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Liu DK, Zhou CY, Tu XD, Zhao Z, Chen JL, Gao XY, Xu SW, Zeng MY, Ma L, Ahmad S, Li MH, Lan S, Liu ZJ. Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes. BMC Genomics 2023; 24:749. [PMID: 38057701 DOI: 10.1186/s12864-023-09847-8] [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: 01/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation. RESULTS We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnNGUU-rpl32 > rpoB-trnCGCA > psbK-psbI > psaC-rps15 > trnEUUC-trnTGGU > accD-psaI) and five coding sequences (ycf1 > rps15 > matK > psbK > ccsA) were selected as potential barcodes based on nucleotide diversity and species discrimination analysis, which suggested that the potential barcode ycf1 was most suitable for species discrimination. A total of 47-56 SSRs and 11-14 long repeats (> 20 bp) were identified in Chiloschista plastomes, and they were mostly located in the large single copy intergenic region. Phylogenetic analysis indicated that Chiloschista was monophyletic. It was clustered with Phalaenopsis and formed the basic clade of the subtribe Aeridinae with a moderate support value. The results also showed that seven Chiloschista species were divided into three major clades with full support. CONCLUSION This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.
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Affiliation(s)
- Ding-Kun Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cheng-Yuan Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiong-De Tu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuang Zhao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jin-Liao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu-Yong Gao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shao-Wei Xu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng-Yao Zeng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liang Ma
- Fujian Health College, Fuzhou, 350101, Fujian, China
| | - Sagheer Ahmad
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ming-He Li
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wee CC, Nor Muhammad NA, Subbiah VK, Arita M, Nakamura Y, Goh HH. Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:930. [PMID: 36840278 PMCID: PMC9966718 DOI: 10.3390/plants12040930] [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] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata, found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups, with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.
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Affiliation(s)
- Ching-Ching Wee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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Zong D, Qiao Z, Zhou J, Li P, Gan P, Ren M, He C. Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes. BMC Genomics 2023; 24:56. [PMID: 36721120 PMCID: PMC9887819 DOI: 10.1186/s12864-023-09154-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important commercial arbor species, which can provide us with the raw lacquer, an excellent adhesive and painting material used to make lacquer ware. Compared with diploid, triploid lacquer tree has a higher yield of raw lacquer and stronger resistance to stress. Triploid T. vernicifluum was a newly discovered natural triploid lacquer tree. However, the taxonomy of triploid T. vernicifluum has remained uncertain. Here, we sequenced and analyzed the complete chloroplast (cp) genome of triploid T. vernicifluum and compared it with related species of Toxicodendron genus based on chloroplast genome and SSR markers. RESULTS The plastome of triploid T. vernicifluum is 158,221 bp in length, including a pair of inverted repeats (IRs) of 26,462 bp, separated by a large single-copy region of 86,951 bp and a small single-copy region of 18,346 bp. In total, 132 genes including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified in the triploid T. vernicifluum. Among these, 16 genes were duplicated in the IR regions, 14 genes contain one intron, while three genes contain two introns. After nucleotide substitutions, seven small inversions were analyzed in the chloroplast genomes, eight hotspot regions were found, which could be useful molecular genetic markers for future population genetics. Phylogenetic analyses showed that triploid T. vernicifluum was a sister to T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi. Moreover, phylogenetic clustering based on the SSR markers showed that all the samples of triploid T. vernicifluum, T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi in one group, while the samples of T. vernicifluum and T. succedaneum in another group, which is consistent with the cp genome and morphological analysis. CONCLUSIONS The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, variety identification, breeding and resource exploitation, and future genetic diversity-related studies of T. vernicifluum.
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Affiliation(s)
- Dan Zong
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Zhensheng Qiao
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jintao Zhou
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Peiling Li
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Peihua Gan
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Meirong Ren
- grid.412720.20000 0004 1761 2943Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Chengzhong He
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
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Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae). BIOMED RESEARCH INTERNATIONAL 2022; 2022:5364094. [PMID: 35252450 PMCID: PMC8893999 DOI: 10.1155/2022/5364094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/11/2022] [Indexed: 01/21/2023]
Abstract
The genus Styrax L. consists of approximately 130 species distributed in the Americas, eastern Asia, and the Mediterranean region. The phylogeny and evolutionary history of this genus are not clear. Knowledge of the phylogenetic relationships and the method for species identification will be critical for the evolution of this genus. In this study, we sequenced the chloroplast genome of 17 Styrax samples and added 17 additional chloroplast genome sequences from GenBank. The data were used to investigate chloroplast genome evolution, infer phylogenetic relationships, and access the species identification rate within Styrax. The Styrax chloroplast genome contains typical quadripartite structures, ranging from 157,641 bp to 159,333 bp. The chloroplast genome contains 114 unique genes. The P distance among the Styrax species ranged from 0.0003 to 0.00611. Seventeen small inversions and SSR sites were discovered in the Styrax chloroplast genome. By comparing with the chloroplast genome sequences, six mutation hotspots were identified, and the markers ycf1b and trnT-trnL were identified as the best Styrax-specific DNA barcodes. The specific barcodes and superbarcode exhibited higher discriminatory power than universal barcodes. Chloroplast phylogenomic results improved the resolution of the phylogenetic relationships of Styrax compared to previous analyses.
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Abstract
The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Robert K Jansen
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Dong W, Xu C, Wen J, Zhou S. Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae. BMC Evol Biol 2020; 20:96. [PMID: 32736519 PMCID: PMC7393888 DOI: 10.1186/s12862-020-01661-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Chloroplast genome sequence data is very useful in studying/addressing the phylogeny of plants at various taxonomic ranks. However, there are no empirical observations on the patterns, directions, and mutation rates, which are the key topics in chloroplast genome evolution. In this study, we used Calycanthaceae as a model to investigate the evolutionary patterns, directions and rates of both nucleotide substitutions and structural mutations at different taxonomic ranks. RESULTS There were 2861 polymorphic nucleotide sites on the five chloroplast genomes, and 98% of polymorphic sites were biallelic. There was a single-nucleotide substitution bias in chloroplast genomes. A → T or T → A (2.84%) and G → C or C → G (3.65%) were found to occur significantly less frequently than the other four transversion mutation types. Synonymous mutations kept balanced pace with nonsynonymous mutations, whereas biased directions appeared between transition and transversion mutations and among transversion mutations. Of the structural mutations, indels and repeats had obvious directions, but microsatellites and inversions were non-directional. Structural mutations increased the single nucleotide mutations rates. The mutation rates per site per year were estimated to be 0.14-0.34 × 10- 9 for nucleotide substitution at different taxonomic ranks, 0.64 × 10- 11 for indels and 1.0 × 10- 11 for repeats. CONCLUSIONS Our direct counts of chloroplast genome evolution events provide raw data for correctly modeling the evolution of sequence data for phylogenetic inferences.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Jo S, Kim YK, Cheon SH, Fan Q, Kim KJ. Characterization of 20 complete plastomes from the tribe Laureae (Lauraceae) and distribution of small inversions. PLoS One 2019; 14:e0224622. [PMID: 31675370 PMCID: PMC6824564 DOI: 10.1371/journal.pone.0224622] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/17/2019] [Indexed: 01/24/2023] Open
Abstract
Lindera Thunb. (Lauraceae) consists of approximately 100 species, mainly distributed in the temperate and tropical regions of East Asia. In this study, we report 20 new, complete plastome sequences including 17 Lindera species and three related species, Actinodaphne lancifolia, Litsea japonica and Sassafras tzumu. The complete plastomes of Lindera range from 152,502 bp (L. neesiana) to 154,314 bp (L. erythrocarpa) in length. Eleven small inversion (SI) sites are documented among the plastomes. Six of the 11 SI sites are newly reported and they locate in rpoB-trnC, psbC-trnS, petA-psbJ, rpoA and ycf2 regions. The distribution patterns of SIs are useful for species identification. An average of 83 simple sequence repeats (SSRs) were detected in each plastome. The mono-SSRs accounted for 72.7% of total SSRs, followed by di- (12.4%), tetra- (9.4%), tri- (4.2%), and penta-SSRs (1.3%). Of these SSRs, 64.6% were distributed in an intergenic spacer (IGS) region. In addition, 79.8% of the SSRs are located in a large single copy (LSC) region. In contrast, almost no SSRs are distributed in inverted repeat (IR) regions. The SSR loci are useful to identifying species but the phylogenetic value is low because the majority of them show autapomorphic status or highly homoplastic characteristics. The nucleotide diversity (Pi) values also indicated the conserved nature of the IR region compared to LSC and small single copy (SSC) regions. Five spacer regions with high Pi values, trnH-psbA, petA-psbJ and ndhF-rpl32, rpl32-trnL and Ψycf1-ndhF, have a potential use for the molecular identification study of Lindera and related species. Lindera species form a paraphyletic group in the plastome tree because of the inclusion of related genera such as Actinodaphne, Laurus, Litsea and Neolitsea. A former member of tribe Laureae, Sassafras, forms a clade with the tribe Cinnamomeae. The SIs do not affect the phylogenetic relationship of Laureae. This result indicated that ancient plastome captures may have contribute to the mixed intergeneric relationship of Laureae. Alternatively, the result may indicate that the morphological characters defined the genera of Lauraceae originated for several times.
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Affiliation(s)
- Sangjin Jo
- School of Life Sciences, Korea University, Seoul, Korea
| | - Young-Kee Kim
- School of Life Sciences, Korea University, Seoul, Korea
| | - Se-Hwan Cheon
- School of Life Sciences, Korea University, Seoul, Korea
| | - Qiang Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ki-Joong Kim
- School of Life Sciences, Korea University, Seoul, Korea
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Zong D, Gan P, Zhou A, Li J, Xie Z, Duan A, He C. Comparative analysis of the complete chloroplast genomes of seven Populus species: Insights into alternative female parents of Populus tomentosa. PLoS One 2019; 14:e0218455. [PMID: 31216332 PMCID: PMC6583991 DOI: 10.1371/journal.pone.0218455] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 06/03/2019] [Indexed: 12/25/2022] Open
Abstract
Populus tomentosa, of section Populus, is distributed mainly in northern China. This species has high resistance to many diseases and insects, and it plays key roles in shelterbelts and urban afforestation in northern China. It has long been suspected to be a hybrid, but its parents remain unknown. In the present study, we report four newly sequenced complete cp genomes from section Populus and comparative genomic analyses of these new sequences and three published cp genome sequences. The seven cp genomes ranged from 155,853 bp (P. tremula var. davidiana) to 156,746 bp (P. adenopoda) in length, and their gene orders, gene numbers and GC contents were similar. We analyzed SNPs, indels, SSRs and repeats among the seven cp genomes, and eight small inversions were detected in the ndhC-trnV, rbcL-accD, petA-psbJ, trnW-trnP, rpl16-rps3, trnL-ycf15, ycf15-trnL, and ndhF-trnL intergenic regions. Furthermore, seven divergent regions (trnH-psbA, matK, psbM-psbD, ndhC-trnV, ycf1, ndhF-ccsA and ccsA-ndhD) were found in more highly variable regions. The phylogenetic tree reveals that P. tomentosa is closely related to P. alba and P. alba var. pyramidalis. Hence, P. alba was involved in the formation of P. tomentosa.
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Affiliation(s)
- Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Peihua Gan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Anpei Zhou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Jinyu Li
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Zhongli Xie
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Anan Duan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
| | - Chengzhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
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Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M. Comparative Chloroplast Genomes of Sorghum Species: Sequence Divergence and Phylogenetic Relationships. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5046958. [PMID: 31016191 PMCID: PMC6444266 DOI: 10.1155/2019/5046958] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/22/2019] [Accepted: 02/26/2019] [Indexed: 11/18/2022]
Abstract
Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.
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Affiliation(s)
- Yun Song
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Yan Chen
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Jizhou Lv
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Jin Xu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - MingFu Li
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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Zong D, Zhou A, Zhang Y, Zou X, Li D, Duan A, He C. Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses. PeerJ 2019; 7:e6386. [PMID: 30809432 PMCID: PMC6387583 DOI: 10.7717/peerj.6386] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/02/2019] [Indexed: 12/28/2022] Open
Abstract
Species of the genus Populus, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five Populus species (Populus cathayana, P. kangdingensis, P. pseudoglauca, P. schneideri, and P. xiangchengensis) were compared. The chloroplast genomes of the five Populus species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (ccsA+ccsA-ndhD, ndhC-trnV, psbZ-trnfM, trnG-atpA, trnL-ndhJ, trnR-trnN, ycf4-cemA, ycf1, and trnR-trnN), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (rpoC2 and rbcL) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that P. schneideri had a close relationship with P. kangdingensis and P. pseudoglauca, while P. xiangchengensis was a sister to P. cathayana.
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Affiliation(s)
- Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan, China
| | - Anpei Zhou
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan, China
| | - Yao Zhang
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan, China
| | - Xinlian Zou
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan, China
| | - Dan Li
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan, China
| | - Anan Duan
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
| | - Chengzhong He
- Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
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11
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Jo S, Kim HW, Kim YK, Sohn JY, Cheon SH, Kim KJ. The complete plastome of tropical fruit Garcinia mangostana (Clusiaceae). Mitochondrial DNA B Resour 2017; 2:722-724. [PMID: 33490474 PMCID: PMC7800348 DOI: 10.1080/23802359.2017.1390406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/06/2017] [Indexed: 01/12/2023] Open
Abstract
The complete plastome sequence of Garcinia mangostana L. (Clusiaceae) is completed in this study (NCBI acc. no. KX822787). This is a first complete plastome sequence from the Clusiaceae. The complete plastome size is 158,179 bp in length and consists of a large single copy of 86,458 bp and a small single copy of 17,703 bp, separated by two inverted repeats of 27,009 bp. The G. mangostana plastome shows four minor structural modifications including infA gene loss, rpl32 gene loss, ycf3 gene intron loss and a 363 bp inversion between trnV-UAC and atpE gene. The plastome contains 111 genes, of which 77 are protein-coding genes, 30 are tRNA genes and four are rRNA genes. The average A-T content of the plastome is 63.9%. A total of 110 simple sequence loci are identified from the genome. Phylogenetic analysis reveals that G. mangostana is a sister group of Erythroxylum novogranatense (Erythroxylaceae) with 78% bootstrap support.
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Affiliation(s)
- Sangjin Jo
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Hoe-Won Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Jung-Yeon Sohn
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul, Korea
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12
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Lhee D, Yang EC, Kim JI, Nakayama T, Zuccarello G, Andersen RA, Yoon HS. Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp. nov. and the Chromatophore Genome Sequence for strain KR01. Protist 2017; 168:155-170. [PMID: 28262587 DOI: 10.1016/j.protis.2017.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/18/2017] [Accepted: 01/31/2017] [Indexed: 11/17/2022]
Abstract
The thecate filose amoeba Paulinella chromatophora is a good model organism for understanding plastid organellogenesis because its chromatophore was newly derived from an alpha-cyanobacterium. Paulinella chromatophora was the only known photosynthetic Paulinella species until recent studies that suggested a species level of diversity. Here, we described a new photosynthetic species P. micropora sp. nov. based on morphological and molecular evidence from a newly established strain KR01. The chromatophore genome of P. micropora KR01 was fully determined; the genome was 976,991bp in length, the GC content was 39.9%, and 908 genes were annotated. A pairwise comparison of chromatophore genome sequences between strains KR01 and FK01, representing two different natural populations of P. micropora, showed a 99.85% similarity. Differences between the two strains included single nucleotide polymorphisms (SNPs) in CDSs, which resulted in 357 synonymous and 280 nonsynonymous changes, along with 245 SNPs in non-coding regions. Indels (37) and microinversions (14) were also detected. Species diversity for photosynthetic Paulinella was surveyed using samples collected from around the world. We compared our new species to two photosynthetic species, P. chromatophora and P. longichromatophora. Phylogenetic analyses using four gene markers revealed three distinct lineages of photosynthetic Paulinella species including P. micropora sp. nov.
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Affiliation(s)
- Duckhyun Lhee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Eun Chan Yang
- Marine Ecosystem Research Center, Korea Institute of Ocean Science & Technology, Ansan 15627, Republic of Korea
| | - Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Takuro Nakayama
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Giuseppe Zuccarello
- School of Biological Sciences, Victoria University of Wellington, Wellington 6041, New Zealand
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, 98250, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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13
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Dong W, Xu C, Li D, Jin X, Li R, Lu Q, Suo Z. Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). PeerJ 2016; 4:e2699. [PMID: 27867769 PMCID: PMC5111891 DOI: 10.7717/peerj.2699] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/18/2016] [Indexed: 12/11/2022] Open
Abstract
The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Delu Li
- Gansu Desert Control Research Institute , Gansu , China
| | - Xiaobai Jin
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing , China
| | - Ruili Li
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing , China
| | - Qi Lu
- Institute of Desertification Studies, Chinese Academy of Forestry , Beijing , China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing , China
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Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species. Gene 2014; 549:58-69. [PMID: 25042453 DOI: 10.1016/j.gene.2014.07.041] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 06/05/2014] [Accepted: 07/12/2014] [Indexed: 11/21/2022]
Abstract
Praxelis (Eupatorium catarium Veldkamp) is a new hazardous invasive plant species that has caused serious economic losses and environmental damage in the Northern hemisphere tropical and subtropical regions. Although previous studies focused on detecting the biological characteristics of this plant to prevent its expansion, little effort has been made to understand the impact of Praxelis on the ecosystem in an evolutionary process. The genetic information of Praxelis is required for further phylogenetic identification and evolutionary studies. Here, we report the complete Praxelis chloroplast (cp) genome sequence. The Praxelis chloroplast genome is 151,410 bp in length including a small single-copy region (18,547 bp) and a large single-copy region (85,311 bp) separated by a pair of inverted repeats (IRs; 23,776 bp). The genome contains 85 unique and 18 duplicated genes in the IR region. The gene content and organization are similar to other Asteraceae tribe cp genomes. We also analyzed the whole cp genome sequence, repeat structure, codon usage, contraction of the IR and gene structure/organization features between native and invasive Asteraceae plants, in order to understand the evolution of organelle genomes between native and invasive Asteraceae. Comparative analysis identified the 14 markers containing greater than 2% parsimony-informative characters, indicating that they are potential informative markers for barcoding and phylogenetic analysis. Moreover, a sister relationship between Praxelis and seven other species in Asteraceae was found based on phylogenetic analysis of 28 protein-coding sequences. Complete cp genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family.
