
Zhi‐Fang Liu, Shi‐Fang Zhang, Alex D. Twyford, Xiu‐Qin Ci, Lang Li, Xiao‐Yan Zhang, Jian‐Lin Hu, Jia‐Chuan Tan, Guang‐Da Tang, Sheng‐Yuan Qin, Ling Hu, Xin Ding, Hong‐Hu Meng, Li‐Na Dong, Ting Huang, Hui Ma, Jian‐Hua Xiao, Chao‐Nan Cai, John G. Conran, Qi Wang, Peter M. Hollingsworth, Jie Li
Species delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well‐supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil‐calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo‐Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of C. filiformis. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones.
物种划分仍然是世界范围内的一项挑战,尤其是在高度多样化的热带和亚热带地区。在本文中,我们采用了一种结合形态学、系统发生组学和物种分布建模(SDM)的综合方法,来阐明中国及邻近地区神秘的半寄生爱子藤(Cassytha filiformis)的隐性分化。我们为该物种分布区的不同样本生成了完整的质粒基因组和核核糖体序列,并将结果与之前发表的质粒数据进行了比较,发现了两个支持良好的单系支系。此外,分析还揭示了两种形态特征和 SDM 的显著差异,表明不同的环境因素影响了它们的分布。通过化石校准分析来估计隐生物种的起源和分化模式,得出的分化年龄估计与中新世晚期一致;这一时期与盛行的东亚季风有关,出现了新的生态机遇。多变量分析支持这样的结论,即华南及其邻近地区有一个不同的、以前未知的丝状藻隐性种系。我们的研究强调了使用多元方法描述植物物种特征的重要性,以及过去的气候变化在推动热带和亚热带地区寄生植物物种变异方面所起的重要作用。
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引用次数: 0
The near-complete genome assembly of Reynoutria multiflora reveals the genetic basis of stilbenes and anthraquinones biosynthesis Reynoutria multiflora 近乎完整的基因组组装揭示了二苯乙烯类和蒽醌类化合物生物合成的遗传基础
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-28 DOI: 10.1111/jse.13068
Qiang He, Yuqing Miao, Xinyuan Zheng, Yaru Wang, Yitao Wang, Zheng Jia, Hongyu Zhang, Yu Wang, Yao Xiao, Cailian Du, Wei Li, Longsheng Xing, Huilong Du
Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti-aging, anti-inflammatory and anti-oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near-complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of long terminal repeats (LTRs) contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole-genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with disease tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in roost, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.
五味子是中国广泛使用的药用植物。其药用化合物主要是二苯乙烯类和蒽醌类化合物,在抗衰老、抗炎和抗氧化方面具有重要的药理活性,但其生物合成途径在很大程度上仍未得到解决。在此,我们报告了一个接近完整的多花蔷薇基因组,该基因组由 1.39 Gb 组成,等位基因 N50 为 122.91 Mb,仅有一个缺口。基因组进化分析表明,最近两次长末端重复序列(LTRs)的爆发极大地增加了多花金花菊的基因组大小,而且在多花金花菊和鞑靼金花菊的基因组之间观察到了许多大的染色体重排。比较基因组学分析表明,最近一次蓼科植物特有的全基因组复制导致多花金银花中与耐病性以及二苯乙烯类和蒽醌类化合物的生物合成有关的基因家族显著扩大。结合转录组学和代谢组学分析,我们阐明了多花连翘根部药用成分含量在不同生长年份动态变化的分子机制。此外,我们还发现了几个负责蒽醌和二苯乙烯生物合成的假定关键基因。我们发现了一个在雄花中高表达的二苯乙烯合成酶基因 PM0G05131,它可能在多花罗汉果中二苯乙烯的积累过程中发挥了重要作用。这些基因组数据将加快药用植物中蒽醌和二苯乙烯类化合物生物合成途径的发现。
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引用次数: 0
Revisiting Xylaria diversity in Southern China: Descriptions of 40 new species 重新审视华南地区的 Xylaria 多样性:40 个新物种的描述
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-26 DOI: 10.1111/jse.13058
Qi‐Rui Li, Kamran Habib, You‐Peng Wu, Si‐Han Long, Xu Zhang, Hong‐Min Hu, Qian‐Zhen Wu, Li‐Li Liu, Yan Lin, Xiang‐Chun Shen, Ji‐Chuan Kang
The genus Xylaria comprises a diverse group of fungi with a global distribution and significant ecological importance, known for being a source of bioactive secondary metabolites with antibacterial, antioxidative, anticarcinogenic, and additional properties. In this study, we present a comprehensive taxonomic revision of the species of Xylaria found in some parts of southern China, characterized by an extensive multilocus phylogeny analysis based on internal transcribed spacer (ITS), TUB2 (β‐tubulin), and DNA‐directed RNA polymerase II subunit 2 (rpb2) gene regions. Morphological examination and detailed comparative analyses of the collected specimens were conducted to determine the distinctiveness of each species. The multilocus phylogeny approach allowed us to infer evolutionary relationships and assess species boundaries accurately, leading to the identification of 40 novel Xylaria species hitherto unknown to science. The newly described species are: X. baoshanensis, X. bawanglingensis, X. botryoidalis, X. dadugangensis, X. doupengshanensis, X. fanglanii, X. glaucae, X. guizhouensis, X. japonica, X. jinghongensis, X. jinshanensis, X. kuankuoshuiensis, X. liboensis, X. negundinis, X. orbiculati, X. ovata, X. pseudoanisopleura, X. pseudocubensis, X. pseudobambusicola, X. pseudoglobosa, X. pseudohemisphaerica, X. pseudohypoxylon, X. puerensis, X. qianensis, X. qiongzhouensis, X. rhombostroma, X. serratifoliae, X. shishangensis, X. shuqunii, X. shuangjiangensis, X. sinensis, X. tongrenensis, X. umbellata, X. xishuiensis, X. yaorenshanensis, X. yinggelingensis, X. yumingii, X. yunnanensis, X. zangmui, and X. zonghuangii. The study's findings shed light on the distinctiveness of the newly described species, supported by both morphological distinctions and ph
木属真菌(Xylaria)是一个种类繁多的真菌群体,分布于全球各地,具有重要的生态意义,是具有抗菌、抗氧化、抗癌和其他特性的生物活性次生代谢产物的来源。本研究通过基于内部转录间隔区(ITS)、TUB2(β-tubulin)和 DNA 引导的 RNA 聚合酶 II 亚基 2(rpb2)基因区的广泛多焦点系统进化分析,对中国南方部分地区发现的木犀属物种进行了全面的分类学修订。对采集的标本进行了形态学检查和详细的比较分析,以确定每个物种的独特性。多焦点系统进化方法使我们能够推断进化关系并准确评估物种边界,从而鉴定出 40 个迄今为止科学界未知的新木犀属物种。这些新描述的物种是X.baoshanensis、X. bawanglingensis、X. botryoidalis、X. dadugangensis、X. doupengshanensis、X. fanglanii、X. glaucae、X. guizhouensis、X. japonica、X. jinghongensis、X.金山ensis、X. kuankuoshuiensis、X. liboensis、X. negundinis、X. orbiculati、X. ovata、X. pseudoanisopleura、X. pseudocubensis、X. pseudobambusicola、X. pseudoglobosa、X.pseudohemisphaerica、X. pseudohypoxylon、X. puerensis、X. qianensis、X. qiongzhouensis、X. rhombostroma、X. serratifoliae、X. shishangensis、X. shuqunii、X. shuangjiangensis、X.X. xishuiensis、X. yaorenshanensis、X. yinggelingensis、X. yumingii、X. yunnanensis、X. zangmui 和 X. zonghuangii。该研究的发现阐明了新描述物种的独特性,并得到了其形态学特征及其与近缘种系统发育关系的支持。此次分类学修订极大地促进了我们对中国木霉菌多样性的了解,并丰富了全球真菌生物多样性的知识。
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引用次数: 0
Spatial phylogenetics of grasses in the Southern Cone provides insights into ecology and evolution of the family in South America 南锥体地区禾本科植物的空间系统发生学为南美洲禾本科植物的生态学和进化提供了启示
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-18 DOI: 10.1111/jse.13067
Lone Aagesen, Diego L. Salariato, María A. Scataglini, Juan M. Acosta, Silvia S. Denham, Carolina Delfini
In this study, we explored the distributions of grass genera in the Southern Cone (SC) of South America, applying several phylogenetic diversity (PD) metrics and randomization tests. Grasses appear to have been present in South America since their early evolution as tropical understory species more than 60 Ma. During the course of evolution, grasses have adapted to all terrestrial biomes and become one of the most successful plant families on earth. At present, the SC contains nearly all terrestrial biomes and a wide range of humid to arid ecoregions. Analyzing 126.514 point occurrences and four plastid markers for 148 genera (91% of the native grass genera), we found that tropical humid regions hold the highest PD, with no observed bias in branch lengths. These results indicate that niche conservatism dominates the diversity pattern of grasses in the SC. We found significantly low PD in the Dry Chaco and in the Patagonian Steppe, which suggest ecological filtering in both warm and cold arid regions. The Patagonian Steppe also holds significantly longer branches than expected by chance, as the native grass flora is mainly composed of distantly related Pooideae genera with a northern hemisphere origin. Short branches are found in the Uruguayan Savanna, suggesting that these grasslands could be a cradle for grass diversity within the SC. The dated phylogeny supported the current view of a relatively recent evolution of the family within the SC, with most diversification taking place from the middle Miocene and onwards.
