Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia

Plant Diversity, Год журнала: 2022, Номер 45(2), С. 147 - 155

Опубликована: Апрель 27, 2022

Fargesia, the largest genus within temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in mountains of Southwest China. The Fargesia bamboos are important components subalpine forest ecosystems that provide food and habitat for many endangered animals, including giant panda. However, species-level identification is difficult. Moreover, rapid radiation slow molecular evolutionary rate pose a significant challenge to using DNA barcoding with standard plant barcodes (rbcL, matK, ITS) bamboos. With progress sequencing technologies, complete plastid genomes (plastomes) nuclear ribosomal (nrDNA) sequences have been proposed as organelle identification; however, these not tested We collected 196 individuals representing 62 comprehensively evaluate discriminatory power plastomes nrDNA compared barcodes. Our analysis indicates substantially higher (28.6%) (5.7%), whereas show moderate improvement (65.4%) ITS (47.2%). also found markers performed better markers, alone had plastomes. study demonstrated can contribute intrageneric phylogenetic resolution Fargesia. neither were able discriminate all sampled species, therefore, need be identified.

Язык: Английский

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Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

Plant Diversity, Год журнала: 2023, Номер 46(3), С. 344 - 352

Опубликована: Июнь 7, 2023

(Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated position of

Язык: Английский

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Phylogenomic and morphological evidence supports the reinstatement of the bamboo genus Clavinodum from Oligostachyum (Poaceae: Bambusoideae)

Molecular Phylogenetics and Evolution, Год журнала: 2025, Номер unknown, С. 108327 - 108327

Опубликована: Март 1, 2025

Язык: Английский

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Cryptic Species Diversification of the Pedicularis siphonantha Complex (Orobanchaceae) in the Mountains of Southwest China Since the Pliocene

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Март 24, 2022

Morphological approaches often fail to delimit species in recently derived complexes. This can be exacerbated historical collections which may have lost key features specimen preparation and preservation. Here, we examine the Pedicularis siphonantha complex, endemic Mountains of Southwest China. complex is characterized by its red/purple/pink long-tubular corolla, twisted, beaked galea. However, herbarium specimens are difficult identify species. Molecular using nrITS or nuclear ribosomal internal transcribed spacer (nrITS) + plastid DNA (ptDNA) been successfully used for identification Pedicularis. To resolve taxonomic confusion reconstructed phylogenies four loci (matK, rbcL, trnH-psbA, trnL-F). recover as much phylogenetic history possible, sampled individuals at population level. Topological incongruence between ptDNA datasets was recovered clades including two widely distributed species, milliana tenuituba. Based on morphological, geographical, genetic evidence, suggest that hybridization/introgression has occurred P. sigmoidea/Pedicularis sp. 1 Yulong Snow Mountain Lijiang, northwest Yunnan, tenuituba leptosiphon Ninglang, Yunnan. After removing conflicting regions dolichosiphon (ptDNA), concatenated distinguish 11 undescribed from Jiaozi Mountains, respectively. Phylogeographical analyses indicate siponantha originated south Hengduan expanding north Himalayas Yunnan-Guizhou Plateau. Moreover, uplift Qinghai-Tibet Plateau climate oscillations driven further diversification complex.

Язык: Английский

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Plant diversity and ecology on the Qinghai–Tibet Plateau

Journal of Systematics and Evolution, Год журнала: 2021, Номер 59(6), С. 1139 - 1141

Опубликована: Ноя. 1, 2021

The Qinghai–Tibet Plateau (QTP) comprises a platform (sometimes called the sensu stricto), Himalayas, and Hengduan Mountains (Liang et al., 2018; Mao 2021). latter two parts adjacent highlands are also Pan-Himalaya. Numerous plants distributed there with many endemic species, probably because of high diverse landscapes created by continuous geological climatic activities (Favre 2015; As well known biodiversity hotspot alpine in world (Sun 2017), studies have been conducted on evolutionary origin ecological adaptation those species occurring QTP (e.g., Wen 2014, 2019; Zhang 2019). In present special issue, we collected 15 related papers this topic. Among them, invited reviews. al. (2021) provide comprehensive review diversity QTP. Especially, they outlined major disputes likely causes research topic, including circumscribing naming QTP, uplifts, dating molecular phylogenetic trees, non-causal correlations between uplifts diversification unified ice sheet. authors summarized genomic advancements to high-altitude both animals. Tong reviewed reproductive strategies animal-pollinated involving pollination system, pollen limitation, self-pollination, sexual system. region, 95.4% pollinated insects (i.e., bees, moths, butterflies, flies) only 4% vertebrates bats birds). Self-pollination through self-compatibility shift from outcrossing has become an effective strategy overcome limitation plants. other 13 aimed address flora three lines evidence: genomics, ecology, paleobotany. We hope that collection these will increase our understanding origin, speciation, Because decreasing cost, it is becoming easy obtain numerous homologous sequences construct high-solved supported phylogeny for genera. Here, collect case studies. A phylogenomic analysis using nuclear plastome genes Zhou was peonies (Paeoniaceae, Paeonia L.). Their results suggest Paeoniaceae relict ancient lineage divergence close relatives late Cretaceous. common ancestor extant may survived Pan-Himalaya during ages. further evolved into subgenera seven sections widespread Northern Hemisphere. addition, oscillations since Pliocene promoted polyploidy speciation allotetraploids autotetraploids. Ye constructed species-rich bamboo genera (Poaceae) Himalayas based simplified genome sequences. They revealed discordance gene topologies extensive hybridization identified lineages. conclude reticulate evolution seems be Chen subtribe Gentianinae (Gentianaceae) regions transcriptomes. Similarly, found inconsistent relationships few clades genes. Both incomplete sorting account discordant relationships. duplication events several nodes. Therefore, might together facilitated addition previously assumed geographic isolation. habitats chances fast adaptive evolution. publish works. Based data, Li (2021b) examined cryptic ginger Roscoea tibetica Batalin (Zingiberaceae) deeply diverged However, flow occurred second contact lineages after initial divergence. For aspens high- low-altitude regions, however, (2021a) clear hybrid zone recovered contacting region species. were experience positive natural selection play important role history Such strong posted arid habitat exist lower used transcriptome data examine one algae. Compared closely algae, involved antioxidative response, DNA repair, translational/post-translational modifications show possibly abiotic stresses, example, UV-B radiation All isolation, (especially stresses), there. It remains interesting topic explore how adapt pollination, climate, functional traits. Harsh environments such as low temperature, wind, solar radiation, change pollinator spectrum Pi compared animal composition pollinators spring-flowering shrub Elaeagnus umbellata Thunb. (Elaeagnaceae) along altitudinal gradients Mountains. flowers individuals became smaller longer floral tubes more nectar sucrose. Correspondingly, number bee decreased while sunbird increased. obvious association altitude, traits, pollinators. paper, He drought distribution limit evergreen oak (Quercus pannosa Hand.-Mazz. s.l.) dry valleys SE Himalaya. measured leaf traits non-monsoon monsoon seasons. growth at stage but increased season. duration factor determining third Zou explored relationship relatedness distributions Rhododendron had trait similarity. convergent among similar distributions. shape coexistence gradients. Paleontology provides direct evidence altitude time. recent past, fossils tropical or subtropical discovered central which suggested climate some subregions very warm humid should not age when formed (Su 2020). four papers. genus Illigera Blume (Hernandiaceae) Africa Asia. first fossil record reported western North America. Wang 10 fruits Eocene. These could placed under eocenica Manchester & O'Leary, America This finding indicates warm, floristic link Del Rio Cissampelos L. Menispermites Lesq. family Menispermaceae Middle Eocene now characterized pantropical temperate distribution. Previous Europe study connection Europe. (2021c) Cercis (Fabaceae) Miocene sediments northeastern currently shows intercontinental disjunct Hemisphere (Li paleo-altitude inferred less than 2400 m stage. include report foot southern Himalaya (Hazra Three reports comprise Miocene. showed connections their historical findings before (Jia Xu Tang Su 2021) still relatively altitudes stages altitudes. total never uplifted elevation certain each subregion subjected different (Mao order fully understand histories adaptations all exemplified here listed reviews 2021; encouraged future (also see Anderson Song, following especially enforced: (1) delimitation statistical analyses morphological population genetic data; (2) pattern radiation; (3) mechanism allelic variation adaptation; (4) linking community; (5) floras

