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Huang Y, Jin XJ, Zhang CY, Li P, Meng HH, Zhang YH. Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae. BMC PLANT BIOLOGY 2024; 24:634. [PMID: 38971744 PMCID: PMC11227234 DOI: 10.1186/s12870-024-05293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. RESULTS The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia. CONCLUSION Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.
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Affiliation(s)
- Yue Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Can-Yu Zhang
- Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
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Pham MH, Tran TH, Le TD, Le TL, Hoang H, Chu HH. The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships. Genes (Basel) 2023; 14:genes14010227. [PMID: 36672968 PMCID: PMC9859165 DOI: 10.3390/genes14010227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/19/2022] [Accepted: 01/07/2023] [Indexed: 01/18/2023] Open
Abstract
Ophiorrhiza baviensis Drake, a flowering medical plant in the Rubiaceae, exists uncertainly within the Ophiorrhiza genus' evolutionary relationships. For the first time, the whole chloroplast (cp) genome of an O. baviensis Drake species was sequenced and annotated. Our findings demonstrate that the complete cp genome of O. baviensis is 154,770 bp in size, encoding a total of 128 genes, including 87 protein-coding genes, 8 rRNAs, and 33 tRNAs. A total of 59 SSRs were screened in the studied cp genome, along with six highly variable loci, which can be applied to generate significant molecular markers for the Ophiorrhiza genus. The comparative analysis of the O. baviensis cp genome with two published others of the Ophiorrhiza genus revealed a high similarity; however, there were some notable gene rearrangements in the O. densa plastome. The maximum likelihood phylogenetic trees were constructed based on the concatenation of the rps16 gene and the trnL-trnF intergenic spacer sequence, indicating a close relationship between the studied O. baviensis and other Ophiorrhiza. This study will provide a theoretical molecular basis for identifying O. baviensis Drake, as well as species of the Ophiorrhiza genus, and contribute to shedding light on the chloroplast genome evolution of Rubiaceae.
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Affiliation(s)
- Mai Huong Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Thu Hoai Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Thi Dung Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Tung Lam Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Ha Hoang
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, VAST, Hanoi 100000, Vietnam
- Correspondence:
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Ouyang ZY, Li ZH, Chen R, Jiang XL, Wu JY. The complete chloroplast genome sequence of Quercus kerrii (Fagaceae), and comparative analysis with related species. Mitochondrial DNA B Resour 2023; 8:527-531. [PMID: 37124995 PMCID: PMC10132218 DOI: 10.1080/23802359.2023.2204167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Quercus kerrii Craib 1911 (section Cyclobalanopsis) is a widespread tree species in the tropical seasonal forests of southwest China and Northern Indo-China areas. In this study, we sequenced, assembled and annotated the complete chloroplast genome of Q. kerrii. The circular genome was 160,743 bp in length and had a GC content of 36.89%. The Q. kerrii chloroplast genome has a typical quadripartite structure, including two inverted repeat regions (length, 25,825 bp; GC content, 42.76%), a large single-copy region (length, 90,196 bp; GC content, 34.74%), and a small single-copy region (length, 18,897 bp; GC content, 30.60%). Genome annotation has indicated that the Q. kerrii chloroplast genome contained 131 genes, including 86 protein-coding genes, 37 tRNA, and eight rRNA. The phylogenetic tree showed that Q. kerrii had a close relationship with Q. schottkyana Rehder & E.H.Wilson 1916.
