The Complete Chloroplast Genomes of Bulbophyllum (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic Analysis Article Swipe
Yuwei Wu
,
Meng-Yao Zeng
,
Huanxin Wang
,
Siren Lan
,
Zhong‐Jian Liu
,
Shi‐Bao Zhang
,
Ming-He Li
,
Yunxiao Guan
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3390/ijms25052665
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3390/ijms25052665
Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations on our study. Here, we report the complete cp genomes of seven Bulbophyllum species, including B. ambrosia, B. crassipes, B. farreri, B. hamatum, B. shanicum, B. triste, and B. violaceolabellum, and compared with related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. A total of 28 Bulbophyllum cp genomes exhibit typical quadripartite structures with lengths ranging from 145,092 bp to 165,812 bp and a GC content of 36.60% to 38.04%. Each genome contained 125–132 genes, encompassing 74–86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The genome arrangements, gene contents, and length were similar, with differences observed in ndh gene composition. It is worth noting that there were exogenous fragment insertions in the IR regions of B. crassipes. A total of 18–49 long repeats and 38–80 simple sequence repeats (SSRs) were detected and the single nucleotide (A/T) was dominant in Bulbophyllum cp genomes, with an obvious A/T preference. An analysis of relative synonymous codon usage (RSCU) revealed that leucine (Leu) was the most frequently used codon, while cysteine (Cys) was the least used. Six highly variable regions (rpl32-trnLUAG > trnTUGU-trnLUAA > trnFGAA-ndhJ > rps15-ycf1 > rbcL-accD > psbI-trnSGCU) and five coding sequences (ycf1 > rps12 > matK > psbK > rps15) were identified as potential DNA markers based on nucleotide diversity. Additionally, 31,641 molecular diagnostic characters (MDCs) were identified in complete cp genomes. A phylogenetic analysis based on the complete cp genome sequences and 68 protein-coding genes strongly supported that 28 Bulbophyllum species can be divided into four branches, sects. Brachyantha, Cirrhopetalum, and Leopardinae, defined by morphology, were non-monophyly. Our results enriched the genetic resources of Bulbophyllum, providing valuable information to illustrate the complicated taxonomy, phylogeny, and evolution process of the genus.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/ijms25052665
- https://www.mdpi.com/1422-0067/25/5/2665/pdf?version=1708854579
- OA Status
- gold
- Cited By
- 10
- References
- 88
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4392168487
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- OpenAlex ID
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https://openalex.org/W4392168487Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3390/ijms25052665Digital Object Identifier
- Title
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The Complete Chloroplast Genomes of Bulbophyllum (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic AnalysisWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-02-25Full publication date if available
- Authors
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Yuwei Wu, Meng-Yao Zeng, Huanxin Wang, Siren Lan, Zhong‐Jian Liu, Shi‐Bao Zhang, Ming-He Li, Yunxiao GuanList of authors in order
- Landing page
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https://doi.org/10.3390/ijms25052665Publisher landing page
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https://www.mdpi.com/1422-0067/25/5/2665/pdf?version=1708854579Direct link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
- OA URL
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https://www.mdpi.com/1422-0067/25/5/2665/pdf?version=1708854579Direct OA link when available
- Concepts
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Orchidaceae, Biology, Phylogenetic tree, Genome, Evolutionary biology, Ornamental plant, Phylogenetics, Botany, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
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10Total citation count in OpenAlex
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2025: 6, 2024: 4Per-year citation counts (last 5 years)
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88Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.Orchidaceae, | 19 |
| abstract_inverted_index.composition. | 150 |
| abstract_inverted_index.encompassing | 124 |
| abstract_inverted_index.phylogenetic | 274 |
| abstract_inverted_index.trnFGAA-ndhJ | 231 |
| abstract_inverted_index.Additionally, | 261 |
| abstract_inverted_index.Bulbophyllum, | 316 |
| abstract_inverted_index.arrangements, | 137 |
| abstract_inverted_index.psbI-trnSGCU) | 237 |
| abstract_inverted_index.quadripartite | 100 |
| abstract_inverted_index.understanding | 82 |
| abstract_inverted_index.(rpl32-trnLUAG | 227 |
| abstract_inverted_index.Cirrhopetalum, | 301 |
| abstract_inverted_index.non-monophyly. | 308 |
| abstract_inverted_index.protein-coding | 126, 285 |
| abstract_inverted_index.trnTUGU-trnLUAA | 229 |
| abstract_inverted_index.characterization | 33 |
| abstract_inverted_index.violaceolabellum, | 72 |
| cited_by_percentile_year.max | 99 |
| cited_by_percentile_year.min | 97 |
| corresponding_author_ids | https://openalex.org/A5107944876, https://openalex.org/A5058508889 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 8 |
| corresponding_institution_ids | https://openalex.org/I61057504 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/15 |
| sustainable_development_goals[0].score | 0.75 |
| sustainable_development_goals[0].display_name | Life in Land |
| citation_normalized_percentile.value | 0.96239323 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |