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学者姓名：李明河
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Abstract ：
Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In this study, we sequenced and analyzed the complete plastome sequences of A. gracile and E. japonica for the first time, aiming to elucidate their plastome characteristics and phylogenetic relationships. Both plastomes exhibited a conserved quadripartite structure, with 158,358 bp in A. gracile and 152,432 bp in E. japonica, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: E. japonica lacked seven ndh genes (ndhC/D/F/G/H/I/K), whereas A. gracile retained a complete ndh gene set. Repetitive sequence analysis identified an abundance of simple sequence repeats (68 and 77), tandem repeats (43 and 30), and long repeats (35 and 40). Codon usage displayed a bias toward the A/U termination, with leucine and isoleucine being the most frequent. Selection pressure analysis indicated that 68 protein-coding genes underwent purifying selection (Ka/Ks < 1), suggesting evolutionary conservation of plastome protein-coding genes. Nucleotide diversity analysis highlighted six hypervariable regions (rps8-rpl14, rps16-trnQ(UUG), psbB-psbT, trnT(UGU)-trnL(UAA), trnF(GAA)-ndhJ, and ycf1), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. A. gracile formed a sister relationship with Mengzia foliosa and E. japonica, whereas Arundina graminifolia exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae.
Keyword ：
Anthogonium gracile Anthogonium gracile Arethusinae Arethusinae Eleorchis japonica Eleorchis japonica phylogenetic analysis phylogenetic analysis plastid genome plastid genome
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| GB/T 7714 | Gao, Xuyong , Chen, Yuming , Xu, Xiaowei et al. Characteristics and Phylogenetic Analysis of the Complete Plastomes of Anthogonium gracile and Eleorchis japonica (Epidendroideae, Orchidaceae) [J]. | HORTICULTURAE , 2025 , 11 (6) . |
| MLA | Gao, Xuyong et al. "Characteristics and Phylogenetic Analysis of the Complete Plastomes of Anthogonium gracile and Eleorchis japonica (Epidendroideae, Orchidaceae)" . | HORTICULTURAE 11 . 6 (2025) . |
| APA | Gao, Xuyong , Chen, Yuming , Xu, Xiaowei , Chen, Hongjiang , Xing, Bingcong , Pan, Jianli et al. Characteristics and Phylogenetic Analysis of the Complete Plastomes of Anthogonium gracile and Eleorchis japonica (Epidendroideae, Orchidaceae) . | HORTICULTURAE , 2025 , 11 (6) . |
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The Fagaceae family, comprising over 900 species, is an essential component of Northern Hemisphere forest ecosystems. However, genomic data for tropical and subtropical genera Castanopsis and Castanea remain limited compared to the well-studied oak. Here, we present chromosome-level genome assemblies of Castanopsis carlesii and Castanea henryi, with assembled genome sizes of 927.24 Mb (N50 = 1.57 Mb) and 780.10 Mb (N50 = 1.07 Mb), respectively, and repetitive sequence contents of 45.79% and 44.88%. Comparative genomic analysis revealed that the estimated divergence time between Castanopsis and Castanea was determined to be 48.3 Mya and provided evidence that both genera experienced only one of the ancient whole genome triplication event (gamma event) shared with most eudicots. The development of C. carlesii flower bracts and cupules was controlled by A- and E-class genes, suggesting that the cupules may originate from the bracts. Additionally, genes involved in sucrose and starch metabolism genes played distinct roles during C. carlesii fruit development. The amplification of the nucleotide-binding leucine-rich repeat (NLR) gene family in Fagaceae exhibited similarities, indicating that this expansion may be an adaptation to similar environmental pressures. This study provides valuable genomic resources for Asian Fagaceae and enhances our understanding of Fagaceae evolution.
