Genome assembly of Stewartia sinensis reveals origin and evolution of orphan genes in Theaceae

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 3, 2025

Orphan genes play crucial roles in diverse biological processes, but the evolutionary trajectories and functional divergence remain largely unexplored. The Theaceae family, including economically culturally important tea plant, offers a distinctive model to examine these aspects. Here, we integrated Nanopore long-read sequencing, Illumina short-read Hi-C methods decode pseudo-chromosomal genome assembly of Stewartia sinensis, from earliest-diverging tribe Theaceae, spanning 2.95 Gb. Comparative genomic analysis revealed absence recent whole-genome duplication events ancestor, highlighting tandem duplications as predominant mechanism gene expansion. We identified 31,331 orphan genes, some which appear have ancient origins, suggesting early emergence with frequent gains losses, while others seem more specific recent. Notably, are distinguished by shorter lengths, fewer exons domains compared that originate much earlier, like transcription factors. Moreover, contributes significantly adaptive evolution characteristic diversity it is also major driving origination genes. This study illuminates dynamics providing valuable resource for understanding origin plant flavor enhancing genetic breeding efforts. nearly complete an early-diverging species, phylogenomic studies provide insights into Theaceae.

Language: Английский

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Climate change impacts the distribution of Quercus section Cyclobalanopsis (Fagaceae), a keystone lineage in East Asian evergreen broadleaved forests

Plant Diversity, Journal Year: 2023, Volume and Issue: 45(5), P. 552 - 568

Published: April 6, 2023

East Asian evergreen broadleaved forests (EBFLs) harbor high species richness, but these ecosystems are severely impacted by global climate change and deforestation. Conserving managing EBLFs requires understanding dominant tree distribution dynamics. In this study, we used 29 in Quercus section Cyclobalanopsis-a keystone lineage EBLFs-as proxies to predict EBLF dynamics using models (SDMs). We examined climatic niche overlap, similarity, equivalency among seven biogeographical regions' 'ecospat'. also estimated the effectiveness of protected areas predicted range elucidate priority conservation regions. Our results showed that niches most geographical groups differ. The western under Indian summer monsoon regime were mainly temperature factors, whereas precipitation eastern regime. simulation a northward expansion Cyclobalanopsis between 2081 2100, except for ranges three Himalayan analyzed, which might shrink significantly. greatest shift highly suitable was South Pacific, with centroid over 300 km. Remarkably, only 7.56% habitat is currently inside areas, percentage continue declining future. To better conserve EBLFs, establishing nature reserves their northern ranges, transplanting populations decreasing numbers degraded habitats future should be high-priority objectives.

Language: Английский

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The Warps and Wefts of a Polyploidy Complex: Integrative Species Delimitation of the Diploid Leucanthemum (Compositae, Anthemideae) Representatives

Plants, Journal Year: 2022, Volume and Issue: 11(14), P. 1878 - 1878

Published: July 19, 2022

Species delimitation-owing to the paramount role of species rank in evolutionary, ecological, and nature conservation studies-is an essential contribution taxonomy biodiversity research. In 'integrative taxonomy' approach delimitation on diploid level, we searched for evolutionary significant units (the warps wefts) that gave rise polyploid complex European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). discovery validation methods based genetic, geographical, morphometric datasets were applied test currently accepted morpho-species, i.e., morphologically delimited species, Leucanthemum. Novel approaches taken analyses RADseq data (consensus clustering), morphometrics reconstructed leaf silhouettes from digitized herbarium specimens, quantification species-distribution overlaps. We show 17 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic remaining three was resolved combining genealogic, ecologic, geographic, morphologic framework von Wettstein's morpho-geographical concept. herewith provide a methodological pipeline fashion using sources evidence genealogical, morphological, geographical philosophy De Queiroz's "Unified Concept".