在这项研究中,我们应用几种系统发育多样性(PD)指标和随机化检验,探索了南美洲南锥体(SC)地区草属的分布情况。禾本科植物似乎自 60 多万年前作为热带林下物种早期演化以来就一直存在于南美洲。在进化过程中,禾本科植物适应了所有陆地生物群落,成为地球上最成功的植物科之一。目前,南极洲几乎包含了所有的陆地生物群落以及从湿润到干旱的各种生态区。通过分析 148 个属(占本地禾本科属的 91%)的 126.514 个点出现和 4 个质体标记,我们发现热带潮湿地区的禾本科属的 PD 最高,而且分支长度没有观察到偏差。这些结果表明,生态位保守性主导了南亚地区草类的多样性模式。我们在干查科和巴塔哥尼亚大草原发现了明显较低的PD,这表明在温暖和寒冷干旱地区都存在生态过滤。巴塔哥尼亚大草原的禾本科禾本科植物主要由起源于北半球的远缘禾本科属植物组成,因此该地区的禾本科禾本科植物的分枝也明显比预期的要长。乌拉圭热带草原的分支较短,这表明这些草原可能是南极洲草类多样性的摇篮。年代系统发育支持目前的观点,即该科属在南美洲的演化相对较新,大部分的多样化发生在中新世中期及以后。
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引用次数: 0
The Bryophyte Phylogeny Group: A revised familial classification system based on plastid phylogenomic data 苔藓植物系统发育组:基于质体系统发生组数据的修订科分类系统
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-13 DOI: 10.1111/jse.13063
Yun‐Feng Li, Lian Luo, Yang Liu, Qiang He, Ning‐Ning Yu, Naren Gaowa, Zhao‐Qin Yi, Jun‐Jie Wang, Wei Han, Tao Peng, Boon‐Chuan Ho, Xiaolan He, Li Zhang, Zhi‐Duan Chen, Yu Jia, Qing‐Hua Wang
Bryophytes, a monophyletic group comprising three major lineages, diversified soon after the terrestrialization of land plants. However, their internal phylogenetic relationships remain controversial. In this study, we reconstructed the ordinal and familial phylogeny of bryophytes using the largest plastid data set to date, including 549 taxa that represent almost all known orders and two‐thirds of families. The strongly supported phylogenetic inference enabled us to propose in mosses seven newly segregated families, that is, Baldwiniellaceae, Calyptrochaetaceae, Ctenidiaceae, Herpetineuraceae, Isodrepaniaceae, Pseudotaxiphyllaceae, and Rozeaceae, and one reduced family, that is, Climaciaceae. We also transferred the liverwort family Calyculariaceae from Fossombroniales to Pelliales. Recent advancements in molecular phylogeny have revolutionized bryophyte classification, tending to be more fragmental. Hence, we further propose a revised familial classification system for bryophytes that includes 45 orders and 142 families in mosses, 23 orders and 85 families in liverworts, and five orders and five families in hornworts.