Keyword ：
Fagaceae Fagaceae Genomics Genomics MADS-box genes MADS-box genes Resistance genes Resistance genes Sucrose-starch metabolism Sucrose-starch metabolism
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| GB/T 7714 | Tu, Xiong-De , Lin, Wen-Jun , Xin, Ya-Xuan et al. Genomic insights into Castanopsis carlesii and Castanea henryi: flower and fruit development and evolution of NLR genes in the beech-oak family [J]. | MOLECULAR HORTICULTURE , 2025 , 5 (1) . |
| MLA | Tu, Xiong-De et al. "Genomic insights into Castanopsis carlesii and Castanea henryi: flower and fruit development and evolution of NLR genes in the beech-oak family" . | MOLECULAR HORTICULTURE 5 . 1 (2025) . |
| APA | Tu, Xiong-De , Lin, Wen-Jun , Xin, Ya-Xuan , Fu, Hou-Hua , Zhou, Cheng-Yuan , Lin, Yi-Zhe et al. Genomic insights into Castanopsis carlesii and Castanea henryi: flower and fruit development and evolution of NLR genes in the beech-oak family . | MOLECULAR HORTICULTURE , 2025 , 5 (1) . |
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为解析石斛属（Dendrobium）灯笼组（Section Densiflora）物种的叶绿体基因组特征及其系统发育关系，本研究采用高通量测序技术首次对该组的四角石斛（D. farmer）、角茎灯笼石斛（D. palpebrae）、具槽石斛（D. sulcatum）和球花石斛（D. thyrsiflorum）叶绿体基因组进行测序，利用生物信息学相关软件对其基因组进行组装、注释、图谱绘制以及序列特征分析，并构建石斛属42个物种（灯笼组10个）的系统发育树。结果显示：灯笼组物种叶绿体基因组全长范围为151 717～160 123 bp，总GC含量为37.1%～37.6%，共注释到129～133个基因；同时检测到46～63个简单重复序列（Simple repeat sequence,SSR）以及48～49个分散重复序列（Interspersed repetitive sequence,INE）；蛋白编码基因的密码子偏好以A/U（T）结尾；灯笼组物种中的trnK
Keyword ：
叶绿体基因组 叶绿体基因组 基因组比较 基因组比较 灯笼组石斛 灯笼组石斛 系统发育分析 系统发育分析
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| GB/T 7714 | 陈育明 , 韦春怡 , 张赛 et al. 石斛属灯笼组物种叶绿体基因组特征及系统发育分析 [J]. | 草地学报 , 2025 , 33 (05) : 1372-1386 . |
| MLA | 陈育明 et al. "石斛属灯笼组物种叶绿体基因组特征及系统发育分析" . | 草地学报 33 . 05 (2025) : 1372-1386 . |
| APA | 陈育明 , 韦春怡 , 张赛 , 黄思铭 , 兰思仁 , 李明河 . 石斛属灯笼组物种叶绿体基因组特征及系统发育分析 . | 草地学报 , 2025 , 33 (05) , 1372-1386 . |
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BackgroundPhalaenopsis orchids, belonging to the Orchidaceae family, one of the largest groups of angiosperms, possess significant commercial value due to their fascinating flowers. Petal size is a vital trait that directly determines flower size and shape of Phalaenopsis. However, the genetic and developmental regulation of petal size in Phalaenopsis remains unexplored.ResultsIn this study, we tracked the petal growth pattern through five stages of flower opening, discovering that cell division stops at stage 2 and stages 3 to 5 are the critical periods of rapid petal expansion. RNA-seq was then conducted to further reveal the molecular mechanisms underlying petal size regulation. Gene ontology (GO) analysis indicated that the differentially expressed genes (DEGs) from the four comparable groups were both enriched in terms related to cell expansion. Endogenous hormone assays showed that auxin, cytokinin, and gibberellin were implicated in the petal growth of Phalaenopsis. Moreover, six auxin signaling pathway genes, 11 cell expansion-related genes, and 30 transcription factors (TFs) identified through trend analysis were abundantly expressed during the critical period of petal expansion, suggesting that they may influence petal size by regulating cell expansion. In contrast, 18 TFs exhibited the highest expression levels at the S1 stage, indicating their potential role in petal cell proliferation. Based on weighted gene co-expression network analysis (WGCNA), six hub genes (PaLOF2, PaSWEET11, PaVNI2, PaHDA3, PaPMEI3, PaXTH30) were screened from the green and yellow module which was highly associated with the petal size.ConclusionOur results lay a foundation for further exploration of the molecular mechanisms regulating petal size development and are significant for molecular breeding programs aimed at generating novel Phalaenopsis with desirable traits.
