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学者姓名：刘仲健
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Abstract ：
Genes that introgress between species can influence the evolutionary and ecological fate of recipients exposed to novel environments. However, key questions on the patterns and molecular mechanisms of introgression in perennial herbaceous plants, which enable distantly related invasive species to thrive in extreme habitats, remain largely unanswered. Here, we report unidirectional introgression from the local species Dendrobium huoshanense to the distantly related invasive species Dendrobium catenatum (Den-drobium officinale) in lithophytic habitats of eastern China. The introgressed regions, which comprise approximately 1% of the genome, contain genes that regulate responses to drought, cold, and metal-ion stresses. Notably, introgressed loci such as CDPK, HHP, PIF, BRI1, and FYshow distinct selection signatures and differential expression compared with their paralogs, each playing a distinct role in drought and cold-stress responses. In addition, CIPK23, PDR9, and HAM demonstrate differential expression relative to their paralogous genes and alleles within introgressed loci, indicating their potential involvement in responses to metal-ion stress. Introgression thus facilitates the colonization of arid, metal-enriched sedimentary habitats by D. catenatum. These findings enhance our understanding of Orchidaceae evolution and reveal the evolutionary role of unidirectional introgression in the adaptation of perennial herbaceous plants to extreme environments.
Keyword ：
Dendrobium Dendrobium distantly related species distantly related species introgression introgression invasive species invasive species metal-ion stress metal-ion stress
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| GB/T 7714 | Jiao Zhenbin , Ren Zhiyao , Hu Chao et al. Unidirectional genomic introgression facilitates the colonization of an invasive orchid in arid, metal-enriched sedimentary habitats [J]. | PLANT COMMUNICATIONS , 2026 , 7 (1) . |
| MLA | Jiao Zhenbin et al. "Unidirectional genomic introgression facilitates the colonization of an invasive orchid in arid, metal-enriched sedimentary habitats" . | PLANT COMMUNICATIONS 7 . 1 (2026) . |
| APA | Jiao Zhenbin , Ren Zhiyao , Hu Chao , Ma Xiaokai , Zhang Guo-Qiang , Chen Li-Jun et al. Unidirectional genomic introgression facilitates the colonization of an invasive orchid in arid, metal-enriched sedimentary habitats . | PLANT COMMUNICATIONS , 2026 , 7 (1) . |
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BackgroundOrchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study.DescriptionRecently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses.ConclusionOrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.
Keyword ：
Cymbidium Cymbidium Genome Genome Orchid Orchid OrchidBase OrchidBase Transcriptome Transcriptome Whole-genome sequencing Whole-genome sequencing
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| GB/T 7714 | Chen, You-Yi , Sun, Ye , Li, Chung-, I et al. OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis [J]. | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
| MLA | Chen, You-Yi et al. "OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis" . | BMC PLANT BIOLOGY 25 . 1 (2025) . |
| APA | Chen, You-Yi , Sun, Ye , Li, Chung-, I , Lin, Shao-Ting , Zheng, Hao-Chen , Zhang, Zhe-Bin et al. OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis . | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
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The GATA transcription factors are a class of DNA-binding proteins that control the expression of target genes by binding to the promoter regions of DNA, thereby affecting the growth and development of plants. In recent years, GATA genes have been discovered and functionally characterized in many plant species. However, there is limited annotation information for GATA genes in the genus Acorus. This study identified 38 and 20 GATA genes in Acorus calamus and A. gramineus, respectively. Based on a phylogenetic tree, they were classified into four subfamilies (I, II, III, and IV). At the same time, an analysis of the GATA domain and motifs revealed that the domains are relatively conserved across all subfamilies. A multiple sequence alignment showed that almost all GATA proteins are highly conserved at the LCNACG site. An analysis of cis-elements, collinearity, and protein-protein interaction networks provided insights into the response mechanisms under biotic stress. Additionally, we found significant changes in the expression of GATA in A. gramineus under drought and salt stress. These results provide useful information for future functional analyses of GATA genes and contribute to a better understanding of the stress response mechanisms and molecular breeding directions in the Acorus species.