苔藓植物是一个单系类群,由三个主要品系组成,在陆生植物陆地化之后不久就出现了多样化。然而,它们的内部系统发育关系仍存在争议。在这项研究中,我们利用迄今为止最大的质体数据集重建了叶绿体的序和科的系统发育,其中包括 549 个分类群,几乎代表了所有已知的目和科的三分之二。得到强有力支持的系统发育推论使我们在苔藓植物中提出了七个新分离的科,即秃头蕨科(Baldwiniellaceae)、萼片蕨科(Calyptrochaetaceae)、栉水母科(Ctenidiaceae)、酢浆草科(Herpetineuraceae)、异酢浆草科(Isodrepaniaceae)、假酢浆草科(Pseudotaxiphyllaceae)和萝茨科(Rozeaceae),以及一个缩小了的科,即攀缘植物科(Climaciaceae)。我们还将肝草科 Calyculariaceae 从 Fossombroniales 转入 Pelliales。分子系统发育的最新进展彻底改变了红叶植物的分类方法,使其更趋于片段化。因此,我们进一步提出了一个经修订的苔藓植物科分类系统,其中包括苔藓植物的 45 目 142 科、肝草植物的 23 目 85 科以及角草植物的 5 目 5 科。
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引用次数: 0
Multi‐omics provides insights into genome evolution and betacyanin biosynthesis in halophyte of Suaeda salsa 多组学揭示 Suaeda salsa 盐生植物基因组进化和甜菜苷生物合成的奥秘
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-13 DOI: 10.1111/jse.13064
Xin Wang, Jiang‐Bao Xia, Jun‐Hong Bai, Shuo Yin, Wei Wang, Da‐Wei Wang, Xin‐Xin Yi, Sheng‐Hong Dai
As an important halophyte in the Yellow River Delta, the Amaranthaceae C3 Suaeda salsa (L.) Pall. has attracted much attention for the “red carpet” landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people's understanding of this species at the molecular level. We constructed a high‐quality chromosome‐scale reference genome by combining high‐throughput sequencing, PacBio single molecule real‐time sequencing, and Hi‐C sequencing techniques with a genome size of 445.10 Mb and contigs N50 of 2.94 Mb. Through the annotation of the S. salsa genome, 298.76 Mb of the repetitive sequences and 23 965 protein‐coding genes were identified, of which the proportion of long terminal repeats type in the repetitive sequences was the most abundant, about 50.74% of the S. salsa genome. Comparative genomics indicated that S. salsa underwent a whole‐genome duplication event about 146.15 million years ago (Ma), and the estimated divergence time between S. salsa and Suaeda aralocaspica was about 16.9 Ma. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6′‐O‐malonyl‐celosianin II were identified and purified in both phenotypes, while two significantly up‐regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerning with betacyanin production were selected in S. salsa.
作为黄河三角洲重要的卤叶植物,苋科 C3 Suaeda salsa (L.) Pall.因其 "红地毯 "景观而备受关注,根据肉质叶片中贝特氰含量的不同,可将其简单分为红色和绿色两种表型。然而,莎莎尚未进行测序,这限制了人们在分子水平上对该物种的了解。我们结合高通量测序、PacBio单分子实时测序和Hi-C测序技术,构建了高质量染色体组规模的参考基因组,基因组大小为445.10 Mb,等位基因N50为2.94 Mb。通过对莎莎鱼基因组的注释,共鉴定出298.76 Mb的重复序列和23 965个编码蛋白质的基因,其中重复序列中长末端重复类型的比例最高,约占莎莎基因组的50.74%。比较基因组学表明,莎草属植物在距今约1.4615亿年前经历了一次全基因组复制事件,估计莎草属植物与Suaeda aralocaspica的分化时间约为16.9Ma。在两种表型中,共鉴定并纯化了四种贝壳杉素,包括贝壳杉素Ⅱ、芹菜素Ⅱ、苋菜素和6′-O-丙二酰基芹菜素Ⅱ,而两种显著上调的贝壳杉素(芹菜素Ⅱ和苋菜素)可能是红色表型中红色的主要原因。此外,我们还对两种表型进行了转录组学和代谢组学研究,以探索色素合成的分子机制,并筛选出了一系列与辣木籽苷产生有关的结构基因和转录因子。
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引用次数: 0
Qineryangia, a new genus from the Hengduan Mountains and new insights into the phylogeny of the subtribe Crepidinae (Cichorieae, Asteraceae) 横断山脉的新属Qineryangia以及对Crepidinae(菊科)亚属系统发育的新认识
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-13 DOI: 10.1111/jse.13066
Lian‐Sheng Xu, Zhu‐Qiu Song, Shu‐Yuan Liao, You‐Sheng Chen
The Crepidinae are the largest subtribe of the Cichorieae (Asteraceae). Debate remains over the circumscription and phylogeny of this subtribe, mainly due to its complex morphology and the poor phylogenetic signal provided by traditional Sanger sequencing markers. In this study, a well‐resolved phylogeny of the subtribe Crepidinae, consisting of seven highly supported clades, was obtained for the first time using nuclear data with a phylogenomics approach (Hyb‐Seq). Using this phylogeny along with other evidence, we propose a new taxonomic framework for the Crepidinae with seven lines and 29 genera, which merges subtribe Chondrillinae with the Crepidinae. We also describe a new monotypic genus, Qineryangia, that is characterized by broad involucres, loose imbricate phyllaries with wavy margins, and thick pappus bristles.
