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Lei W, Zhou P, Pei Z, Liu Y, Luo Y, Xiang X. Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae). Int J Mol Sci 2024; 25:9538. [PMID: 39273486 PMCID: PMC11394697 DOI: 10.3390/ijms25179538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/29/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024] Open
Abstract
Vanda R.Br. is an epiphytic orchid genus with significant horticultural and ornamental value. Previous molecular studies expanded Vanda including some members from five other genera. However, the interspecific relationships of this recently radiated genus have remained unclear based on several DNA markers until now. In this study, the complete plastome has been used to infer the phylogenetic relationships of Vanda s.l. The five newly obtained plastomes ranged from 146,340 bp to 149,273 bp in length, with a GC content ranging from 36.5% to 36.7%. The five plastomes contained 74 protein-coding genes (CDSs), 38 tRNAs, and 8 rRNAs, and their ndh genes underwent loss or pseudogenization. Comparative plastome analyses of 13 Vanda species revealed high conservation in terms of genome size, structure, and gene order, except for a large inversion from trnGGCC to ycf3 in V. coerulea. Moreover, six CDSs and five non-CDSs were selected as candidate DNA barcodes. Our phylogenetic analyses demonstrated that Vanda s.l. is a monophyletic group with high supporting values based on five different datasets (complete plastome with one IR, 68 CDSs, LSC, five hypervariable non-CDSs, and six hypervariable CDSs), while the phylogenetic relationships among species were fully resolved based on the complete plastome with one IR dataset. Our results confirmed that the complete plastome has a great power in resolving the phylogenetic relationships of recently radiated lineages.
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Affiliation(s)
- Wanshun Lei
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Peng Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Zelong Pei
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Yizhen Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666300, China
| | - Xiaoguo Xiang
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China
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Hu Q, Wu J, Fan C, Luo Y, Liu J, Deng Z, Li Q. Comparative analysis of codon usage bias in the chloroplast genomes of eighteen Ampelopsideae species (Vitaceae). BMC Genom Data 2024; 25:80. [PMID: 39223463 PMCID: PMC11370015 DOI: 10.1186/s12863-024-01260-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The tribe Ampelopsideae plants are important garden plants with both medicinal and ornamental values. The study of codon usage bias (CUB) facilitates a deeper comprehension of the molecular genetic evolution of species and their adaptive strategies. The joint analysis of CUB in chloroplast genomes (cpDNA) offers valuable insights for in-depth research on molecular genetic evolution, biological resource conservation, and elite breeding within this plant family. RESULTS The base composition and codon usage preferences of the eighteen chloroplast genomes were highly similar, with the GC content of bases at all positions of their codons being less than 50%. This indicates that they preferred A/T bases. Their effective codon numbers were all in the range of 35-61, which indicates that the codon preferences of the chloroplast genomes of the 18 Ampelopsideae plants were relatively weak. A series of analyses indicated that the codon preference of the chloroplast genomes of the 18 Ampelopsideae plants was influenced by a combination of multiple factors, with natural selection being the primary influence. The clustering tree generated based on the relative usage of synonymous codons is consistent with some of the results obtained from the phylogenetic tree of chloroplast genomes, which indicates that the clustering tree based on the relative usage of synonymous codons can be an important supplement to the results of the sequence-based phylogenetic analysis. Eventually, 10 shared best codons were screened on the basis of the chloroplast genomes of 18 species. CONCLUSION The codon preferences of the chloroplast genome in Ampelopsideae plants are relatively weak and are primarily influenced by natural selection. The codon composition of the chloroplast genomes of the eighteen Ampelopsideae plants and their usage preferences were sufficiently similar to demonstrate that the chloroplast genomes of Ampelopsideae plants are highly conserved. This study provides a scientific basis for the genetic evolution of chloroplast genes in Ampelopsideae species and their suitable strategies.
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Affiliation(s)
- Qun Hu
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi, Hubei, 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi, Hubei, 445000, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Jiaqi Wu
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi, Hubei, 445000, China
| | - Chengcheng Fan
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi, Hubei, 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi, Hubei, 445000, China
| | - Yongjian Luo
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Jun Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi, Hubei, 445000, China.
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi, Hubei, 445000, China.
| | - Qing Li
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China.
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Huang K, Li B, Chen X, Qin C, Zhang X. Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1430191. [PMID: 39224852 PMCID: PMC11366656 DOI: 10.3389/fpls.2024.1430191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.
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Affiliation(s)
| | | | | | | | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, China
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Zhou P, Lei WS, Shi YK, Liu YZ, Luo Y, Li JH, Xiang XG. Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla. Int J Mol Sci 2024; 25:8500. [PMID: 39126069 PMCID: PMC11312641 DOI: 10.3390/ijms25158500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7-36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).