Language: Английский

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Genomics and ecological modelling clarify species integrity in a confusing group of butterflies

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(8), P. 2400 - 2417

Published: Feb. 25, 2022

Recent advances in both genomics and ecological modelling present new, multidisciplinary opportunities for resolving species boundaries understanding the mechanisms that maintain their integrity regions of contact. Here, we use a combination high-throughput DNA sequencing niche to resolve divergence within Speyeria atlantis-hesperis (Lepidoptera: Nymphalidae) complex, confusing group North American butterflies. This complex is notorious its muddled delimitations, morphological ambiguity, extensive mitonuclear discordance. Our admixture multispecies coalescent-based analyses single nucleotide polymorphisms identified substantial divergences between S. atlantis hesperis areas contact, as well distinct northern southern lineages hesperis. results also provide evidence past introgression relating another species, zerene, which previous work has shown be more distantly related complex. We then used models predict habitat suitability each three recovered genomic assessed pairwise divergence. These resolved these are significantly diverged respective niches not separated by discontinuities suitable might barriers gene flow. therefore infer ecologically-mediated selection resulting disparate associations principal mechanism reinforcing integrity. Overall, our unambiguously support significant evolutionary hesperis, sufficient recognize lineage called nausicaa based on taxonomic priority.

Language: Английский

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Species boundaries and conservation implications of Cinnamomum japonicum, an endangered plant in China

Journal of Systematics and Evolution, Journal Year: 2023, Volume and Issue: 62(1), P. 73 - 83

Published: Feb. 20, 2023

Abstract Clear species boundaries are crucial for plans and actions on biodiversity conservation. However, morphological similarities among allied can result in taxonomic difficulties, thus impeding conservation efforts. In China, Cinnamomum japonicum Siebold is a well‐known endangered plant, yet suffers from longstanding issues. Here, we explicitly evaluate whether C. , chenii chekiangense the same phylogenetic basis of multi‐individual sampling strategy. We identified three sets low‐copy orthologous genes 19 Lauraceae taxa inferences. Both concatenation coalescent‐based phylogenies supported that individuals were embedded clade indicating these two conspecific . Meanwhile, accessions formed monophyly which was not sister to This result, together with differences leaves glabrous faveolate pattern venation while those have trichomes inevident lateral veins, led us consider both as distinct species. Based 17 728 neutral single nucleotide polymorphisms ( SNPs ), ADMIXTURE analysis suggested Chinese populations Zhoushan Archipelago (= ) genetically differentiated Japanese Korean ones. Furthermore, ecological niche modeling predicted present distribution area likely be unsuitable under global warming scenarios. Together its limited genetic uniqueness, recommend deserves priorities.

Language: Английский

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Two Species Delimitation of Pseudaulacaspis (Hemiptera: Diaspididae) Based on Morphology, Molecular Clustering, and Niche Differentiation

Insects, Journal Year: 2023, Volume and Issue: 14(8), P. 666 - 666

Published: July 25, 2023

Pseudaucalaspis pentagona and P. prunicola are notorious pests commonly feed on various ornamental plants fruit trees worldwide. The two species share many host-plant species, similar in morphological characteristics life cycle, making it difficult to distinguish between them. In this study, characteristics, molecular evidence, ecological niches were used define these species. We performed PCA analysis 22 that allowed the delineation of then sequenced COI gene both revealing five populations one population prunicola, higher support rate could also identified potential distribution area based MaxEnt niche model, which showed degree overlap was high, but they occupied different niches. Ultimately, we combined three lines evidence show distinctly different. This study supports definition using morphology, genetics, ecology provides a theoretical basis for effective control future.

Language: Английский

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The Origin and Evolution of Orphan Genes: A Case Study in Tea Plant Family

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 6, 2024

Abstract Orphan genes and transcription factor (TFs) are pervasive across genomes, play pivotal roles as regulators in a myriad of biological processes. Despite their ubiquity, the evolutionary trajectories functional divergence these remain largely unexplored. Theaceae family, encompassing economically culturally significant tea plant, presents unique opportunity to study dynamics. Here, we decoded nearly complete, chromosome-scale reference genome Stewartia gemmata spanning 2.95 Gb. This is enhanced by integrating S. , an early-diverging species within Theaceae, crucial for phylogenomic analyses understanding dynamics orphan this family. Our analysis confirmed absence recent specific whole-genome duplication (WGD) event, with tandem duplications emerging predominant mechanism gene at ancestral nodes Theaceae. By conducting extensive comparative genomics 13 comparing wide array eukaryotic prokaryotic proteins, identified 37,618 25,884 TFs Interestingly, some appear have ancient origins plant ancestors, suggesting relatively early frequent gains losses, conversely, many others seem more recent. Notably, characterized shorter lengths, fewer exons domains than TFs, implying simpler roles. These demonstrate diverse cellular localization functions predicted GO/KEGG analysis, implicated environmental response flavor formation plants. not only sheds light on distinct histories divergences between but also contributes our genetic complexity adaptability valuable Short summary: The complete studies provide insights into new evolution

Language: Английский

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Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae)

Annals of Botany, Journal Year: 2024, Volume and Issue: 133(7), P. 1007 - 1024

Published: March 1, 2024

Abstract Background and Aims Introgressive hybridization poses a challenge to taxonomic phylogenetic understanding of taxa, particularly when there are high numbers co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks highly diverse in sympatry cross freely, creating syngameons interfertile Although well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many more recently derived clades remain be defined, young exceptionally Mexican white clade. Here, we adopted an approach bridging micro- macroevolutionary scales resolve rapidly diversifying clade endemic Mexico. Methods Ecological data sequences 155 low-copy nuclear genes were used identify distinct lineages laeta complex. Concatenated coalescent approaches assess placement these relative Phylogenetic network methods applied evaluate timing genomic significance recent or historical introgression among lineages. Key Results Q. complex comprises six well-supported lineages, each restricted geographically with mostly divergent climatic niches. Species trees corroborated that different closely related other species oaks than other, suggesting polyphyletic. networks estimated events ancient involved ancestors three present-day Conclusions morphologically ecologically group rather Currently, phylogenetics at turning point, which it necessary integrate ecology broad regional samples figure out boundaries. Our study illuminates one complicated groups lays groundwork further study.

Language: Английский

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An integrative approach to the taxonomy of Oxymycterus paramensis (Rodentia, Cricetidae) and related nominal forms

Journal of Mammalogy, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 3, 2024

Abstract Oxymycterus includes 17 species of small- to medium-sized sigmodontine rodents. The taxonomy this genus has been widely studied, but several unresolved issues persist. One example is the Paramo Hocicudo, paramensis, which over its extended latitudinal range associated with nominal forms that have not evaluated an integrative approach. Based on phylogenetic analyses Cytb gene, qualitative and quantitative morphological characters, environmental niche modeling, we reexamined taxonomic status akodontius, jacentior, paramensis while considering recently recognized O. willkaurco. reconstruction guided subsequent analysis variation development models. Considering results in framework, observed congruence among phylogenetic, distribution models, models (a proxy indicating different preferences), support recognition 2 within concept s.l. At same time, did observe congruent for hypothesis from evidence, absence diagnostic or characters differentiating taxa. some lines evidence suggest interruption gene flow, see more recognizing existing names taxa at level: endemic Bolivia; akodontius (which priority jacentior), distributed southern Bolivia northwestern Argentina. However, recommend detailed studies test scenario advanced here.

Language: Английский

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Collections‐based systematics in the new age of discovery: Celebrating the legacy and life of Professor Wen‐Tsai Wang

Journal of Systematics and Evolution, Journal Year: 2023, Volume and Issue: 61(1), P. 1 - 10

Published: Jan. 1, 2023

Professor Wen-Tsai Wang (王文采, June 5, 1926–November 16, 2022) was an academician of the Chinese Academy Sciences (CAS) and a legendary plant taxonomist at Institute Botany CAS (Fig. 1). Herein, we organize virtual special issue in Journal Systematics Evolution (JSE) to celebrate legacy life Wang, who leading China made important contributions toward advancing understanding flora China, biogeography eastern Asia, biodiversity research vast Hengduan Mountains. He served as Editor-in-Chief Acta Phytotaxonomica Sinica (now JSE) for 6 years from 1982 1988, trained several generations taxonomists (Li, 2001). graduated Beijing Normal University 1949 joined Plant Taxonomy Botany), CAS, assistant 1950. promoted professor rank 1982, elected 1993. had long, productive career Herbarium Botany, 2), published more than 250 taxonomic floristic papers monographs 3). described 28 new genera, 303 taxa tribal, sectional, series ranks, ca. 1370 species, 242 combinations. one most participants compilation enormous 8-volume Iconographia Cormophytorum Sinicorum (Institute 1972–1983) 4). first assigned be charge preparation book 1965 set foundation preparing Flora Reipublicae Popularis Sinicae (FRPS) help with identifications China. The included 11 000 higher species brief descriptions on morphology, ecology, distribution, uses, 9082 which line drawings. contributed treatments families this series, including Boraginaceae, Geraniaceae, Gesneriaceae, Papaveraceae, Proteaceae, Ranunculaceae, Urticaceae, Vitaceae. This has been widely used by scientific institutions, colleges, universities train botanists young students biology throughout became botanical classics authority difficult Rubiaceae, Vitaceae, through his extensive herbarium field 5). Sinicae, treating part Ranunculaceae (Aconitum, Delphinium, Anemone, small genera) (Wang, 1979, 1980), Gesneriaceae 1990), Boraginaceae (Kung & 1989; 1993), Urticaceae (Wang Chen, 1995; 2014, 2016). retired 1986, but he continued Gesneriaceae. From early 1990s 2000s, visited major herbaria abroad Europe United States, BM, E, G, GH, K, LE, MHA, MO, NY, P, S, UPS, US. 77 after turned 85 old, only stopped quite recently spring 2021 (e.g., 1993, 1994, 2000, 2002, 2003, 2004, 2006, 2016, 2018, 2019, 2020, 2021). also collaborative project treated (in collaboration De-Zhi Fu Liang-Qian Li) Kai-Yu Pan Zhen-Yu Li). In 1996, States National (US) Smithsonian Institution, Gray Harvard (GH), New York Botanical Garden (NY), Missouri (MO). During trip, completed revision Dr. Laurence E. Skog (Smithsonian Institution) et al., 1998). Beyond studies, distribution patterns migration routes Eastern Asiatic Region 1989, 1992). These have inspired many studies Asian (Wen 2014; Nie 2016; Liu 2021; Mao Zhang 2022). two volumes vascular plants Mountains that edited 1994) documented all collected region based specimens created western collectors. achievement time when collections were not easily available online or digitized. completion systematic, biogeographic, conservation work evolutionary hotspot Asia. numerous workers taxonomy courses universities, institutes 6). always humble, modest, approachable, taught younger colleagues informally PE 7). well known training such Fu, Li, other 8). editorial board 1973. May 1981, Deputy Editor-in-Chief, chaired standing meeting reach some agreements journal, publishing significant academic value innovation, soliciting high-quality manuscripts, adopting strict peer-review process, implemented journal until today. JSE leaving position, serve various ways. April 1995, wrote office suggest type should deposited recognized is committed long-term maintenance. helped revise approve Latin description diagnosis authors even 80s. received awards honors, prestigious First Prize Natural Science Award twice 1987 2009) (Figs. 9, 10), Qiu Shi Technologies Foundation Technology Achievement Ho Leung Lee 1997. named Lifetime Honorary CAS. Commemorative Badge Celebrating 70th Anniversary Founding People′s Republic government. To honor Wang′s taxonomy, floristics, efforts next-generation taxonomists, herein, selected 16 last 3 collections-based systematics legacy. articles showcase advances biogeography, floristics age discovery 2015, 2017; Funk, 2018). dedicated We present discuss four emphasize diversity assembly Hu al. (2020) provided updated phylogenetic tree plants, generating mega-phylogenetic 15 092 tips 14 878 13 663 (44.0%) 2953 genera (95.7%) are native tremendous framework flora, study identified hotspots angiosperms both genus levels; hence, paper great significance utilizing information diversity. Xie (2021) reviewed analyzed data Species Catalogue China: Volume 1: Plants (SCCP), comprehensive inventory plants. database freely accessible at: http://www.sp2000.org.cn/, includes