Crepidinae 是菊科(Cichorieae)中最大的亚科。主要由于其复杂的形态以及传统的 Sanger 测序标记所提供的系统发育信号较差,该亚支系的划分和系统发育仍存在争议。在本研究中,利用核数据和系统发生组学方法(Hyb-Seq),首次获得了由七个高度支持的支系组成的蝶形花亚科的系统发生。利用这一系统发育以及其他证据,我们提出了一个新的蝶形花科分类框架,包括 7 个支系和 29 个属,并将 Chondrillinae 亚支与蝶形花科合并。我们还描述了一个新的单型属--Qineryangia,其特点是总苞宽大,叶片松散覆瓦状,边缘呈波浪形,叶被刚毛粗大。
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引用次数: 0
Phylogenomics of Puya (Bromeliaceae): Evolution in the Andean slopes and sky island ecosystems Puya(凤梨科)的系统发生组学:安第斯山坡和天空岛生态系统的演变
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-08 DOI: 10.1111/jse.13062
Julián Aguirre-Santoro, Alejandro Zuluaga, Emma Stonesmyth, Julio Betancur, Rachel S. Jabaily
Phylogenomics enhances our understanding of plant radiations in the biodiverse Andes. Our study focuses on Puya, primarily Andean and a part of the Bromeliaceae family. Using a phylogenomic framework based on the Angiosperms353 probe set for 80 species, we explored Puya′s phenotypic evolution and biogeography. Divergence time analyses and ancestral area estimations suggested that Puya originated in Central Coastal Chile around 9 million years ago (Ma). Subsequently, it dispersed to the dry valleys of the Central Andes and Puna regions between 5–8 Ma, leading to the emergence of major lineages. Key events in the last 2–4 million years include the recolonization of Chilean lowlands and dispersal to the northern Andes via Peru's Jalcas, facilitating passage through the Huancabamba depression. This event gave rise to the high-elevation Northern Andes clade. Using phylogenetic comparative methods, we tested the hypothesis that adaptation to the Andes' island-like high-elevation ecosystems was facilitated by unique leaf and floral traits, life history, and inflorescence morphology. Our findings suggest correlations between inflorescence axis compression, protective bract overlap, and high-elevation living, potentially preventing reproductive structure freezing. Semelparity evolved exclusively at high elevations, although its precise adaptive value remains uncertain. Our framework offers insights into Andean evolution, highlighting that lineages adapted to life in dry ecosystems can easily transition to high-elevation biomes. It also underscores how the island-like nature of high-elevation ecosystems influences phenotypic evolution rates. Moreover, it opens avenues to explore genetic mechanisms underlying adaptation to extreme mountain conditions.
系统发生组学加深了我们对生物多样性丰富的安第斯山脉植物辐射的了解。我们的研究重点是主要生长在安第斯山脉、属于凤梨科(Bromeliaceae)的Puya。我们利用基于 Angiosperms353 探针集的系统发生组框架,对 80 个物种的表型进化和生物地理学进行了探索。分异时间分析和祖先地区估计表明,蒲葵起源于智利中部沿海地区,距今约900万年(Ma)。随后,在距今5-8百万年之间,它扩散到了安第斯山脉中部的干旱山谷和普纳地区,导致了主要品系的出现。在过去的 200-400 万年间发生的关键事件包括智利低地的再殖民化以及通过秘鲁的 Jalcas 向安第斯山脉北部的扩散,为穿越万卡班巴洼地提供了便利。这一事件产生了高海拔的北安第斯支系。利用系统发生比较方法,我们检验了一个假设,即独特的叶和花特征、生活史和花序形态有助于适应安第斯山脉岛屿般的高海拔生态系统。我们的研究结果表明,花序轴压缩、保护性苞片重叠和高海拔生活之间存在相关性,有可能防止生殖结构冻结。雌雄同株只在高海拔地区进化,但其确切的适应价值仍不确定。我们的框架为安第斯山脉的进化提供了见解,强调了适应干旱生态系统生活的品系很容易过渡到高海拔生物群落。它还强调了高海拔生态系统类似岛屿的性质是如何影响表型进化速度的。此外,它还为探索适应极端山区条件的遗传机制开辟了道路。
{"title":"Phylogenomics of Puya (Bromeliaceae): Evolution in the Andean slopes and sky island ecosystems","authors":"Julián Aguirre-Santoro, Alejandro Zuluaga, Emma Stonesmyth, Julio Betancur, Rachel S. Jabaily","doi":"10.1111/jse.13062","DOIUrl":"https://doi.org/10.1111/jse.13062","url":null,"abstract":"Phylogenomics enhances our understanding of plant radiations in the biodiverse Andes. Our study focuses on <i>Puya</i>, primarily Andean and a part of the Bromeliaceae family. Using a phylogenomic framework based on the Angiosperms353 probe set for 80 species, we explored <i>Puya</i>′s phenotypic evolution and biogeography. Divergence time analyses and ancestral