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Abstract
The plastid genome (plastome) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations are allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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16
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Huotari T, Korpelainen H. Comparative analyses of plastid sequences between native and introduced populations of aquatic weeds Elodea canadensis and E. nuttallii. PLoS One 2013; 8:e58073. [PMID: 23620722 PMCID: PMC3631202 DOI: 10.1371/journal.pone.0058073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 01/30/2013] [Indexed: 11/23/2022] Open
Abstract
Non-indigenous species (NIS) are species living outside their historic or native range. Invasive NIS often cause severe environmental impacts, and may have large economical and social consequences. Elodea (Hydrocharitaceae) is a New World genus with at least five submerged aquatic angiosperm species living in fresh water environments. Our aim was to survey the geographical distribution of cpDNA haplotypes within the native and introduced ranges of invasive aquatic weeds Elodea canadensis and E. nuttallii and to reconstruct the spreading histories of these invasive species. In order to reveal informative chloroplast (cp) genome regions for phylogeographic analyses, we compared the plastid sequences of native and introduced individuals of E. canadensis. In total, we found 235 variable sites (186 SNPs, 47 indels and two inversions) between the two plastid sequences consisting of 112,193 bp and developed primers flanking the most variable genomic areas. These 29 primer pairs were used to compare the level and pattern of intraspecific variation within E. canadensis to interspecific variation between E. canadensis and E. nuttallii. Nine potentially informative primer pairs were used to analyze the phylogeographic structure of both Elodea species, based on 70 E. canadensis and 25 E. nuttallii individuals covering native and introduced distributions. On the whole, the level of variation between the two Elodea species was 53% higher than that within E. canadensis. In our phylogeographic analysis, only a single haplotype was found in the introduced range in both species. These haplotypes H1 (E. canadensis) and A (E. nuttallii) were also widespread in the native range, covering the majority of native populations analyzed. Therefore, we were not able to identify either the geographic origin of the introduced populations or test the hypothesis of single versus multiple introductions. The divergence between E. canadensis haplotypes was surprisingly high, and future research may clarify mechanisms that structure native E. canadensis populations.
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Affiliation(s)
- Tea Huotari
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
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17
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de Bivort BL, Clouse RM, Giribet G. A cladistic reconstruction of the ancestral mite harvestman (Arachnida, Opiliones, Cyphophthalmi): portrait of a Paleozoic detritivore. Cladistics 2012; 28:582-597. [DOI: 10.1111/j.1096-0031.2012.00407.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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18
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Yi DK, Kim KJ. Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS One 2012; 7:e35872. [PMID: 22606240 PMCID: PMC3351433 DOI: 10.1371/journal.pone.0035872] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 03/23/2012] [Indexed: 01/08/2023] Open
Abstract
Sesamum indicum is an important crop plant species for yielding oil. The complete chloroplast (cp) genome of S. indicum (GenBank acc no. JN637766) is 153,324 bp in length, and has a pair of inverted repeat (IR) regions consisting of 25,141 bp each. The lengths of the large single copy (LSC) and the small single copy (SSC) regions are 85,170 bp and 17,872 bp, respectively. Comparative cp DNA sequence analyses of S. indicum with other cp genomes reveal that the genome structure, gene order, gene and intron contents, AT contents, codon usage, and transcription units are similar to the typical angiosperm cp genomes. Nucleotide diversity of the IR region between Sesamum and three other cp genomes is much lower than that of the LSC and SSC regions in both the coding region and noncoding region. As a summary, the regional constraints strongly affect the sequence evolution of the cp genomes, while the functional constraints weakly affect the sequence evolution of cp genomes. Five short inversions associated with short palindromic sequences that form step-loop structures were observed in the chloroplast genome of S. indicum. Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum. Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum. Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors. The complete cp DNA sequences of S. indicum reported in this paper are prerequisite to modifying this important oilseed crop by cp genetic engineering techniques.