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Affiliation(s)
- Peng Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Wan-Shun Lei
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Ying-Kang Shi
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yi-Zhen Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666300, China;
| | - Ji-Hong Li
- Kadoorie Farm and Botanic Garden, Hong Kong Lam Kam Road, Tai Po, New Territories, Hong Kong 999077, China;
| | - Xiao-Guo Xiang
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
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Wu J, Gao Y, Wang J, Guo A, Qin N, Xing G, Li S. Comparative analysis of chloroplast genome and evolutionary history of Hemerocallis. Front Genet 2024; 15:1433548. [PMID: 39130749 PMCID: PMC11310003 DOI: 10.3389/fgene.2024.1433548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/07/2024] [Indexed: 08/13/2024] Open
Abstract
Members of the genus Hemerocallis have significant value as ornamental, edible, and medicinal plants, particularly in China, where they have been utilized for thousands of years as both a vegetable and Traditional Chinese Medicine. Hemerocallis species exhibit strict control over flowering time, with individuals flowering either diurnally or nocturnally. However, our understanding of the evolutionary history of this genus, especially concerning important horticultural traits, remains limited. In this study, sequencing and assembly efforts were conducted on 73 samples within the Hemerocallis genus. All accessions were classified into two distinct groups based on their diurnal (daylilies) or nocturnal (nightlilies) flowering habits. Comparative analysis of the chloroplast genomes from these two groups identified fifteen variant hotspot regions, including fourteen SNPs and one deletion, which hold promise for the development of molecular markers for interspecific identification. Phylogenetic trees, generated through both maximum-likelihood and Bayesian inference methods using 76 shared protein-coding sequences, revealed that diurnal flowering evolved prior to nocturnal flowering. The divergence between the two groups is estimated to have occurred approximately 0.82 MYA (95% CI: 0.35-1.45 MYA). The ancestral state of Hemerocallis is hypothesized to have featured diurnal flowering with orange yellow petals. This study marks the first reconstruction of the evolutionary history and ancestral state of the genus Hemerocallis. The findings contribute significantly to our understanding of the adaptation and speciation history within the genus.
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Affiliation(s)
- Jiang Wu
- College of Horticulture, Shanxi Agriculture University, Taiyuan, China
| | - Yang Gao
- College of Horticulture, Shanxi Agriculture University, Taiyuan, China
| | - Jinyao Wang
- College of Horticulture, Shanxi Agriculture University, Taiyuan, China
| | - Aihua Guo
- Department of Life Science, Lyuliang University, Lüliang, China
| | - Nannan Qin
- College of Horticulture, Shanxi Agriculture University, Taiyuan, China
| | - Guoming Xing
- College of Horticulture, Shanxi Agriculture University, Taiyuan, China
- Datong Daylily Industrial Development Research Institute, Datong, China
| | - Sen Li
- College of Horticulture, Shanxi Agriculture University, Taiyuan, China
- Datong Daylily Industrial Development Research Institute, Datong, China
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Shen Z, Liu Q, Hao J, Bi S, Fu Y, Zhang L. The Complete Chloroplast Genome Sequence of the Medicinal Moss Rhodobryum giganteum (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses. Genes (Basel) 2024; 15:900. [PMID: 39062679 PMCID: PMC11275618 DOI: 10.3390/genes15070900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Rhodobryum giganteum (Bryaceae, Bryophyta), a rare medicinal bryophyte, is valued for its cardiovascular therapeutic properties in traditional Chinese medicine. This study presents the first complete chloroplast genome sequence of R. giganteum, including its assembly and annotation. The circular chloroplast genome of R. giganteum is 124,315 bp in length, displaying a typical quadripartite structure with 128 genes: 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Analyses of codon usage bias, repetitive sequences, and simple sequence repeats (SSRs) revealed an A/U-ending codon preference, 96 repetitive sequences, and 385 SSRs in the R. giganteum chloroplast genome. Nucleotide diversity analysis identified 10 high mutational hotspots. Ka/Ks ratio analysis suggested potential positive selection in rpl20, rps18, petG, and psbM genes. Phylogenetic analysis of whole chloroplast genomes from 38 moss species positioned R. giganteum within Bryales, closely related to Rhodobryum laxelimbatum. This study augments the chloroplast genomic data for Bryales and provides a foundation for molecular marker development and genetic diversity analyses in medicinal bryophytes.
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Affiliation(s)
- Zhengyuan Shen
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
| | - Qin Liu
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin 537000, China
| | - Jiewei Hao
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
| | - Sheng Bi
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
| | - Yezhen Fu
- Bawangling Branch of Hainan Tropical Rainforest National Park Administration, Changjiang 572700, China
| | - Lina Zhang
- Center for Eco-Environment Restoration Engineering of Hainan Province, School of Ecology, Hainan University, Haikou 570228, China; (Z.S.)
