1
|
Shi Y, Chen Z, Jiang J, Wu W, Yu W, Zhang S, Zeng W. The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata. FRONTIERS IN PLANT SCIENCE 2024; 15:1439245. [PMID: 39290737 PMCID: PMC11405213 DOI: 10.3389/fpls.2024.1439245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024]
Abstract
Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.
Collapse
Affiliation(s)
- Yujie Shi
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Zhen Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Jingyong Jiang
- Institute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry (A&F) University, Hangzhou, China
| | - Weifu Yu
- Zhejiang Hongshiliang Group Tiantai Mountain Wu-Yao Co., Ltd., RedRock Group, Taizhou, China
| | - Shumeng Zhang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Wei Zeng
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| |
Collapse
|
2
|
Lan ZQ, Zheng W, Talavera A, Nie ZL, Liu J, Johnson G, Yin XM, Zhao WQ, Zhao ZY, Handy SM, Wen J. Comparative and phylogenetic analyses of plastid genomes of the medicinally important genus Alisma (Alismataceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1415253. [PMID: 39233910 PMCID: PMC11372848 DOI: 10.3389/fpls.2024.1415253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Alisma L. is a medicinally important genus of aquatic and wetland plants consisting of c. 10 recognized species. However, largely due to polyploidy and limited taxon and gene sampling, the phylogenomic relationships of Alisma remain challenging. In this study, we sequenced 34 accessions of Alismataceae, including eight of the ten species of Alisma, one species of Echinodorus and one species of Luronium, to perform comparative analyses of plastid genomes and phylogenetic analyses. Comparative analysis of plastid genomes revealed high sequence similarity among species within the genus. Our study analyzed structural changes and variations in the plastomes of Alisma, including IR expansion or contraction, and gene duplication or loss. Phylogenetic results suggest that Alisma is monophyletic, and constitutes four groups: (1) A. lanceolatum and A. canaliculatum; (2) the North American clade of A. subcordatum and A. triviale; (3) A. wahlenbergii and A. gramineum; and (4) A. plantago-aquatica from Eurasia and northern Africa with the eastern Asian A. orientale nested within it. Hence the results challenge the recognition of A. orientale as a distinct species and raise the possibility of treating it as a synonym of the widespread A. plantago-aquatica. The well-known Alismatis Rhizoma (Zexie) in Chinese medicine was likely derived from the morphologically variable Alisma plantago-aquatica throughout its long history of cultivation in Asia. The plastome phylogenetic results also support the tetraploid A. lanceolatum as the likely maternal parent of the hexaploid eastern Asian A. canaliculatum.
Collapse
Affiliation(s)
- Zhi-Qiong Lan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Wen Zheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Alicia Talavera
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Málaga, Spain
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Jing Liu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Xian-Mei Yin
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wen-Qi Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zong-Yi Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy/College of Modern Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, United States
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| |
Collapse
|
3
|
Tian X, Guo J, Song Y, Yu Q, Liu C, Fu Z, Shi Y, Shao Y, Yuan Z. Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses. Ecol Evol 2024; 14:e11119. [PMID: 38469045 PMCID: PMC10927362 DOI: 10.1002/ece3.11119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/08/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis-related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.
Collapse
Affiliation(s)
- Xiangyu Tian
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| | - Jia Guo
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education)Guangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinGuangxiChina
| | - Qunfei Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnanChina
| | - Chao Liu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Zhixi Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Yuhua Shi
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yizhen Shao
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhiliang Yuan
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| |
Collapse
|
4
|
Shi Y, Chen Z, Jiang J, Li X, Zeng W. Comparative Analysis of Chloroplast Genomes of "Tiantai Wu-Yao" ( Lindera aggregata) and Taxa of the Same Genus and Different Genera. Genes (Basel) 2024; 15:263. [PMID: 38540322 PMCID: PMC10970223 DOI: 10.3390/genes15030263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 06/15/2024] Open
Abstract
Lindera aggregata is a species of the Lauraceae family, which has important medicinal, economic and ornamental values. In this study, we sequenced, assembled and annotated the chloroplast genome of L. aggregata and reannotated and corrected eight unverified annotations in the same genus. The chloroplast genomes taxa from Lindera and from different genera of Lauraceae were compared and analyzed, and their phylogenetic relationship and divergence time were speculated. All the 36 chloroplast genomes had typical quadripartite structures that ranged from 150,749 to 154,736 bp in total length. These genomes encoded 111-112 unique genes, including 78-79 protein-coding genes, 29-30 tRNA and 4 rRNA. Furthermore, there were 78-97 SSRs loci in these genomes, in which mononucleotide repeats were the most abundant; there were 24-49 interspersed repeats, and forward repeat types were the most frequent. The codon bias patterns of all species tended to use codons ending with A or U. Five and six highly variable regions were identified within genus and between genera, respectively, and three common regions (ycf1, ndhF-rpl32 and rpl32-trnL) were identified, which can be used as important DNA markers for phylogeny and species identification. According to the evaluation of the Ka/Ks ratio, most of the genes were under purifying selection, and only 10 genes were under positive selection. Finally, through the construction of the evolutionary tree of 39 chloroplast genomes, the phylogenetic relationship of Lauraceae was clarified and the evolutionary relationship of Lindera was revealed. The species of genus Lindera experienced rapid adaptive radiation from Miocene to Pleistocene. The results provided valuable insights for the study of chloroplast genomes in the Lauraceae family, especially in the genus Lindera.
Collapse
Affiliation(s)
- Yujie Shi
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou 318000, China; (Y.S.); (Z.C.)
| | - Zhen Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou 318000, China; (Y.S.); (Z.C.)
| | - Jingyong Jiang
- Institute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai 317000, China;
| | - Xiaobai Li
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Wei Zeng
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou 318000, China; (Y.S.); (Z.C.)
| |
Collapse
|
5
|
Cao Z, Yang L, Xin Y, Xu W, Li Q, Zhang H, Tu Y, Song Y, Xin P. Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1205051. [PMID: 37484476 PMCID: PMC10362447 DOI: 10.3389/fpls.2023.1205051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/29/2023] [Indexed: 07/25/2023]
Abstract
The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.
Collapse
Affiliation(s)
- Zhengying Cao
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Linyi Yang
- Yunnan Forestry Vocational and Technical College, Kunming, Yunnan, China
| | - Yaxuan Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Wenbin Xu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qishao Li
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Haorong Zhang
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yuxiang Tu
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| |
Collapse
|
6
|
Zhang Y, Zhou J, Tng DYP, Wang S, Wang Y, Peng Y, Liu H, Wang Z. Phylogeny and Systematics of Sassafras (Lauraceae), an Interesting Genus with Disjunct Distributions in Eastern North America and East Asia. PLANTS (BASEL, SWITZERLAND) 2023; 12:1419. [PMID: 36987107 PMCID: PMC10058790 DOI: 10.3390/plants12061419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
The Lauraceae is a family of the order Laurales, with 2500-3000 species comprising 50 genera, mainly distributed in tropical and subtropical evergreen broad-leaved forests. Up to two decades ago, the systematic classification of the Lauraceae was based on floral morphology, but molecular phylogenetic approaches have made tremendous advances in elucidating tribe- and genus-level relationships within the family in recent decades. Our review focused on the phylogeny and systematics of Sassafras, a genus of three species with highly disjunct distributions in eastern North America and East Asia, whose tribe affiliation within the Lauraceae has long been controversial. By synthesizing information on the floral biology and molecular phylogeny of Sassafras, this review aimed to explore the position of Sassafras within the Lauraceae, and to provide suggestions and implications for future phylogenetic studies. Our synthesis highlighted Sassafras as a transitional type between Cinnamomeae and Laureae with a closer genetic relationship with Cinnamomeae, as revealed by molecular phylogenetic evidence, while it shares many similar characteristics with Laureae in morphology. We therefore discovered that several molecular and morphological methods should be concurrently considered to illuminate the phylogeny and systematics of Sassafras in Lauraceae.