Keyword ：
abiotic stress abiotic stress Acorus Acorus expression pattern analysis expression pattern analysis GATA gene family GATA gene family
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| GB/T 7714 | Ma, Liang , Zhou, Cheng-Yuan , Gong, Chen-Yu et al. Genome-Wide Identification of GATA Transcription Factors in Acorus and Expression Patterns Under Abiotic Stress [J]. | HORTICULTURAE , 2025 , 11 (4) . |
| MLA | Ma, Liang et al. "Genome-Wide Identification of GATA Transcription Factors in Acorus and Expression Patterns Under Abiotic Stress" . | HORTICULTURAE 11 . 4 (2025) . |
| APA | Ma, Liang , Zhou, Cheng-Yuan , Gong, Chen-Yu , He, Yao , Chang, Meng-Lin , Fu, Hou-Hua et al. Genome-Wide Identification of GATA Transcription Factors in Acorus and Expression Patterns Under Abiotic Stress . | HORTICULTURAE , 2025 , 11 (4) . |
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The MADS-box transcription factor gene family is essential for the differentiation and development of floral organs. Genome-wide and transcriptome data from Phoebe bournei provide the foundation for studying its floral development. In this study, phylogenetic relationships, protein characteristics, conserved domains, gene structures, and cis-acting elements in promoter regions of P. bournei MADS-box genes were systematically analyzed through bioinformatics methodologies. A total of 69 PbMADS genes were identified and classified into 15 subfamilies based on their phylogenetic relationships. The potential functions of these genes were inferred based on transcriptomic data and GO classification. In addition, we selected genes from the ABCDE model to analyze protein interactions and performed RT-qPCR to analyze their expression in each floral organ whorl (outer tepals, inner tepals, stamens, and carpel). Based on these analyses, we rationally constructed a model for the floral organ development in P. bournei. This study, thus, provides a theoretical reference for germplasm innovation in P. bournei and offers insights into the floral development in other Lauraceae species.
Keyword ：
ABCDE model ABCDE model flowering flowering Lauraceae Lauraceae MADS-box MADS-box Phoebe bournei Phoebe bournei
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| GB/T 7714 | Bi, Yuanyang , Fu, Houhua , Jiang, Zihan et al. Integrating Genome and Transcriptome-Wide Data to Explore the Expression Dynamics of ABCDE-like MADS-Box Genes in Phoebe bournei Floral Organs [J]. | FORESTS , 2025 , 16 (2) . |
| MLA | Bi, Yuanyang et al. "Integrating Genome and Transcriptome-Wide Data to Explore the Expression Dynamics of ABCDE-like MADS-Box Genes in Phoebe bournei Floral Organs" . | FORESTS 16 . 2 (2025) . |
| APA | Bi, Yuanyang , Fu, Houhua , Jiang, Zihan , Jiang, Yan , You, Limei , Li, Can et al. Integrating Genome and Transcriptome-Wide Data to Explore the Expression Dynamics of ABCDE-like MADS-Box Genes in Phoebe bournei Floral Organs . | FORESTS , 2025 , 16 (2) . |
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Colorful leaves, particularly red ones, represent an important ornamental trait of Cymbidium ensifolium. However, the mechanisms underlying red leaf formation in C. ensifolium are not well understood. In this study, we examined the phenotypic, physiological, and transcriptomic differences between red and green leaves at various developmental stages. We found that red leaves exhibited significantly lower levels of chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll across all stages, while anthocyanin levels were notably higher. Ultrastructural analysis revealed abnormalities in the chloroplast structure of red leaves, including fewer chloroplasts, ruptured thylakoid membranes, an indistinct matrix layer, and the accumulation of osmiophilic particles, which led to reduced photosynthetic capacity. In addition, transcriptomic analysis showed significant differences in the expression of genes related to anthocyanin biosynthesis, chlorophyll metabolism, and photosynthesis between red and green leaves at different stages of growth. Therefore, we suggest that red leaf formation in C. ensifolium is driven by reduced expression of chlorophyll metabolism genes, resulting in impaired chloroplast development and chlorophyll synthesis, while upregulation of anthocyanin biosynthesis genes promotes anthocyanin accumulation, leading to the red coloration. These findings provide valuable insights into color formation mechanisms of red leaves in C. ensifolium.