Keyword ：
Cell division Cell division Cell expansion Cell expansion Differentially expressed genes Differentially expressed genes Petal growth Petal growth Phalaenopsis Phalaenopsis RNA-seq RNA-seq
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| GB/T 7714 | Guan, Yunxiao , Zhang, Qiaoyu , Zhang, Ting et al. Transcriptome analysis reveals the mechanisms underlying petal growth during the flower opening process in Phalaenopsis orchids [J]. | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
| MLA | Guan, Yunxiao et al. "Transcriptome analysis reveals the mechanisms underlying petal growth during the flower opening process in Phalaenopsis orchids" . | BMC PLANT BIOLOGY 25 . 1 (2025) . |
| APA | Guan, Yunxiao , Zhang, Qiaoyu , Zhang, Ting , Li, Minghe , Ai, Ye , Zhai, Junwen et al. Transcriptome analysis reveals the mechanisms underlying petal growth during the flower opening process in Phalaenopsis orchids . | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
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本研究通过CiteSpace软件分析2003-2023年间中国知网和Web of Science数据库中的文献。分析显示，中国和美国是主要发文国家，且发文量呈增长趋势。研究热点集中在“可持续性”“城市绿地功能”和“生态系统服务”，凸显了城市绿地在生态平衡和居民福祉中的重要性。随着城市化的推进，研究趋势转向如何优化绿地布局以提升生态系统服务和城市韧性。文章呼吁制定全面政策，以实现城市生态系统的可持续管理。
Keyword ：
城市绿地 城市绿地 时空变化 时空变化 演变 演变 绿地格局 绿地格局 趋势 趋势
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| GB/T 7714 | 黄雅芬 , 黄博洵 , 黄雅凌 et al. 基于CiteSpace的城市绿地演化研究热点与趋势分析 [J]. | 智能建筑与智慧城市 , 2025 , 3 (03) : 38-40 . |
| MLA | 黄雅芬 et al. "基于CiteSpace的城市绿地演化研究热点与趋势分析" . | 智能建筑与智慧城市 3 . 03 (2025) : 38-40 . |
| APA | 黄雅芬 , 黄博洵 , 黄雅凌 , 陈美芬 , 刘明悦 , 李明河 . 基于CiteSpace的城市绿地演化研究热点与趋势分析 . | 智能建筑与智慧城市 , 2025 , 3 (03) , 38-40 . |
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[目的]报道贵州省兰科羊耳蒜属植物一新记录种，为生物多样性的研究和兰科植物的保护提供基础信息。[方法]测量该物种的形态特征，并与羊耳蒜属已知物种进行比较；联合核基因片段ITS和质体基因matK进行系统发育分析。[结果]在贵州省发现1种兰科新记录种：北方羊耳蒜(Liparis makinoana Schltr.),凭证标本保存于福建农林大学林学院植物标本馆(FJFC)。[结论]该物种系贵州省新记录，此次发现丰富了贵州省兰科植物的物种多样性。
Keyword ：
兰科 兰科 北方羊耳蒜 北方羊耳蒜 新记录 新记录 贵州省 贵州省
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| GB/T 7714 | 王焕鑫 , 吴宇苇 , 韦春怡 et al. 基于形态和分子证据记述贵州省兰科一新记录种 [J]. | 亚热带农业研究 , 2024 , 20 (01) : 43-47 . |
| MLA | 王焕鑫 et al. "基于形态和分子证据记述贵州省兰科一新记录种" . | 亚热带农业研究 20 . 01 (2024) : 43-47 . |
| APA | 王焕鑫 , 吴宇苇 , 韦春怡 , 黄明忠 , 兰思仁 , 李明河 . 基于形态和分子证据记述贵州省兰科一新记录种 . | 亚热带农业研究 , 2024 , 20 (01) , 43-47 . |
