Xue-Jun Ge

Xue-Jun Ge
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Xue-Jun verified their affiliation via an institutional email.
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Xue-Jun verified their affiliation via an institutional email.
South China Botanical Garden

Ph D.

About

242
Publications
77,568
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7,128
Citations
Additional affiliations
South China Botanical Garden, Guangzhou, China
Position
  • Professor (Full)
January 2008 - March 2017
South China Botanical Garden, Guangzhou, China
Position
  • Professor (Full)
July 2005 - December 2007
Sun Yat-sen University
Position
  • Professor

Publications

Publications (242)
Article
The family Primulaceae s.l. is estimated to comprise approximately 60 genera and 2600 species worldwide. Although extensive research has been conducted on the family Primulaceae and its subfamily boundaries, there is a lack of systematic studies utilizing complete plastid genome data, leading to uncertainties in the phylogenetic positions of certai...
Article
Full-text available
Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitat-adapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing; however, molecular resources for the genus still need improvement. We conducted a genome skimming ap...
Article
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Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome‐wide patterns of diversity, especially in long‐lived semelparous plants. Puya raimondii is a high‐altitude semelpar...
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Musa ornata and Musa velutina are members of the Musaceae family and are indigenous to the South and Southeast Asia. They are very popular in the horticultural market, but the lack of genomic sequencing data and genetic studies has hampered efforts to improve their ornamental value. In this study, we generated the first chromosome-level genome asse...
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Background Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. Howev...
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Background The ephemeral flora of northern Xinjiang, China, plays an important role in the desert ecosystems. However, the evolutionary history of this flora remains unclear. To gain new insights into its origin and evolutionary dynamics, we comprehensively sampled ephemeral plants of Brassicaceae, one of the essential plant groups of the ephemeral...
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The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library...
Article
Plant odours are central for pollinator attraction. This is particularly true in obligate brood site pollination mutualisms. However, we know little about the evolution of olfactory signalling in these mutualisms. Here, we investigate geographic variation of floral odour in the obligate host-specific brood site pollination mutualism between Ficus h...
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Global environmental changes drive biodiversity loss and community compositional change. Yet whether and how both factors simultaneously impact biomass dynamics in natural ecosystems remains elusive, especially considering their multidimensional effects (e.g., taxonomic, functional, and phylogenetic) over spatial scales. To fill this knowledge gap,...
Article
Aim: The equator-to-poles decline in the number of species, namely the latitudinal diversity gradient (LDG), is the most conspicuous pattern in biology, yet the underlying mechanisms of this pattern remain controversial. Species dispersal could have strong effects on large-scale species distributions but has rarely been considered in understanding...
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Musa acuminata is a main wild contributor to banana cultivars. Here, we reported a haplotype-resolved and telomere-to-telomere reference genome of M. acuminata by incorporating PacBio HiFi reads, Nanopore ultra-long reads, and Hi-C data. The genome size of the two haploid assemblies was estimated to be 469.83 Mb and 470.21 Mb, respectively. Multipl...
Preprint
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Endemic to the Neotropics, Monnina is the second largest genus of Polygalaceae, yet little is known about its phylogenetic history, biogeog-raphy, and morphological character evolution. To address these knowledge gaps, we conducted Bayesian and maximum likelihood (ML) analyses of nuclear ITS and plastid trnL-F regions to test the monophyly of Monni...
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Banana is one of the most important crops of the world. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half of the global banana production, thereby are of great significance for human societies. However, until now, the high-quality haplotype-resolved reference genome was still undecoded for banana...
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Background Lysimachia L., the second largest genus within the subfamily Myrsinoideae of Primulaceae, comprises approximately 250 species worldwide. China is the species diversity center of Lysimachia, containing approximately 150 species. Despite advances in the backbone phylogeny of Lysimachia, species-level relationships remain poorly understood...
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Lomas formations or "fog oases" are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world's deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA infor...
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DNA barcoding is a well-established tool for rapid species identification and biodiversity monitoring. A reliable and traceable DNA barcode reference library with extensive coverage is necessary but unavailable for many geographic regions. The arid region in northwestern China, a vast area of about 2.5 million km2 , is ecologically fragile and ofte...
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Background and aims: Artemisia is a mega-diverse genus consisting of ca. 400 species. Despite its medicinal importance and ecological significance, a well-resolved phylogeny for global Artemisia, a natural generic delimitation and infrageneric taxonomy heretofore remain missing, owing to the obstructions from limited taxon sampling and insufficien...
Article
Hyperdominant trees in Amazonia account for half of the individual trees (>10 cm dbh) in the forest, and thus play a crucial role in ecosystem dynamics. However, several of these widespread hyperdominant species may be complexes hiding cryptic diversity that can affect species richness estimates and conservation priorities. Here, we study the intra...
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Background Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical...
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Background Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. M...
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Background Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula , an important ornamental taxon, is more limited than the information on their nuclear and plas...
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Background Tribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly seq...
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The Andean plant endemic Puya is a striking example of recent and rapid diversifica-tion from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of t...
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Genome size varies 2400‐fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat ‘communities’ are analogous to those structuring ecological communiti...
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Puya raimondii is an endemic species from the high Andes of Peru and Bolivia. In Peru it is distributed from 8.068501°S, 16.170280°W to 16.180580°S, 70.658873°W, between 3600 and 4800 m, living in extreme climatic conditions typical of the Puna, where it plays an important ecological role. Despite the wide distribution of P. raimondii populations i...
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Background Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. Findings Using Oxford Nanopore Technologies, ch...
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Background and Aims Ongoing global warming is a challenge for humankind. A series of drastic climatic changes have been proven to have occurred throughout the Cenozoic based on a variety of geological evidence, which helps to better understand our planet’s future climate. Notably, extant biomes have recorded drastic environmental shifts. The climat...
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The strength of biodiversity-biomass production relationships increases with increasing environmental stress and time. However, we know little about the effects of abiotic (e.g., climate) and biotic (e.g., species pool and community composition) factors on this trend. Whether variation in biomass production is best explained by phylogenetic diversi...
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Background and aims: The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative co...
Article
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Background Musaceae is an economically important family consisting of 70-80 species. Elucidation of the interspecific relationships of this family is essential for a more efficient conservation and utilization of genetic resources for banana improvement. However, the scarcity of herbarium specimens and quality molecular markers have limited our und...
Article
Climate warming and atmospheric nitrogen deposition threaten plant biodiversity in mountain ecosystems; however, their influences on soil microbial diversity and community composition remain poorly understood. We conducted randomized block factorial experiments in three mountain meadows of different elevations on Yulong Snow Mountain, China. These...
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Background: The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. How‑ ever, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential plant groups, the tribe Perseeae (Lauraceae). Results: Our plastid tree...
Preprint
Full-text available
Background Ensete glaucum (2 n = 2 x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana ( Musa ). A high-quality reference genome sequence of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete , the Musaceae, and more widely in the Zingiberales. Findings Using...
Preprint
Full-text available
Genome size varies 2,400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants’ environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat ‘communities’ are analogous to those structuring ecological communit...
Article
Full-text available
The complete chloroplast genome of Isatis minima, a typical ephemeral plant of Brassicaceae in the Central Asia desert, was sequenced and characterized in this study. The genome 153,642 bp in size, contains a typical quadripartite genome organization including LSC and SSC regions of 83,423 bp and 17,709 bp, and two copies of the IR regions of 26,25...
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Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic‐tree generated using V.PhyloMaker, a barcode‐tree generated using rbcL+matK+trnH‐psbA, and a plastome‐t...
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Lithocarpus hancei (Benth.) Rehd is a widely distributed evergreen tree with broad-leaves that dominates the lower stories of the forest in China. Here, we sequenced and assembled the complete chloroplast genome of L. hancei. The genome is 161,304 bp with one large single copy (LSC: 90,585 bp), one small single copy (SSC: 18,959 bp), and two invert...
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Aims Species diversity-productivity relationships (DPR) in natural ecosystems have been well documented in the literature. However, biotic and abiotic factors that determine their relationships are still poorly understood, especially under future climate change scenarios. Methods Randomized block factorial experiments were performed in three meado...
Article
Puya raimondii, the Queen of the Andes, is an endangered high Andean species in the Bromeliaceae family. Here, we report its first genome to promote its conservation and evolutionary study. Comparative genomics showed P. raimondii diverged from Ananas comosus about 14.8 million years ago, and the long terminal repeats were likely to contribute to t...