Keyword ：
Anthocyanin Anthocyanin Chlorophyll metabolism Chlorophyll metabolism Cymbidium ensifolium Cymbidium ensifolium Red leaves Red leaves
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| GB/T 7714 | Xiong, Longwei , Ou, Yue , Li, Peng et al. Comparative physiology and transcriptome analysis revealed the mechanisms underlying red leaf formation in Cymbidium ensifolium [J]. | SCIENTIA HORTICULTURAE , 2025 , 340 . |
| MLA | Xiong, Longwei et al. "Comparative physiology and transcriptome analysis revealed the mechanisms underlying red leaf formation in Cymbidium ensifolium" . | SCIENTIA HORTICULTURAE 340 (2025) . |
| APA | Xiong, Longwei , Ou, Yue , Li, Peng , Tian, Yang , Guo, Liting , Li, Jinjin et al. Comparative physiology and transcriptome analysis revealed the mechanisms underlying red leaf formation in Cymbidium ensifolium . | SCIENTIA HORTICULTURAE , 2025 , 340 . |
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LBD transcription factors are critical regulators of plant growth and development. Recent studies highlighted their significant role in the transcriptional regulation of plant growth and metabolism. Thus, identifying the CeLBD gene in Cymbidium ensifolium, a species abundant in floral scent metabolites, could provide deeper insights into its functional significance. A total of 34 LBD genes were identified in C. ensifolium. These CeLBDs fell into two major groups: Class I and Class II. The Class I group contained 30 genes, while the Class II group included only 4 genes. Among the 30 Class I genes, several genes in the Ie branch exhibited structural variations or partial deletions (CeLBD20 and CeLBD21) in the coiled-coil motif (LX6LX3LX6L). These changes may contribute to the difficulty in root hair formation in C. ensifolium. The variations may prevent normal transcription, leading to low or absent expression, which may explain the fleshy and corona-like root system of C. ensifolium without prominent lateral roots. The expansion for CeLBDs was largely due to special WGD events in orchids during evolution, or by segmental duplication and tandem duplication. CeLBDs in different branches exhibit similar functions and expression characteristics. Promoter analysis enriched environmental response elements, such as AP2/ERF, potentially mediating the specific expression of CeLBDs under different stresses. CeLBDs were predicted to interact with multiple transcription factors or ribosomal proteins, forming complex regulatory networks. CeLBD20 was localized in the cytoplasm, it may act as a signaling factor to activate other transcription factors. CeLBD6 in Class II was significantly up-regulated under cold, drought, and ABA treatments, suggesting its role in environmental responses. Furthermore, metabolic correlation analysis revealed that its expression was associated with the release of major aromatic compounds, such as MeJA. These findings offer valuable insights for further functional studies of CeLBD genes in C. ensifolium.
Keyword ：
flower development flower development LBD gene family LBD gene family Orchidaceae Orchidaceae scent formation scent formation structure variation structure variation
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| GB/T 7714 | Peng, Yukun , Zhan, Suying , Tang, Feihong et al. Characterization of LBD Genes in Cymbidium ensifolium with Roles in Floral Development and Fragrance [J]. | HORTICULTURAE , 2025 , 11 (2) . |
| MLA | Peng, Yukun et al. "Characterization of LBD Genes in Cymbidium ensifolium with Roles in Floral Development and Fragrance" . | HORTICULTURAE 11 . 2 (2025) . |
| APA | Peng, Yukun , Zhan, Suying , Tang, Feihong , Zhao, Yuqing , Wu, Haiyan , Li, Xiangwen et al. Characterization of LBD Genes in Cymbidium ensifolium with Roles in Floral Development and Fragrance . | HORTICULTURAE , 2025 , 11 (2) . |
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A new species of Cymbidium (Orchidaceae) from Hubei Province, China, is described as C. huikanran, which is like C. kanran and C. faberi. Morphologically, it can be distinguished from the former by its basally non-articulate leaves, and arching, short scape; from the latter by its narrowly oblong-lanceolate sepals and narrowly ovate-lanceolate petals. Molecular analysis based on nuclear ribosomal ITS and the plastid sequences (matK and rbcL) clearly indicated that is a new species as a sister to C. faberi in C. subgenus Jensoa.