entries 478 families, 4052 41 687 specific infraspecific taxa. origin Qinghai-Tibetan Plateau (QTP), well-known discussed issues circumscribing naming QTP, QTP uplifts, dating molecular trees, processes diversification high-altitude adaptation. Low tropical Typhonium s.s. Araceae reconstruct biogeographic paleotropical flora. inferred originated Indochina during early–middle Miocene subsequent within may triggered intensification monsoons around middle Miocene. provides hypotheses studying evolution elements. phylogenetics become classification 2017). Phylogenetic progressed tremendously decade additional sampling characteristics genomics) taxa, especially team (Zimmer Wen, 2015). five systematics, realm classification. Soreng (2022) worldwide large economically grass family Poaceae. revised 12 subfamilies, 7 supertribes, 54 tribes, 5 supersubtribes, 109 subtribes, list number each 787 accepted setting investigations family. another landmark paper, Larridon phylogenomic target enrichment sequences conjunction morphology traditional sources propose Cyperaceae tribal rearrangements re-circumscriptions. Roalson re-evaluated infrageneric taxonomically challenging Carex using organizing principles will roadmap ongoing progress classification, reflect current state our knowledge while being made. hybrid organized into six subgenera, then classified 62 sections plus 49 informal groups. data, network approaches infer phylogeny Caprifoliaceae. They integrated evidence divergence times Zabelioideae subfamily Jiang report case focused assessment monotypic Pseudobartsia yunnanensis (Orobanchaceae), single specimen. obtained chloroplast genome nuclear ribosome sequence specimen 1940, analyses Orobanchaceae plastomes support reinstatement Pseudobartsia. showcases importance today′s research. Two insights delimitations (Li Lin One goals discover describe species; yet, delimitation remained highly controversial due phenotypic plasticity, indistinguishable complex hybridizations (Wiens, 2007; Wen 2018; Hillis Li examined cryptic widespread Roscoea tibetica genotyping sequencing, morphological traits, models, simulating demographic history. Phylogenomic genetic structure inferences supported distinct lineages R. tibetica, discovered common garden observations, ecological models. Phylogenomic, morphological, hence recent contact likely occurred between lineages. However, plasticity heterogeneous environments convergence similar habitats complicated variational patterns. explored complex, Stewartia sinensis (Theaceae), showing continuum variations. phylogenomics, morphology. multispecies coalescent-based 572 orthologs anchored reciprocal (but sister) monophyly northern lineage (NL) southern (SL). Significant climatic niche differentiation detected NL SL populations, modeling further their separation. Morphometric suggested multiple traits. Hence, suggested: gemmata S. NL. highlight applying integrative approach assessing Asia Northern Hemisphere. Zhou sequenced 20 single-copy genes regions Paeonia Paeoniaceae document parents tetraploids. dated late Cretaceous diverged clades, woody herbaceous clades Oligocene survived Pan-Himalaya, where they migrated Northwestern America, Middle Europe. glacial interglacial cycles Pliocene Pleistocene polyploidy speciation allotetraploids autotetraploids. Xu karst endemic Primulina model identify areas Nanling north Guangdong northeast Guangxi southeast Yungui southwest Guangxi. categorical analysis neo- paleoendemism “museums” “cradles” deserve priority. Lu hypothesis Japan–East probably ancestral area cradle sects. Confertiflorae Molliculae. highlights geographic heterogeneity diversification. Dong utilized SNPs plastome explore Magnolia revealed cytonuclear discordances. Their hybridization events sect. Yulania, Magnolia. Dating three disjunctions tracing mid Eocene, temperate much later Miocene, supporting boreotropical (Nie 2008). Yao constructed history holly genus, Ilex (Aquifoliaceae). subtropical colonized South America c. 30 million ago (Ma), North 23 Ma, Australia 8 Africa 4 times. efficient seed dispersal mechanisms rapidly colonize suitable mesic areas. near-cosmopolitan reflected dynamic balance dispersal, diversification, extinction, long-distance 2013). achievements community. Finally, would like share what said about American friends Hayden Wetzel Washington, DC: “he delightful guest friend—gentle, direct, positive helpful. Almost every evening I came home prepared dinner (always same beef dish, fine me). When traveling week told me afterward gone house seemed lonely ate local restaurant. What sweet guy! A few later, Beijing, showed up my hotel morning took town, tired out afternoon. fond pleasant memories lovely man.”

Language: Английский

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