Collapse
Affiliation(s)
- Yunyan Zhang
- College of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.Z.)
| | - Jingbo Zhou
- College of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.Z.)
| | - David Y. P. Tng
- Centre for Rainforest Studies, The School for Field Studies, Yungaburra, Queensland 4884, Australia
| | - Shuang Wang
- College of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.Z.)
| | - Ying Wang
- College of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.Z.)
| | - Ye Peng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hong Liu
- Center for Tropical Plant Conservation, Fairchild Tropical Botanic Garden, Coral Gables, Miami, FL 33156, USA
- Department of Earth and Environment, Florida International University, Miami, FL 33199, USA
| | - Zhongsheng Wang
- College of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.Z.)
| |
Collapse
|
7
|
Shi W, Song W, Chen Z, Cai H, Gong Q, Liu J, Shi C, Wang S. Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin. PeerJ 2023; 11:e14573. [PMID: 36755871 PMCID: PMC9901306 DOI: 10.7717/peerj.14573] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/28/2022] [Indexed: 02/05/2023] Open
Abstract
The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA-psbE, ndhF-rpl32, and psbM-trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.
Collapse
Affiliation(s)
- Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Zimeng Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Haohong Cai
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Qin Gong
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| |
Collapse
|
8
|
Du S, Hu X, Guo Y, Wang S, Yang X, Wu Z, Huang Y. A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube. AOB PLANTS 2023; 15:plad006. [PMID: 37025103 PMCID: PMC10071050 DOI: 10.1093/aobpla/plad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/17/2023] [Indexed: 06/19/2023]
Abstract
Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.
Collapse
Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoyan Hu
- College of Food Science and Technology, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yuanting Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shengji Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | | | - Zhenzhen Wu
- Taian Dushihuaxiang Agricultural Technology Co., Ltd, Taian, Shandong, China
| | - Yuyin Huang
- Shandong Huinongtianxia Science and Technology Information Consulting Co., Ltd, Taian, Shandong, China
| |
Collapse
|
9
|
Li X, Zhang Q, Weng G, Zhu M, Wang X. Analysis and characterization of the chloroplast genome of Stephania cepharantha Hayata. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2100719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Xinran Li
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Qingyan Zhang
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Guiying Weng
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Miao Zhu
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| | - Xuying Wang
- Department of Plant Science and Technology, School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, PR China
| |
Collapse
|
10
|
Han L, Cai J, Chen H, Liu C. Complete plastid genome of Litsea honghoensis Liou 1933, an endangered evergreen species in China. Mitochondrial DNA B Resour 2022; 7:1707-1708. [PMID: 36188668 PMCID: PMC9518278 DOI: 10.1080/23802359.2022.2122884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Litsea honghoensis Liou is an endangered tree endemic to south China. In this study, the first complete plastid genome of L. honghoensis was presented, which had a length of 152,605 base pairs (bp) with a GC content of 39.20%. The genome consisted of a large single-copy (LSC) region of 93,560 bp, a small single-copy (SSC) region of 18,905 bp, and two inverted repeat regions (IRa and IRb) of 20,070 bp. There were 125 genes in the plastid genome, including 81 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Phylogenomic analysis based on 52 complete plastomes of Laureae in the family Lauraceae supports the close relationships among L. honghoensis, Lindera communis, Lindera nacusua, Lindera angustifolia, and Lindera glauca.