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Affiliation(s)
- Ze-Yi Ouyang
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
- Hunan Botanical Garden, Changsha, China
| | - Zhi-Hui Li
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Ran Chen
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Xiao-Long Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
- CONTACT Xiao-Long Jiang College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ji-You Wu
- Hunan Academy of Forestry, Changsha, China
- Ji-You Wu Hunan Academy of Forestry, Changsha, Hunan, China
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Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications. BIOLOGY 2022; 11:biology11121779. [PMID: 36552287 PMCID: PMC9775174 DOI: 10.3390/biology11121779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
The genus Crassula is the second-largest genus in the family Crassulaceae, with about 200 species. As an acknowledged super-barcode, plastomes have been extensively utilized for plant evolutionary studies. Here, we first report 10 new plastomes of Crassula. We further focused on the structural characterizations, codon usage, aversion patterns, and evolutionary rates of plastomes. The IR junction patterns-IRb had 110 bp expansion to rps19-were conservative among Crassula species. Interestingly, we found the codon usage patterns of matK gene in Crassula species are unique among Crassulaceae species with elevated ENC values. Furthermore, subgenus Crassula species have specific GC-biases in the matK gene. In addition, the codon aversion motifs from matK, pafI, and rpl22 contained phylogenetic implications within Crassula. The evolutionary rates analyses indicated all plastid genes of Crassulaceae were under the purifying selection. Among plastid genes, ycf1 and ycf2 were the most rapidly evolving genes, whereas psaC was the most conserved gene. Additionally, our phylogenetic analyses strongly supported that Crassula is sister to all other Crassulaceae species. Our findings will be useful for further evolutionary studies within the Crassula and Crassulaceae.
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Liu D, Xie X, Tong B, Zhou C, Qu K, Guo H, Zhao Z, El-Kassaby YA, Li W, Li W. A high -quality genome assembly and annotation of Quercus acutissima Carruth. FRONTIERS IN PLANT SCIENCE 2022; 13:1068802. [PMID: 36507419 PMCID: PMC9729791 DOI: 10.3389/fpls.2022.1068802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation. METHODS Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. acutissima genome. RESULTS We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Ab initio, homology-based and RNA sequence-based gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. Phylogenetic analysis showed that Q. acutissima and Q. variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication. CONCLUSION The assembled and annotated high-quality Q. acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.
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Affiliation(s)
- Dan Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Chengcheng Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai Qu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Zhiheng Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Wei Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wenqing Li
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
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Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China. Int J Mol Sci 2022; 23:ijms231911617. [PMID: 36232915 PMCID: PMC9569570 DOI: 10.3390/ijms231911617] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022] Open
Abstract
Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China.
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Li Y, Wang TR, Kozlowski G, Liu MH, Yi LT, Song YG. Complete Chloroplast Genome of an Endangered Species Quercus litseoides, and Its Comparative, Evolutionary, and Phylogenetic Study with Other Quercus Section Cyclobalanopsis Species. Genes (Basel) 2022; 13:genes13071184. [PMID: 35885967 PMCID: PMC9316884 DOI: 10.3390/genes13071184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
Quercus litseoides, an endangered montane cloud forest species, is endemic to southern China. To understand the genomic features, phylogenetic relationships, and molecular evolution of Q. litseoides, the complete chloroplast (cp) genome was analyzed and compared in Quercus section Cyclobalanopsis. The cp genome of Q. litseoides was 160,782 bp in length, with an overall guanine and cytosine (GC) content of 36.9%. It contained 131 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. A total of 165 simple sequence repeats (SSRs) and 48 long sequence repeats with A/T bias were identified in the Q. litseoides cp genome, which were mainly distributed in the large single copy region (LSC) and intergenic spacer regions. The Q. litseoides cp genome was similar in size, gene composition, and linearity of the structural region to those of Quercus species. The non-coding regions were more divergent than the coding regions, and the LSC region and small single copy region (SSC) were more divergent than the inverted repeat regions (IRs). Among the 13 divergent regions, 11 were in the LSC region, and only two were in the SSC region. Moreover, the coding sequence (CDS) of the six protein-coding genes (rps12, matK, atpF, rpoC2, rpoC1, and ndhK) were subjected to positive selection pressure when pairwise comparison of 16 species of Quercus section Cyclobalanopsis. A close relationship between Q. litseoides and Quercus edithiae was found in the phylogenetic analysis of cp genomes. Our study provided highly effective molecular markers for subsequent phylogenetic analysis, species identification, and biogeographic analysis of Quercus.
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Affiliation(s)
- Yu Li
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
| | - Tian-Rui Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland
| | - Mei-Hua Liu
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
| | - Li-Ta Yi
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
- Correspondence: (L.-T.Y.); (Y.-G.S.)
| | - Yi-Gang Song
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (Y.L.); (M.-H.L.)
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (T.-R.W.); (G.K.)
- Correspondence: (L.-T.Y.); (Y.-G.S.)
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