Keyword ：
Chinese orchids Chinese orchids Cymbidiinae Cymbidiinae Cymbidium subgenus Jensoa Cymbidium subgenus Jensoa new species new species
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| GB/T 7714 | Li, Jun , Zeng, Meng-yao , Chen, Gui-zhen et al. Cymbidium huikanran (Orchidaceae; Epidendroideae), a new species from China: evidence from morphology and molecular analyses [J]. | PHYTOTAXA , 2025 , 683 (2) : 177-183 . |
| MLA | Li, Jun et al. "Cymbidium huikanran (Orchidaceae; Epidendroideae), a new species from China: evidence from morphology and molecular analyses" . | PHYTOTAXA 683 . 2 (2025) : 177-183 . |
| APA | Li, Jun , Zeng, Meng-yao , Chen, Gui-zhen , Li, Yuan-yuan , Liu, Zhong-jian , Lan, Siren . Cymbidium huikanran (Orchidaceae; Epidendroideae), a new species from China: evidence from morphology and molecular analyses . | PHYTOTAXA , 2025 , 683 (2) , 177-183 . |
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Angraecum sesquipedale, also known as Darwin's orchid, possesses an exceptionally long nectar spur. Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis, later identified as Xanthopan praedicta. In this plant-pollinator interaction, the A. sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes (R1R2C = N-OH) to attract crepuscular and nocturnal pollinators. The molecular mechanism of oxime biosynthesis remains unclear in orchids. Here, we present the chromosome-level genome of A. sesquipedale. The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes. Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A. sesquipedale genome nor the genomes of other members of the orchid family. Metabolomic analysis of the A. sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage. By integrating metabolomic and transcriptomic correlation approaches, flavin-containing monooxygenases (FMOs) encoded by six tandem-repeat genes in the A. sesquipedale genome are identified as catalyzing the formation of oximes present. Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis. We designate these FMOs as orchid oxime synthases 1-6. The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin's orchid provide new insights into the convergent evolution of biosynthetic pathways.
Keyword ：
Angraecum sesquipedale Angraecum sesquipedale convergent evolution convergent evolution CYP79 absence CYP79 absence flavin monooxygenase flavin monooxygenase white floral scent white floral scent whole genome sequence whole genome sequence
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| GB/T 7714 | Jiang, Kai , Moller, Birger Lindberg , Luo, Shaofan et al. Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid [J]. | MOLECULAR PLANT , 2025 , 18 (3) : 392-415 . |
| MLA | Jiang, Kai et al. "Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid" . | MOLECULAR PLANT 18 . 3 (2025) : 392-415 . |
| APA | Jiang, Kai , Moller, Birger Lindberg , Luo, Shaofan , Yang, Yu , Nelson, David R. , Neilson, Elizabeth Heather Jakobsen et al. Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid . | MOLECULAR PLANT , 2025 , 18 (3) , 392-415 . |
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Sucrose non-fermenting 1-related protein kinases (SnRKs) are crucial for modulating plant responses to abiotic stresses, linking metabolism with stress signaling pathways. Investigating the roles and stress responses of SnRKs in plants paves the way for developing stress-tolerant strategies in orchid species. Here, 362 SnRK members were identified from nine current orchid genomes, highlighting the conservation of these genes in evolution. Among these, 33 CeSnRKs were found across 20 chromosomes of C. ensifolium genome. Multiple duplication events increased the complexity of CeSnRKs during independent evolution. Moreover, distinct functional domains beyond the kinase domain differentiated the subfamilies. These multi-copy members existed tissue specific expressions falling into 6 main trends, especially CeSnRK1, CeCIPK9, CeCIPK23 displayed a strict floral expression. ABA-related elements were enriched in the promoters of CeSnRKs, and stress-related miRNA binding sites were identified on partial CeSnRKs. Consequently, most CeSnRKs exhibited up-regulated expression during ABA treatment. Several genes, such as CeSnRK2.1 and CeCIPK28 involved growth and development at different times and various tissues. The up-regulation of SnRK2.1, along with high expression of SnRK1 and CIPK27 under drought stress, and the differential expression patterns of CeSnRKs under cold stress, underscore the involvement of CeSnRK genes in different stress responses. Additionally, the diverse interactions of CeSnRKs with proteins highlighted a multifaceted functional network.These findings offer valuable insights for the future functional characterization formation of CeSnRKs and the adaptive evolution of genes in orchids.