Collapse
Affiliation(s)
- Lihong Han
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, China
| | - Jian Cai
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, China
| | - Huanhuan Chen
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, China
| | - Chao Liu
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, China
| |
Collapse
|
11
|
Liu C, Chen HH, Tang LZ, Khine PK, Han LH, Song Y, Tan YH. Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae). PLANT DIVERSITY 2022; 44:377-388. [PMID: 35967258 PMCID: PMC9363652 DOI: 10.1016/j.pld.2021.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 06/15/2023]
Abstract
Litsea, a non-monophyletic group of the tribe Laureae (Lauraceae), plays important roles in the tropical and subtropical forests of Asia, Australia, Central and North America, and the islands of the Pacific. However, intergeneric relationships between Litsea and Laurus, Lindera, Parasassafras and Sinosassafras of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced Litsea plastomes, together with 47 Laureae plastomes obtained from public databases, representing six genera of the Laureae. Our results highlight two highly supported monophyletic groups of Litsea taxa. One is composed of 16 Litsea taxa and two Lindera taxa. The 18 plastomes of these taxa were further compared for their gene structure, codon usage, contraction and expansion of inverted repeats, sequence repeats, divergence hotspots, and gene evolution. The complete plastome size of newly sequenced taxa varied between 152,377 bp (Litsea auriculata) and 154,117 bp (Litsea pierrei). Seven of the 16 Litsea plastomes have a pair of insertions in the IRa (trnL-trnH) and IRb (ycf2) regions. The 18 plastomes of Litsea and Lindera taxa exhibit similar gene features, codon usage, oligonucleotide repeats, and inverted repeat dynamics. The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots, which are located in the same regions. We also identified six protein coding genes (accD, ndhJ, rbcL, rpoC2, ycf1 and ycf2) under positive selection in Litsea; these genes may play important roles in adaptation of Litsea species to various environments.
Collapse
Affiliation(s)
- Chao Liu
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Huan-Huan Chen
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Li-Zhou Tang
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Phyo Kay Khine
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Li-Hong Han
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, 541004, China
| | - Yun-Hong Tan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| |
Collapse
|
12
|
Dong Z, Zhang R, Shi M, Song Y, Xin Y, Li F, Ma J, Xin P. The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis. PLoS One 2022; 17:e0269819. [PMID: 35771795 PMCID: PMC9246242 DOI: 10.1371/journal.pone.0269819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022] Open
Abstract
Brassaiopsis angustifolia K.M. Feng belongs to the family Araliaceae, and is an endangered shrub species in southwest China. Despite the importance of this species, the plastid genome has not been sequenced and analyzed. In this study, the complete plastid genome of B. angustifolia was sequenced, analyzed, and compared to the eight species in the Araliaceae family. Our study reveals that the complete plastid genome of B. angustifolia is 156,534 bp long, with an overall GC content of 37.9%. The chloroplast genome (cp) encodes 133 genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. Five highly divergent regions were successfully identified that could be used as potential genetic markers of Brassaiopsis and Asian Palmate group. Phylogenetic analysis of 47 plastomes, representing 19 genera of Araliaceae and two related families, was performed to reconstruct highly supported relationships for the Araliaceae, which highlight four well-supported clades of the Hydrocotyle group, Greater Raukaua group, Aralia-Panax group, and Asian Palmate group. The genus Brassaiopsis can be divided into four groups using internal transcribed spacer (ITS) data. The results indicate that plastome and ITS data can contribute to investigations of the taxonomy, and phylogeny of B. angustifolia. This study provides a theoretical basis for species identification and future biological research on resources of the genus Brassaiopsis.
Collapse
Affiliation(s)
- Zhanghong Dong
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Ruli Zhang
- Sympodial Bamboos Technological and Engineering Research Center, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Ming Shi
- Sympodial Bamboos Technological and Engineering Research Center, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Normal University, Guilin, China
| | - Yaxuan Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Feng Li
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Jianzhong Ma
- Yunnan Academy of Forestry and Grassland, Kunming, China
- * E-mail: (JM); (PX)
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- * E-mail: (JM); (PX)
| |
Collapse
|
13
|
Guzmán-Díaz S, Núñez FAA, Veltjen E, Asselman P, Larridon I, Samain MS. Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030448. [PMID: 35161429 PMCID: PMC8838774 DOI: 10.3390/plants11030448] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 05/13/2023]
Abstract
Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.