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石斛顶叶组(Dendrobium section Densiflora)物种具有重要的观赏和药用价值，为更科学高效地对其进行育种和栽培管理，以该组所有国产的8个原生物种：长苏石斛(D.brymerianum)、鼓槌石斛(D.chrysotoxum)、密花石斛(D.densiflorum)、苏瓣石斛(D.harveyanum)、具槽石斛(D.sulcatum)、球花石斛(D.thyrsiflorum)、小黄花石斛(D.jenkinsii)和聚石斛(D.lindleyi)为研究对象，通过进行稳定碳同位素分馏值(δ~(13)C)、全天CO_2净吸收值和早晚可滴定酸值测定，探究其光合碳同化途径类型。结果表明：聚石斛和小黄花石斛的δ~(13)C值大于-20‰,为景天酸代谢(CAM)途径植物；其余6种均小于-20‰，为C_3植物。干旱胁迫后，小黄花石斛的整个夜间净CO_2吸收速率为正值，聚石斛2/3以上的夜间净CO_2吸收速率为正值，聚石斛和小黄花石斛的暗期CO_2净吸收量显著高于昼期，同时早晚可滴定酸差值(△H~+)显著高于C_3植物，进一步支持聚石斛和小黄花石斛为CAM植物; C_3植物昼期CO_2净吸收量均显著高于暗期，其中长苏石斛的△H~+小于0，为C_3植物中的专性C_3物种，而其余5个物种的△H~+均大于4 mmol·kg~(-1)，为C_3植物中的兼性CAM物种。
Keyword ：
干旱胁迫 干旱胁迫 景天酸代谢 景天酸代谢 石斛属 石斛属 碳同化途径 碳同化途径 顶叶组 顶叶组
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| GB/T 7714 | 林雅君 , 吴宇苇 , 韦春怡 et al. 石斛顶叶组物种的碳同化途径类型 [J]. | 森林与环境学报 , 2024 , 44 (04) : 441-446 . |
| MLA | 林雅君 et al. "石斛顶叶组物种的碳同化途径类型" . | 森林与环境学报 44 . 04 (2024) : 441-446 . |
| APA | 林雅君 , 吴宇苇 , 韦春怡 , 兰思仁 , 李明河 . 石斛顶叶组物种的碳同化途径类型 . | 森林与环境学报 , 2024 , 44 (04) , 441-446 . |
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Malaxidinae is one of the most confusing groups in the Orchidaceae classification. Previous phylogenetic analyses have revealed that the relationships between the taxa in Malaxidinae have not yet been reliably established, using only a few plastome regions and nuclear ribosomal internal transcribed spacer (nrITS). In the present study, the complete plastomes of Oberonia integerrima and Crepidium purpureum were assembled using high-throughput sequencing. Combined with publicly available complete plastome data, this resulted in a dataset of 19 plastomes, including 17 species of Malaxidinae. The plastome features and phylogenetic relationships were compared and analyzed. The results showed the following: (1) Malaxidinae species plastomes possess the quadripartite structure of typical angiosperms, with sizes ranging from 142,996 to 158,787 bp and encoding from 125 to 133 genes. The ndh genes were lost or pseudogenized to varying degrees in six species. An unusual inversion was detected in the large single-copy region (LSC) of Oberonioides microtatantha. (2) Eight regions, including ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trnFGAA-ndhJ, and trnSGCU-trnGUCC, were identified as mutational hotspots. (3) Based on complete plastomes, 68 protein-coding genes, and 51 intergenic regions, respectively, our phylogenetic analyses revealed the genus-level relationships in this subtribe with strong support. The Liparis was supported as non-monophyletic.