Keyword ：
ABA response ABA response Abiotic stress Abiotic stress Evolution Evolution Expression patterns Expression patterns Orchidaceae Orchidaceae
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| GB/T 7714 | Zheng, Ruiyue , Zhao, Kai , Chen, Jiemin et al. Genomic signatures of SnRKs highlighted conserved evolution within orchids and stress responses through ABA signaling in the Cymbidium ensifolium [J]. | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
| MLA | Zheng, Ruiyue et al. "Genomic signatures of SnRKs highlighted conserved evolution within orchids and stress responses through ABA signaling in the Cymbidium ensifolium" . | BMC PLANT BIOLOGY 25 . 1 (2025) . |
| APA | Zheng, Ruiyue , Zhao, Kai , Chen, Jiemin , Zhu, Xuanyi , Peng, Yukun , Shen, Mingli et al. Genomic signatures of SnRKs highlighted conserved evolution within orchids and stress responses through ABA signaling in the Cymbidium ensifolium . | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
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The fully mycoheterotrophic orchid Gastrodia Brown (1810: 330; Gastrodieae, Epidendroideae) comprises 103 species (POWO, 2024) and is widespread from India, southern China throughout Southeast Asia to Japan, eastern Australia, New Zealand, Pacific islands, Madagascar-Mascarene Islands and tropical Africa (Pridgeon et al. 2005, Chase et al. 2015, Chen et al. 2023). In China the members of this genus are distributed mainly in southern China, including Fujian, Guangxi, Guangdong, Hong Kong, Hainan, Yunnan and Taiwan (Liu et al. 2021, Zhou et al. 2021, Huang et al. 2021). On Hainan Island, four species, namely Gastrodia longitubularis Meng, Song & Luo (2007: 23), G. punctata Aver. (2006: 21, Lu et al. 2017), G. menghaiensis Tsi & Chen (2021: 703), and G. bawanglingensis Z.H.Chen, Z.Y.Zhang & X.Q.Song in Chen et al. (2023: 39) have been reported from the tropical rainforest. Here, we add another new species to this genus. This new species was found during our field investigation in the karst forests of Hainan Island. After undertaking a review of the literature (Meng et al. 2008, Chen et al. 2009, Chen et al. 2023, POWO 2024), we confirmed that it is a new species, described below.
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| GB/T 7714 | Huang, Ming-zhong , Wei, Chunyi , Li, Ruyi et al. Gastrodia exianlingensis (Gastrodieae, Epidendroideae), a new species of Orchidaceae from Hainan, China [J]. | PHYTOTAXA , 2025 , 689 (1) : 158-162 . |
| MLA | Huang, Ming-zhong et al. "Gastrodia exianlingensis (Gastrodieae, Epidendroideae), a new species of Orchidaceae from Hainan, China" . | PHYTOTAXA 689 . 1 (2025) : 158-162 . |
| APA | Huang, Ming-zhong , Wei, Chunyi , Li, Ruyi , Tu, Xiongde , Zhao, Xuewei , Lan, Siren et al. Gastrodia exianlingensis (Gastrodieae, Epidendroideae), a new species of Orchidaceae from Hainan, China . | PHYTOTAXA , 2025 , 689 (1) , 158-162 . |
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