Collapse
Affiliation(s)
- Salvador Guzmán-Díaz
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Correspondence:
| | - Fabián Augusto Aldaba Núñez
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
| | - Emily Veltjen
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Ghent University Botanical Garden, Ghent University, 9000 Gent, Belgium
| | - Pieter Asselman
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
| | - Isabel Larridon
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Marie-Stéphanie Samain
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro 61600, Mexico; (F.A.A.N.); (M.-S.S.)
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, 9000 Gent, Belgium; (E.V.); (P.A.); (I.L.)
| |
Collapse
|
14
|
Trofimov D, Cadar D, Schmidt-Chanasit J, Rodrigues de Moraes PL, Rohwer JG. A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex. Sci Rep 2022; 12:1120. [PMID: 35064146 PMCID: PMC8782842 DOI: 10.1038/s41598-021-04635-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/28/2021] [Indexed: 12/15/2022] Open
Abstract
The genus Ocotea (Lauraceae) includes about 450 species, of which about 90% are Neotropical, while the rest is from Macaronesia, Africa and Madagascar. In this study we present the first complete chloroplast genome sequences of seven Ocotea species, six Neotropical and one from Macaronesia. Genome sizes range from 152,630 (O. porosa) to 152,685 bp (O. aciphylla). All seven plastomes contain a total of 131 (114 unique) genes, among which 87 (80 unique) encode proteins. The order of genes (if present) is the same in all Lauraceae examined so far. Two hypervariable loci were found in the LSC region (psbA-trnH, ycf2), three in the SSC region (ycf1, ndhH, trnL(UAG)-ndhF). The pairwise cp genomic alignment between the taxa showed that the LSC and SSC regions are more variable compared to the IR regions. The protein coding regions comprise 25,503-25,520 codons in the Ocotea plastomes examined. The most frequent amino acids encoded in the plastomes were leucine, isoleucine, and serine. SSRs were found to be more frequent in the two dioecious Neotropical Ocotea species than in the four bisexual species and the gynodioecious species examined (87 vs. 75-84 SSRs). A preliminary phylogenetic analysis based on 69 complete plastomes of Lauraceae species shows the seven Ocotea species as sister group to Cinnamomum sensu lato. Sequence divergence among the Ocotea species appears to be much lower than among species of the most closely related, likewise species-rich genera Cinnamomum, Lindera and Litsea.
Collapse
Affiliation(s)
- Dimitrij Trofimov
- Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststraße 18, 22609, Hamburg, Germany.
- Institute of Ecology and Evolution, Universität Jena, Philosophenweg 16, 07743, Jena, Germany.
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359, Hamburg, Germany
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359, Hamburg, Germany
| | - Pedro Luís Rodrigues de Moraes
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Av. 24 A 1515, Bela Vista, Rio Claro, Caixa Postal 199, São Paulo, CEP 13506-900, Brazil
| | - Jens G Rohwer
- Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststraße 18, 22609, Hamburg, Germany.
| |
Collapse
|
15
|
Li C, Cai C, Tao Y, Sun Z, Jiang M, Chen L, Li J. Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:754209. [PMID: 34721483 PMCID: PMC8551639 DOI: 10.3389/fpls.2021.754209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 06/02/2023]
Abstract
Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.