Keyword ：
comparative genomics comparative genomics Malaxidinae Malaxidinae phylogeny phylogeny plastid genome plastid genome
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| GB/T 7714 | Zeng, Meng-Yao , Li, Ming-He , Lan, Siren et al. Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (20) . |
| MLA | Zeng, Meng-Yao et al. "Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 25 . 20 (2024) . |
| APA | Zeng, Meng-Yao , Li, Ming-He , Lan, Siren , Yin, Wei-Lun , Liu, Zhong-Jian . Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (20) . |
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Gastrochilus pseudodresslerii (Aeridinae), a new species from Maguan County, Yunnan Province, China, is described and illustrated. Morphological comparisons indicated that this new species is similar to G. dresslerii, but differs by its longer and broadly lanceolate to oblong leaves, larger and elliptic dorsal sepal, longer and elliptic petals, subcupular hypochile, and narrowed toward apex of column. Phylogenetic analysis based on nuclear ribosomal ITS and four plastid sequences (atpI, matK, psbA and trnL-F) indicated that G. pseudodresslerii is also closely related to G. formosanus and G. raraensis, but can be easily distinguished from these two species based on its leaves, epichile and hypochile.
Keyword ：
Asian orchids Asian orchids Epidendroideae Epidendroideae Gastrochilus phylogenetics Gastrochilus phylogenetics
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| GB/T 7714 | Zhou, Cheng-Yuan , Zeng, Meng-Yao , Wu, Yu-Wei et al. Gastorchilus pseudodresslerii (Orchidaceae; Vandeae), a new species from China: evidence from morphological and DNA analysis [J]. | PHYTOTAXA , 2024 , 634 (1) : 71-78 . |
| MLA | Zhou, Cheng-Yuan et al. "Gastorchilus pseudodresslerii (Orchidaceae; Vandeae), a new species from China: evidence from morphological and DNA analysis" . | PHYTOTAXA 634 . 1 (2024) : 71-78 . |
| APA | Zhou, Cheng-Yuan , Zeng, Meng-Yao , Wu, Yu-Wei , Li, Ming-He . Gastorchilus pseudodresslerii (Orchidaceae; Vandeae), a new species from China: evidence from morphological and DNA analysis . | PHYTOTAXA , 2024 , 634 (1) , 71-78 . |
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The taxonomic status of Vanda coelestis (Rchb.f.) Motes remains a matter of discussion. So far, molecular systematic work has not been used to investigate. Here, we conducted the phylogenetic analyses using two datasets, the complete plastome and a combination of traditional molecular sequences (nrITS, matK, psbA-trnH, and trnL-trnF). Plastid-based phylogenetic trees indicated that this species was deeply embedded within the genus Vanda. In the analysis based on combined traditional sequences dataset, this species was further supported as sister to V. vietnamica with strong support.
Keyword ：
foxtail orchid foxtail orchid orchid phylogenetics orchid phylogenetics plastome plastome taxonomic treatment taxonomic treatment
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| GB/T 7714 | Zeng, Meng-yao , Chen, Jin-liao , Huang, Ming-zhong et al. Phylogenetic position of Vanda coelestis (Rchb.f.) Motes (Orchidaceae; Aeridinae): evidence from complete plastome and combined traditional sequences [J]. | PHYTOTAXA , 2024 , 638 (3) : 285-293 . |
| MLA | Zeng, Meng-yao et al. "Phylogenetic position of Vanda coelestis (Rchb.f.) Motes (Orchidaceae; Aeridinae): evidence from complete plastome and combined traditional sequences" . | PHYTOTAXA 638 . 3 (2024) : 285-293 . |
| APA | Zeng, Meng-yao , Chen, Jin-liao , Huang, Ming-zhong , Li, Ming-he . Phylogenetic position of Vanda coelestis (Rchb.f.) Motes (Orchidaceae; Aeridinae): evidence from complete plastome and combined traditional sequences . | PHYTOTAXA , 2024 , 638 (3) , 285-293 . |
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