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, China
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Wu Y, Zeng MY, Wang HX, Lan S, Liu ZJ, Zhang S, Li MH, Guan Y. The Complete Chloroplast Genomes of Bulbophyllum (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic Analysis. Int J Mol Sci 2024; 25:2665. [PMID: 38473912 DOI: 10.3390/ijms25052665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
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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Affiliation(s)
- Yuwei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huan-Xin Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shibao Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunxiao Guan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Cai H, Xu R, Tian P, Zhang M, Zhu L, Yin T, Zhang H, Liu X. Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom. Int J Mol Sci 2023; 25:257. [PMID: 38203426 PMCID: PMC10778623 DOI: 10.3390/ijms25010257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.
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Affiliation(s)
| | | | | | | | | | - Tuo Yin
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (H.C.); (R.X.); (P.T.); (M.Z.); (L.Z.); (T.Y.)
| | - Hanyao Zhang
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (H.C.); (R.X.); (P.T.); (M.Z.); (L.Z.); (T.Y.)
| | - Xiaozhen Liu
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (H.C.); (R.X.); (P.T.); (M.Z.); (L.Z.); (T.Y.)
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Ma L, Zhou CY, Chen JL, Liu DK, Lan S, Liu ZJ. Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation. Genes (Basel) 2023; 15:20. [PMID: 38254910 PMCID: PMC10815154 DOI: 10.3390/genes15010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Luisia, a genus of the subtribe Aeridinae of Orchidaceae, comprises ca. 40 species. Members of Luisia exhibit unique morphological characteristics and represent a valuable ornamental orchid genus. However, due to the scarcity of distinct morphological characters, species identification within this genus is ambiguous and controversial. In the present study, next-generation sequencing (NGS) methods were used to assemble the plastomes of five Luisia species and compare them with one publicly available Luisia plastid genome data. The plastomes of Luisia possessed a quadripartite structure, with sizes ranging from 146,243 bp to 147,430 bp. The plastomes of six Luisia species contained a total of 120 genes, comprising 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. Notably, all ndh genes were pseudogenized or lost. An analysis of codon usage bias showed that leucine (Leu) exhibited the highest frequency, while cysteine (Cys) exhibited the lowest frequency. A total of 57 to 64 SSRs and 42 to 49 long repeats were identified. Five regions and five coding sequences were identified for DNA barcodes, based on the nucleotide diversity (Pi) analysis. The species of Luisia constituted a monophyletic group and were sister to Paraphalaenopsis with strong support. Our study deepens the understanding of species identification, plastome evolution and the phylogenetic positions of Luisia.
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Affiliation(s)
- Liang Ma
- Fujian Health College, Fuzhou 350101, China;
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Cheng-Yuan Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Jin-Liao Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.-Y.Z.); (J.-L.C.); (D.-K.L.); (S.L.)
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10
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Wei Z, Chen F, Ding H, Liu W, Yang B, Geng J, Chen S, Guo S. Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera ( Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers. Genes (Basel) 2023; 14:2183. [PMID: 38137004 PMCID: PMC10743295 DOI: 10.3390/genes14122183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Species within the genus Chenopodium hold significant research interest due to their nutritional richness and salt tolerance. However, the morphological similarities among closely related species and a dearth of genomic resources have impeded their comprehensive study and utilization. In the present research, we conduct the sequencing and assembly of chloroplast (cp) genomes from six Chenopodium and related species, five of which were sequenced for the first time. These genomes ranged in length from 151,850 to 152,215 base pairs, showcased typical quadripartite structures, and encoded 85 protein-coding genes (PCGs), 1 pseudogene, 37 tRNA genes, and 8 rRNA genes. Compared with the previously published sequences of related species, these cp genomes are relatively conservative, but there are also some interspecific differences, such as inversion and IR region contraction. We discerned 929 simple sequence repeats (SSRs) and a series of highly variable regions across 16 related species, predominantly situated in the intergenic spacer (IGS) region and introns. The phylogenetic evaluations revealed that Chenopodium is more closely related to genera such as Atriplex, Beta, Dysphania, and Oxybase than to other members of the Amaranthaceae family. These lineages shared a common ancestor approximately 60.80 million years ago, after which they diverged into distinct genera. Based on InDels and SNPs between species, we designed 12 pairs of primers for species identification, and experiments confirmed that they could completely distinguish 10 related species.
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Affiliation(s)
- Zixiang Wei
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Fangjun Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Hongxia Ding
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Wenli Liu
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Bo Yang
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Jiahui Geng
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shihua Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shanli Guo
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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11
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Zhao Z, Zeng MY, Wu YW, Li JW, Zhou Z, Liu ZJ, Li MH. Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species. Int J Mol Sci 2023; 24:14437. [PMID: 37833887 PMCID: PMC10572996 DOI: 10.3390/ijms241914437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78-82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25-38 long repeats and 130-149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA-petN, trnDGUC-trnYGUA, trnSGCU-trnGUCC, and rpl32-trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.
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Affiliation(s)
- Zhuang Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Meng-Yao Zeng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Yu-Wei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Jin-Wei Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
| | - Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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