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学者姓名：李明河
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Abstract ：
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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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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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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Angraecum, commonly known as Darwin's orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of Angraecum were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine-cytosine (GC) content of 36.6-36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all ndh genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (trnS(GCU)-trnG(GCC), ycf1-trnN(GGU), trnN(GUU)-rpl32, psaC-ndhE and trnS(GCU)-trnG(GCC)) and five protein-coding genes (rpl32, rps16, psbK, rps8, and ycf1) were identified. The consistent and robust phylogenetic relationships of Angraecum were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus Angraecum was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for Angraecum.
Keyword ：
Angraecinae Angraecinae Darwin's orchid Darwin's orchid Orchidaceae Orchidaceae phylogenetic analysis phylogenetic analysis plastid genome plastid genome
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| GB/T 7714 | Zhou, Cheng-Yuan , Lin, Wen-Jun , Li, Ruyi et al. Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (1) . |
| MLA | Zhou, Cheng-Yuan et al. "Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 25 . 1 (2024) . |
| APA | Zhou, Cheng-Yuan , Lin, Wen-Jun , Li, Ruyi , Wu, Yuhan , Liu, Zhong-Jian , Li, Ming-He et al. Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (1) . |
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Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants.
Keyword ：
high-throughput sequencing high-throughput sequencing multichromosomal mitogenome multichromosomal mitogenome mycoheterotrophic plants mycoheterotrophic plants organelle genomes organelle genomes phylogenetic analysis phylogenetic analysis
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| GB/T 7714 | Zhao, Zhuang , Li, Yuanyuan , Zhai, Jun-Wen et al. Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (3) . |
| MLA | Zhao, Zhuang et al. "Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 25 . 3 (2024) . |
| APA | Zhao, Zhuang , Li, Yuanyuan , Zhai, Jun-Wen , Liu, Zhong-Jian , Li, Ming-He . Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (3) . |
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Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.
Keyword ：
bacterial-type PEPC bacterial-type PEPC crassulacean acid metabolism (CAM) crassulacean acid metabolism (CAM) evolution evolution orchids orchids PEPC gene family PEPC gene family
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| GB/T 7714 | Li, Ruyi , Gao, Xuyong , Wu, Yuwei et al. Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (4) . |
| MLA | Li, Ruyi et al. "Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 25 . 4 (2024) . |
| APA | Li, Ruyi , Gao, Xuyong , Wu, Yuwei , Wei, Chunyi , Li, Ming-He , Liu, Ding-Kun et al. Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (4) . |
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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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[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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