Genome-based identification of the CYP75 gene family in Orchidaceae and its expression patterns in Cymbidium goeringii by Yuanyuan Li, Xuewei Zhao, Meng-Meng Zhang, Xin He, Ye Huang, Sagheer Ahmad, Zhong-Jian Liu, Zhong-Jian Liu, Siren Lan, Siren Lan

“…We also discovered unique conserved motifs in each subfamily that serve as specific recognition features (motif 19 belong to CYP75A; motif 17 belong to CYP75B). …”
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Genome-wide identification and expression analysis of the GRAS gene family in Dendrobium chrysotoxum by Xuewei Zhao, Xuewei Zhao, Ding-Kun Liu, Ding-Kun Liu, Qian-Qian Wang, Shijie Ke, Shijie Ke, Yuanyuan Li, Diyang Zhang, Qinyao Zheng, Cuili Zhang, Zhong-Jian Liu, Zhong-Jian Liu, Siren Lan, Siren Lan

“…Forty-six DchGRAS genes were identified from the D. chrysotoxum genome and divided into ten subfamilies according to their phylogenetic relationships. …”
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General Analysis of Heat Shock Factors in the <i>Cymbidium ensifolium</i> Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature by Ruiyue Zheng, Jiemin Chen, Yukun Peng, Xuanyi Zhu, Muqi Niu, Xiuming Chen, Kai Xie, Ruiliu Huang, Suying Zhan, Qiuli Su, Mingli Shen, Donghui Peng, Sagheer Ahmad, Kai Zhao, Zhong-Jian Liu, Yuzhen Zhou

“…According to phylogenetic analysis, 59.1% of HSFs were grouped into the A subfamily, while subfamily HSFC contained only two HSFs. …”
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<i>Apostasia</i> Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics by Shi-Jie Ke, Ding-Kun Liu, Xiong-De Tu, Xin He, Meng-Meng Zhang, Meng-Jia Zhu, Di-Yang Zhang, Cui-Li Zhang, Si-Ren Lan, Zhong-Jian Liu

“…<i>Apostasia shenzhenica</i> belongs to the subfamily Apostasioideae and is a primitive group located at the base of the Orchidaceae phylogenetic tree. …”
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Comparative Analysis of Six Complete Plastomes of <i>Tripterospermum</i> spp. by Xiong-De Tu, Wen-Jun Lin, Hou-Hua Fu, Yi-Zhe Lin, Jun Shen, Shuai Chen, Zhong-Jian Liu, Ming-He Li, Shi-Pin Chen

“…Therefore, we first analyzed the 86 Gentianae plastid genomes to explore the phylogenetic relationships within the Gentianae subfamily where <i>Tripterospermum</i> is located. …”
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Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots by Cheng-Yuan Zhou, Wen-Jun Lin, Ruyi Li, Yuhan Wu, Zhong-Jian Liu, Ming-He Li

“…The consistent and robust phylogenetic relationships of <i>Angraecum</i> were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus <i>Angraecum</i> was strongly supported as a monophyletic group and sister to Aeridinae. …”
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Genome-Wide Identification and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in <i>Cymbidium ensifolium</i> by Meng-Jie Wang, Yue Ou, Zuo Li, Qing-Dong Zheng, Yu-Jie Ke, Hui-Ping Lai, Si-Ren Lan, Dong-Hui Peng, Zhong-Jian Liu, Ye Ai

“…Here, 94 bHLH transcription factors were identified from the <i>Cymbidium ensifolium</i> genome and divided into 18 subfamilies. Most <i>CebHLHs</i> contain numerous <i>cis-acting</i> elements associated with abiotic stress responses and phytohormone responses. …”
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Genome-Wide Identification of TCP Gene Family in <i>Dendrobium</i> and Their Expression Patterns in <i>Dendrobium chrysotoxum</i> by Ye Huang, Xuewei Zhao, Qinyao Zheng, Xin He, Meng-Meng Zhang, Shijie Ke, Yuanyuan Li, Cuili Zhang, Sagheer Ahmad, Siren Lan, Zhong-Jian Liu

“…A total of 50 <i>TCP</i>s were identified across three <i>Dendrobium</i> species; they were divided into two clades—Class-I (PCF subfamily) and Class-II (CIN and CYC/TB1 subfamilies)—based on their phylogenetic relationships. …”
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Identification, Molecular Characteristics, and Evolution of YABBY Gene Family in <i>Melastoma dodecandrum</i> by Jie Huang, Gui-Zhen Chen, Sagheer Ahmad, Qin Wang, Song Tu, Xiao-Ling Shi, Yang Hao, Yu-Zhen Zhou, Si-Ren Lan, Zhong-Jian Liu, Dong-Hui Peng