area estimations suggested that <i>Puya</i> originated in Central Coastal Chile around 9 million years ago (Ma). Subsequently, it dispersed to the dry valleys of the Central Andes and Puna regions between 5–8 Ma, leading to the emergence of major lineages. Key events in the last 2–4 million years include the recolonization of Chilean lowlands and dispersal to the northern Andes via Peru's Jalcas, facilitating passage through the Huancabamba depression. This event gave rise to the high-elevation Northern Andes clade. Using phylogenetic comparative methods, we tested the hypothesis that adaptation to the Andes' island-like high-elevation ecosystems was facilitated by unique leaf and floral traits, life history, and inflorescence morphology. Our findings suggest correlations between inflorescence axis compression, protective bract overlap, and high-elevation living, potentially preventing reproductive structure freezing. Semelparity evolved exclusively at high elevations, although its precise adaptive value remains uncertain. Our framework offers insights into Andean evolution, highlighting that lineages adapted to life in dry ecosystems can easily transition to high-elevation biomes. It also underscores how the island-like nature of high-elevation ecosystems influences phenotypic evolution rates. Moreover, it opens avenues to explore genetic mechanisms underlying adaptation to extreme mountain conditions.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140073089","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}
引用次数: 0
Comparative analysis of 326 chloroplast genomes in Chinese jujube (Ziziphus jujuba): Structural variations, horizontal gene transfer events, and evolutionary patterns impacting its domestication from wild jujube 中国大枣(Ziziphus jujuba)326 个叶绿体基因组的比较分析:结构变异、水平基因转移事件以及影响从野生枣驯化而来的进化模式
IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-03-01 DOI: 10.1111/jse.13065
Meng Yang, Shu-Feng Zhang, Bin Li, Yun-Xin Lan, Yi-Han Yang, Meng-Jun Liu
Jujube (Ziziphus jujuba Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 nonredundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast-to-nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, Z. jujuba. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species.
大枣(Ziziphus jujuba Mill.)以其营养价值和保健功效而闻名,据信起源于中国黄河中下游地区,在那里经历了从野生大枣到栽培大枣的驯化过程。然而,野生大枣和栽培大枣之间的进化轨迹和物种分化仍有待进一步阐明。与核基因组相比,叶绿体基因组(质体)的突变率相对较低,是进化和比较基因组研究的绝佳模型。在这项研究中,我们分析了分布在中国各地的 133 个红枣栽培品种和 193 个野生红枣基因型的 326 个非冗余质粒体。值得注意的是,这些质粒的大小差异主要是由大的单拷贝区域的变化造成的,这影响了从野生枣到栽培品种的进化。水平基因转移(HGT)揭示了一个独特的叶绿体到细胞核的转移事件,转移的片段主要影响了核基因组的进化,而质体则相对不受影响。种群遗传学分析揭示了从野生红枣到栽培红枣的两条不同的进化途径:一条是由自然选择驱动的,人为干扰极少;另一条是人类驯化和栽培的结果。基于系统发育分析的分子测年支持了野生大枣和栽培大枣属于同一分类学类别(Z. jujuba)的可能性。总之,我们的研究全面考察了红枣质体结构和 HGT 事件,同时对红枣物种进化和驯化的复杂过程提出了新的见解。
{"title":"Comparative analysis of 326 chloroplast genomes in Chinese jujube (Ziziphus jujuba): Structural variations, horizontal gene transfer events, and evolutionary patterns impacting its domestication from wild jujube","authors":"Meng Yang, Shu-Feng Zhang, Bin Li, Yun-Xin Lan, Yi-Han Yang, Meng-Jun Liu","doi":"10.1111/jse.13065","DOIUrl":"https://doi.org/10.1111/jse.13065","url":null,"abstract":"Jujube (<i>Ziziphus jujuba</i> Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 nonredundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast-to-nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, <i>Z. jujuba</i>. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140011477","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}
引用次数: 0
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Journal of Systematics and Evolution
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