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Affiliation(s)
- Dong-Keun Yi
- School of Life Sciences, Korea University, Seoul, Korea
| | - Ki-Joong Kim
- School of Life Sciences, Korea University, Seoul, Korea
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19
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Braun EL, Kimball RT, Han KL, Iuhasz-Velez NR, Bonilla AJ, Chojnowski JL, Smith JV, Bowie RCK, Braun MJ, Hackett SJ, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Witt CC, Yuri T. Homoplastic microinversions and the avian tree of life. BMC Evol Biol 2011; 11:141. [PMID: 21612607 PMCID: PMC3123225 DOI: 10.1186/1471-2148-11-141] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 05/25/2011] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. RESULTS We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. CONCLUSIONS Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies.
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Affiliation(s)
- Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | | | - Amber J Bonilla
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Jena L Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Jordan V Smith
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Rauri CK Bowie
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Shannon J Hackett
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
| | - John Harshman
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
- 4869 Pepperwood Way, San Jose, CA 95124, USA
| | - Christopher J Huddleston
- Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Ben D Marks
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kathleen J Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - William S Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Sushma Reddy
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
- Biology Department, Loyola University Chicago, Chicago, IL 60626, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Christopher C Witt
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
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20
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Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, Al-Mssallem IS, Yu J. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 2010; 5:e12762. [PMID: 20856810 PMCID: PMC2939885 DOI: 10.1371/journal.pone.0012762] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 08/23/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Date palm (Phoenix dactylifera L.), a member of Arecaceae family, is one of the three major economically important woody palms--the two other palms being oil palm and coconut tree--and its fruit is a staple food among Middle East and North African nations, as well as many other tropical and subtropical regions. Here we report a complete sequence of the data palm chloroplast (cp) genome based on pyrosequencing. METHODOLOGY/PRINCIPAL FINDINGS After extracting 369,022 cp sequencing reads from our whole-genome-shotgun data, we put together an assembly and validated it with intensive PCR-based verification, coupled with PCR product sequencing. The date palm cp genome is 158,462 bp in length and has a typical quadripartite structure of the large (LSC, 86,198 bp) and small single-copy (SSC, 17,712 bp) regions separated by a pair of inverted repeats (IRs, 27,276 bp). Similar to what has been found among most angiosperms, the date palm cp genome harbors 112 unique genes and 19 duplicated fragments in the IR regions. The junctions between LSC/IRs and SSC/IRs show different features of sequence expansion in evolution. We identified 78 SNPs as major intravarietal polymorphisms within the population of a specific cp genome, most of which were located in genes with vital functions. Based on RNA-sequencing data, we also found 18 polycistronic transcription units and three highly expression-biased genes--atpF, trnA-UGC, and rrn23. CONCLUSIONS Unlike most monocots, date palm has a typical cp genome similar to that of tobacco--with little rearrangement and gene loss or gain. High-throughput sequencing technology facilitates the identification of intravarietal variations in cp genomes among different cultivars. Moreover, transcriptomic analysis of cp genes provides clues for uncovering regulatory mechanisms of transcription and translation in chloroplasts.
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Affiliation(s)
- Meng Yang
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Xiaowei Zhang
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Guiming Liu
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Yuxin Yin
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Kaifu Chen
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Quanzheng Yun
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Duojun Zhao
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Ibrahim S. Al-Mssallem
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Department of Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Hssa, Hofuf, Kingdom of Saudi Arabia
| | - Jun Yu
- The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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Whitlock BA, Hale AM, Groff PA. Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PLoS One 2010; 5:e11533. [PMID: 20644717 PMCID: PMC2903610 DOI: 10.1371/journal.pone.0011533] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/17/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. METHODOLOGY/PRINCIPAL FINDINGS Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. CONCLUSIONS/SIGNIFICANCE Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.
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WORTH JRP, JORDAN GJ, MARTHICK JR, MCKINNON GE, VAILLANCOURT RE. Chloroplast evidence for geographic stasis of the Australian bird-dispersed shrub Tasmannia lanceolata (Winteraceae). Mol Ecol 2010; 19:2949-63. [DOI: 10.1111/j.1365-294x.2010.04725.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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