“…The transcriptomic data and real-time reverse transcription quantitative PCR (RT-qPCR) expression pattern analyses showed that <i>MdYABBY</i> genes were involved in organ development and differentiation of <i>M. dodecandrum</i>, and some <i>MdYABBYs</i> in the subfamily may have function differentiation. The RT-qPCR analysis showed high expression of flower bud and medium flower. …”
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Genome-Wide Identification of the MYB Gene Family in <i>Cymbidium</i><i>ensifolium</i> and Its Expression Analysis in Different Flower Colors by Yu-Jie Ke, Qing-Dong Zheng, Ya-He Yao, Yue Ou, Jia-Yi Chen, Meng-Jie Wang, Hui-Ping Lai, Lu Yan, Zhong-Jian Liu, Ye Ai

“…The analysis of the <i>CeMYB</i><i>s</i> expression based on transcriptome data showed that <i>CeMYB52</i>, and <i>CeMYB104</i> of the S6 subfamily may be the key genes leading to flower color variation. …”
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Genome-Wide Identification and Drought Stress Response Pattern of the NF-Y Gene Family in <i>Cymbidium sinense</i> by Linying Wang, Xuewei Zhao, Ruiyue Zheng, Ye Huang, Cuili Zhang, Meng-Meng Zhang, Siren Lan, Zhong-Jian Liu

“…Protein structure analysis revealed that different subfamilies contained different motifs, but all of them contained Motif 2. …”
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OrchidBase 5.0: updates of the orchid genome knowledgebase by You-Yi Chen, Chung‐I Li, Yu-Yun Hsiao, Sau-Yee Ho, Zhe-Bin Zhang, Chien-Chi Liao, Bing-Ru Lee, Shao-Ting Lin, Wan-Lin Wu, Jeen-Shing Wang, Diyang Zhang, Ke-Wei Liu, Ding-Kun Liu, Xue-Wei Zhao, Yuan-Yuan Li, Shi-Jie Ke, Zhuang Zhou, Ming-Zhong Huang, Yong-Shu Wu, Dong-Hui Peng, Si-Ren Lan, Hong-Hwa Chen, Zhong-Jian Liu, Wei-Sheng Wu, Wen-Chieh Tsai

“…OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. …”
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Genome-wide identification and analysis of anthocyanin synthesis-related R2R3-MYB genes in Cymbidium goeringii by Jiating Chen, Jiating Chen, Yuan-Yang Bi, Yuan-Yang Bi, Qian-Qian Wang, Qian-Qian Wang, Ding-Kun Liu, Ding-Kun Liu, Diyang Zhang, Diyang Zhang, Xiangqing Ding, Xiangqing Ding, Zhong-Jian Liu, Zhong-Jian Liu, Shi-Pin Chen, Shi-Pin Chen

“…The R2R3-MYB genes of Arabidopsis thaliana were used as a reference to determine 104 CgMYB genes and categorize them into 22 subfamilies. Exon/intron organizations and conserved motif analysis revealed that the majority of CgMYB genes were highly conserved, and chromosome localization and collinearity analysis provided evidence of tandem duplication and segmental duplication events, indicating the phenomenon of gene family expansion and contraction. …”
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Bioinformatic Assessment and Expression Profiles of the <i>AP2/ERF</i> Superfamily in the <i>Melastoma dodecandrum</i> Genome by Yuzhen Zhou, Ruiyue Zheng, Yukun Peng, Jiemin Chen, Xuanyi Zhu, Kai Xie, Qiuli Su, Ruiliu Huang, Suying Zhan, Donghui Peng, Kai Zhao, Zhong-Jian Liu

“…A significant number of genes, totaling 218, were discovered to possess the AP2 domain sequence and displayed notable structural variations among five subfamilies. An uneven distribution of these genes was observed on 12 pseudochromosomes as the result of gene expansion facilitated by segmental duplications. …”
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The <i>bZIP</i> Transcription Factors in Current Jasmine Genomes: Identification, Characterization, Evolution and Expressions by Kai Zhao, Xianmei Luo, Mingli Shen, Wen Lei, Siqing Lin, Yingxuan Lin, Hongyan Sun, Sagheer Ahmad, Guohong Wang, Zhong-Jian Liu

“…The <i>HTbZIP</i> genes were categorized into 12 subfamilies compared with <i>A. thaliana</i>. In cis-acting element analysis, all genes contained light-responsive elements. …”
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Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i> by Qinyao Zheng, Xuewei Zhao, Ye Huang, Meng-Meng Zhang, Xin He, Shijie Ke, Yuanyuan Li, Cuili Zhang, Sagheer Ahmad, Siren Lan, Minghe Li, Zhong-Jian Liu

“…The 24 YABBY genes were classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3) based on their phylogenetic analysis. …”
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