Язык: Английский

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Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Окт. 27, 2022

Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of phylogeography evolutionary history plants there remains limited. The genus Heteroplexis (Asteraceae) is one typical representative isolated by habitat islands, also an endangered endemic to China. In this study, species-level phylogeographic analysis was conducted using restriction site-associated DNA sequencing (RADseq). genetic structure showed a clear consistent with current species boundaries H. microcephala, incana, vernonioides, sericophylla, impressinervia. significant global (R = 0.37, P < 0.01) regional 0.650.95, 0.05) isolation distance (IBD) signals among indicate strong geographic mountains, which may result chronically restricted gene flow increased drift differentiation. Furthermore, suggested southward migration since last glacial period. Demographic revealed mountains as refuge for species. Finally, both Treemix ABBA-BABA statistic detected historical between Significant long-term stability effective population size (Ne) together explain high genome-wide (π 0.05370.0838). However, recent collapse Ne, widespread inbreeding within populations, contemporary suggest that probably facing risk loss. Our results help understand guide conservation.

Язык: Английский

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Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

Ecology and Evolution, Год журнала: 2022, Номер 12(8)

Опубликована: Июль 29, 2022

The Andean plant endemic

Язык: Английский

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Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae)

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Дек. 4, 2023

Neomicrocalamus and Temochloa are closely related to bamboo genera. However, when considered with newly discovered morphologically similar material from China Vietnam, the phylogenetic relationship among these three groups was ambiguous in analyses based on DNA regions. Here, as a means of investigating relationships exploring potential sources genomic conflicts, we present phylogenomic examination whole plastome, single-nucleotide polymorphism (SNP), single-copy nuclear (SCN) gene datasets. Three different hypotheses were found. The inconsistency is attributed combination incomplete lineage sorting introgression. origin bamboos introgressive hybridization between liliana (which contributed 80.7% genome) prainii (19.3%), indicating that closer T. genetics. more morphology distribution elevation also imply bamboos.

Язык: Английский

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Yushania dezhui (Poaceae, Bambusoideae), a new bamboo species from Yunnan, China

PhytoKeys, Год журнала: 2024, Номер 246, С. 1 - 14

Опубликована: Авг. 16, 2024

A new bamboo species, Yushania dezhui , from Kunming, Yunnan, China is described and illustrated in this paper. The species used to be misidentified as Y. polytricha . Based on careful comparison of morphological features molecular phylogeny evidence, we confirmed its identity a member the genus resembles maculata weixiensis several aspects, such culm height branch complement structure. However, glabrous leaf sheaths internodes, absence auricles oral setae most foliage leaves, except one-year-old pubescence adaxial surface leaves limestone habitat preference can readily distinguish related taxa. Moreover, emphasise that individuals various populations markers with different inheritance patterns for reconstruction should included discovery, especially plant groups complex evolutionary histories.

Язык: Английский

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New insights into intergeneric relationships of Hickeliinae (Poaceae: Bambusoideae) revealed by complete plastid genomes

Plant Diversity, Год журнала: 2022, Номер 45(2), С. 125 - 132

Опубликована: Июнь 9, 2022

The Hickeliinae (Poaceae: Bambusoideae) is an ecologically and economically significant subtribe of tropical bamboos restricted to Madagascar, Comoros, Reunion Island, a small part continental Africa (Tanzania). Because these rarely flower, field identification challenging, inferring the evolutionary history from herbarium specimens even more so. Molecular phylogenetic work critical understanding this group bamboos. Here, comparative analysis 22 newly sequenced plastid genomes showed that members all genera share evolutionarily conserved plastome structures. We also determined sequences are informative for reconstructions. Phylogenetic monophyletic, except Nastus, which paraphyletic forms two distant clades. type species Nastus (Clade II) endemic Island not closely related other sampled Madagascar VI). Clade VI (Malagasy Nastus) sister Sokinochloa + Hitchcockella clade V), both clades have clumping habit with short-necked pachymorph rhizomes. monotypic Decaryochloa remarkable in having longest floret Bambuseae distinct IV. III, has highest generic diversity, consists Cathariostachys, Perrierbambus, Sirochloa, Valiha, morphologically diverse. This provides resources further genetic phylogenomic studies Hickeliinae, understudied bamboo.

Язык: Английский

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