Collapse
Affiliation(s)
- Chenxin Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Yutian Tao
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| |
Collapse
|
16
|
Lugon MD, dos Santos PHD, Oliveira PV, de Almeida FAN, Luber J, Forzza RC, Jardim MAG, Paneto GG. Is Your Açaí Really from Amazon? Using DNA Barcoding to Authenticate Commercial Products. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-01998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
17
|
Research Progress in Plant Molecular Systematics of Lauraceae. BIOLOGY 2021; 10:biology10050391. [PMID: 34062846 PMCID: PMC8147330 DOI: 10.3390/biology10050391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Lauraceae, as an angiosperm group with high ecological and economic value, has been widely studied. With the development of science and technology, the research of Lauraceae has changed from morphology to molecular systematics. Our paper reviewed the molecular phylogeny of Lauraceae in recent years. From the aspects of gene fragments, chloroplast genome and DNA barcodes, we mainly discussed the establishment of Cinnamomeae in the ‘Core Lauraceae’ and the tribal controversial genera (Actinodaphne, Sassafras, Caryodaphnopsis, Neocinnamomum and Cassytha). We think that the whole genome and inflorescence characteristics are the breakthrough to solve the tribal problem of Lauraceae. Using reliable molecular and morphological evidence to reconstruct the phylogenetic relationship of Lauraceae will provide an important theoretical basis for the rational utilization of Lauraceae resources, the development of potential resources and the protection of rare plants. Abstract Lauraceae is a large family of woody plants with high ecological and economic value. The tribal and generic division and phylogenetic relationship of Lauraceae have long been controversial. Based on morphological and molecular evidence, phylogenetic relationships within the Cinnamomeae, Laureae and Perseeae tribes, also called ‘the Core Lauraceae’, have arisen particular attention. In this review, we comprehensively collated the literatures on the phylogeny of Lauraceae published in recent years and summarized progress made in molecular systematic researches employing gene fragments, chloroplast genomes and DNA barcodings analyses. We clarified the phylogenetic relationships and main controversies of ‘the Core Lauraceae’, the systemic position of fuzzy genera (Neocinnamomum, Caryodaphnopsis and Cassytha) and the development of chloroplast genome and DNA barcodes. We further suggested and proposed the whole genome analysis and different inflorescence types would be possible to provide more information for further research on phylogenetic relationships and taxonomy of Lauraceae.
Collapse
|
18
|
Xavier JKAM, Maia L, Figueiredo PLB, Folador A, Ramos AR, Andrade EH, Maia JGS, Setzer WN, da Silva JKR. Essential Oil Composition and DNA Barcode and Identification of Aniba species (Lauraceae) Growing in the Amazon Region. Molecules 2021; 26:1914. [PMID: 33805452 PMCID: PMC8036375 DOI: 10.3390/molecules26071914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022] Open
Abstract
Lauraceae species are widely represented in the Amazon, presenting a significant essential oil yield, large chemical variability, various biological applications, and high economic potential. Its taxonomic classification is difficult due to the accentuated morphological uniformity, even among taxa from a different genus. For this reason, the present work aimed to find chemical and molecular markers to discriminate Aniba species collected in the Pará State (Brazil). The chemical composition of the essential oils from Aniba canelilla, A. parviflora, A. rosaeodora, and A. terminalis were grouped by multivariate statistical analysis. The major compounds were rich in benzenoids and terpenoids such as 1-nitro-2-phenylethane (88.34-70.85%), linalool (15.2-75.3%), α-phellandrene (36.0-51.8%), and β-phellandrene (11.6-25.6%). DNA barcodes were developed using the internal transcribed spacer (ITS) nuclear region, and the matK, psbA-trnH, rbcL, and ycf1 plastid regions. The markers psbA-trnH and ITS showed the best discrimination for the species, and the phylogenic analysis in the three- (rbcL + matK + trnH - psbA and rbcL + matK + ITS) and four-locus (rbcL + matK + trnH - psbA + ITS) combination formed clades with groups strongly supported by the Bayesian inference (BI) (PP:1.00) and maximum likelihood (ML) (BS ≥ 97%). Therefore, based on statistical multivariate and phylogenetic analysis, the results showed a significant correlation between volatile chemical classes and genetic characteristics of Aniba species.
Collapse
Affiliation(s)
- Júlia Karla A. M. Xavier
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-900, Brazil; (J.K.A.M.X.); (L.M.)
| | - Leonardo Maia
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-900, Brazil; (J.K.A.M.X.); (L.M.)
| | - Pablo Luis B. Figueiredo
- Departamento de Ciências Naturais, Centro de Ciências Sociais e Educação, Universidade do Estado do Pará, Belém, PA 66050-540, Brazil;
| | - Adriana Folador
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, PA 66075-900, Brazil;
| | - Alessandra R. Ramos
- Instituto de Estudos em Saúde e Biológicas, Universidade Federal do Sul e Sudeste do Pará, Marabá, PA 68507-590, Brazil;
| | - Eloísa H. Andrade
- Coordenação de Botânica, Museu Paraense Emílio Goeldi, Belém, PA 66040-170, Brazil;
| | - José Guilherme S. Maia
- Programa de Pós-Graduação em Química, Universidade Federal do Maranhão, São Luís, MA 64080-040, Brazil;
| | - William N. Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA;
- Aromatic Plant Research Center, 230 N 1200 E, Suite 102, Lehi, UT 84043, USA
| | - Joyce Kelly R. da Silva
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-900, Brazil; (J.K.A.M.X.); (L.M.)
- Aromatic Plant Research Center, 230 N 1200 E, Suite 102, Lehi, UT 84043, USA
| |
Collapse
|
19
|
Wen F, Wu X, Li T, Jia M, Liu X, Liao L. The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China. BMC Genomics 2021; 22:161. [PMID: 33676415 PMCID: PMC7937279 DOI: 10.1186/s12864-021-07484-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. RESULTS A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. CONCLUSIONS This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
Collapse
Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| |
Collapse
|
20
|
Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes. Sci Rep 2021; 11:5153. [PMID: 33664414 PMCID: PMC7933167 DOI: 10.1038/s41598-021-84705-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/19/2021] [Indexed: 11/29/2022] Open
Abstract
Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.
Collapse
|
21
|
Yuan C, Sha X, Xiong M, Zhong W, Wei Y, Li M, Tao S, Mou F, Peng F, Zhang C. Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications. Sci Rep 2021; 11:988. [PMID: 33441833 PMCID: PMC7806627 DOI: 10.1038/s41598-020-80225-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.
Collapse
Affiliation(s)
- Can Yuan
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Xiufen Sha
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Miao Xiong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Wenjuan Zhong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Yu Wei
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingqian Li
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, Zhejiang, China
| | - Shan Tao
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Fangsheng Mou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China
| | - Fang Peng
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
| | - Chao Zhang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
| |
Collapse
|
22
|
Rono PC, Dong X, Yang JX, Mutie FM, Oulo MA, Malombe I, Kirika PM, Hu GW, Wang QF. Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships. Front Genet 2020; 11:560368. [PMID: 33362846 PMCID: PMC7756076 DOI: 10.3389/fgene.2020.560368] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.
Collapse
Affiliation(s)
- Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Millicent A Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Paul M Kirika
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
23
|
Xiao TW, Xu Y, Jin L, Liu TJ, Yan HF, Ge XJ. Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae). PeerJ 2020; 8:e10155. [PMID: 33088627 PMCID: PMC7568859 DOI: 10.7717/peerj.10155] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.
Collapse
Affiliation(s)
- Tian-Wen Xiao
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lu Jin
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tong-Jian Liu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Hai-Fei Yan
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Xue-Jun Ge
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| |
Collapse
|
24
|
Park J, Xi H, Kim Y. The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana. Int J Genomics 2020; 2020:3236461. [PMID: 32964010 PMCID: PMC7492873 DOI: 10.1155/2020/3236461] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 01/18/2023] Open
Abstract
Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.