Preprint
Phylogenetic trees have been extensively used in community ecology. However, how the phylogenetic reconstruction affects ecological inferences is poorly understood. In this study, we reconstructed three different types of phylogenetic trees (a synthetic-tree generated using VPhylomaker, a barcode-tree generated using rbcL+matK+trnH-psbA and a genom...
Preprint
Full-text available
Ecological scale has been widely assumed to influence various biodiversity-productivity relationships in ecological communities; however, its robustness has not been extensively studied. In this study, we tested the scale dependency of biodiversity-productivity relationships by evaluating their direct linkages while considering other confounders, a...
Article
Full-text available
Aims Species diversity-productivity relationships in natural ecosystems have been well documented in the literature. However, biotic and abiotic factors that determine their relationships are still poorly understood, especially under future climate change scenarios. Methods Randomized block factorial experiments were performed in three meadows alon...
Preprint
Full-text available
The colonization success of a species depends on phenotypic plasticity, adaptive potential and population structure. Assessing their relative contributions during a colonization process is challenging, and a large-scale experiment had yet to be done. In this study, we attempted to tease apart their effects on the fitness of one of the most common p...
Article
Full-text available
Aims Phylogenetic diversity metrics can discern the relative contributions of ecological and evolutionary processes associated with the assembly of plant communities. However, the magnitude of the potential variation associated with phylogenetic methodologies, and its effect on estimates of phylogenetic diversity, remains poorly understood. Here, w...
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Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for i...
Article
Full-text available
Understanding the genetic basis underpinning local adaptation is one of the fundamental issues in ecological and evolutionary biology. In this study, we investigated the genomic basis underlying local adaptation of the Chinese wingnut (Pterocarya stenoptera C. DC). Our population genomic analyses revealed nine spatial genetic clusters across the cu...
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Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae...
Article
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The palm family (Arecaceae) is of high ecological and economic value, yet identification in the family remains a challenge for both taxonomists and horticulturalists. The family consists of approximately 2600 species across 181 genera and DNA barcoding may be a useful tool for species identification within the group. However, there have been few sy...
Article
Full-text available
Tropical race 4 of Fusarium oxysporum f. sp. cubense (FocTR4) is seriously threatening the banana industry worldwide. Resistant genotypes are present in wild relatives of banana, but little is known about the genetic and molecular mechanisms driving resistance responses. In this work, through in-depth expression analysis, we compared the responses...
Article
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Background: Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligon...
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The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera ( D. acuminata , D. peruviana , D. montana , D. ruiziana and D. mucronata ) in this study. These cp...
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Premise: Microsatellite primers were developed for Puya raimondii (Bromeliaceae), an endangered species distributed in the Andean Mountains of Bolivia and Peru. Methods and results: Genome skimming of P. raimondii, P. macrura, and P. hutchisonii resulted in the selection of 46 pairs of cross-species microsatellite markers. Of these, 12 microsate...
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Crop wild relatives (CWRs) play a key role in crop breeding by providing beneficial trait characteristics for improvement of related crops. CWRs are more efficiently used in breeding if the plant material is genetically characterized, but the diversity in CWR genetic resources has often poorly been assessed. Seven seed collections of Musa balbisian...
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The application of quantifying phylogenetic information into measures of forest β-diversity is increasing for investigating the underlying drivers of community assembly along environmental gradients. In terms of assessing evolutionary inferences of community processes, a variety of plant DNA barcodes has been widely used in phylogenetic diversity m...
Article
The Cornales is a relatively small but morphologically diverse order in the basal position of the Asterids clade. Previous study hypothesized that the order might have undergone ancient rapid radiation during the Cretaceous when major angiosperm lineages were established. We conducted the phylogenomic analysis of Cornales using 81 plastid genome se...
Article
The Northern Hemisphere was widely covered by a tropical flora (i.e., the Boretropical flora) in the Eocene and the evaluation of plant diversifications in the post-Boreotropical era has become an important challenge to understanding the modern biogeographic complexity in this vast region. Toxicodendron or the poison ivy genus of the sumac family h...
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Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mech...
Article
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To elucidate potential ecological and evolutionary processes associated with the assembly of plant communities, there is now widespread use of estimates of phylogenetic diversity that are based on a variety of DNA barcode regions and phylogenetic construction methods. However, relatively few studies consider how estimates o