Collapse
Affiliation(s)
- Jongsun Park
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| |
Collapse
|
25
|
Han K, Shi C, Li L, Seim I, Lee SMY, Xu X, Yang H, Fan G, Liu X. Lineage-specific evolution of mangrove plastid genomes. THE PLANT GENOME 2020; 13:e20019. [PMID: 33016609 DOI: 10.1002/tpg2.20019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/26/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
Mangroves is an umbrella term for plants located across the tropics and sub-tropics that live in the coastal region, between the sea and the land. All mangroves evolved from terrestrial plants, providing the opportunity to assess convergence, as well as the lineage-specific features, at the genetic level. In this study, we compared chloroplast genomes from 21 mangrove species, covering main phylogenetic clades. We demonstrate that chloroplast gene order, content, and genome size is largely conserved in mangroves. The exceptions are loss of the photosystem I gene psaZ in Acanthus ilicifolius and inversion of the ribosomal protein gene rpl23 in Avicennia germinans. The repeat content of mangrove chloroplast varied between species, but was conserved within species of the same order. Sequence diversity analysis revealed that the IR (invert repeat) region was highly conserved compared to the SC (single-copy) region in most phylogenetic clades, except clade core leptosporangiates (ferns). The ribosomal protein gene rps7 was under positive selection in Kandelia obovato, Rhizophora stylosa, Bruguiera sexangular and Rhizophora mangle, a monophyletic branch of clade fabids, while no evidence of positive selection was found in other mangrove lineages. Taken together, our data suggests that convergent evolutionary dynamics leaves no significant signal on the plastid genome of mangroves. The complete chloroplast genomes provided in this study shed light on the evolution of these important plastids and provides a valuable resource for further research efforts.
Collapse
Affiliation(s)
- Kai Han
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Chengcheng Shi
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Liangwei Li
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xun Xu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guangyi Fan
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| |
Collapse
|
26
|
Li H, Liu B, Davis CC, Yang Y. Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae). Mol Phylogenet Evol 2020; 151:106901. [PMID: 32619568 DOI: 10.1016/j.ympev.2020.106901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/06/2020] [Accepted: 06/26/2020] [Indexed: 01/27/2023]
Abstract
Intergeneric relationships of the Beilschmiedia group (Lauraceae) remain unresolved, hindering our understanding of their classification and evolutionary diversification. To remedy this, we sequenced and assembled complete plastid genomes (plastomes) from 25 species representing five genera spanning most major clades of Beilschmiedia and close relatives. Our inferred phylogeny is robust and includes two major clades. The first includes a monophyletic Endiandra nested within a paraphyletic Australasian Beilschmiedia group. The second includes (i) a subclade of African Beilschmiedia plus Malagasy Potameia, (ii) a subclade of Asian species including Syndiclis and Sinopora, (iii) the lone Neotropical species B. immersinervis, (iv) a subclade of core Asian Beilschmiedia, sister to the Neotropical species B. brenesii, and v) two Asian species including B. turbinata and B. glauca. The rampant non-monophyly of Beilschmiedia we identify necessitates a major taxonomic realignment of the genus, including but not limited to the mergers of Brassiodendron and Sinopora into the genera Endiandra and Syndiclis, respectively. Along these lines, the high degree of continental, clade-wide endemism we identify suggests that geographical distribution may be a good proxy for delineating taxa within this group. Our molecular divergence time estimates indicate that stem Beilschmiedia group members date to the Early Eocene (~50 Ma); their crown age dates to the Eocene-Oligocene boundary (~34 Ma). These findings contradict older estimates of the group and support mounting evidence that the origin and diversification of many pantropical angiosperm clades are not easily attributed to strict western Gondwanan vicariance. Finally, our study highlights the phylogenetic utility of plastomes in Lauraceace, and lays a solid foundation for future phylogenomic and biogeographic investigations within the family.
Collapse
Affiliation(s)
- Haiwen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China.
| |
Collapse
|
27
|
Liu C, Chen H, Han L, Tang L. The complete plastid genome of an evergreen tree Litsea elongata (Lauraceae: Laureae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2483-2484. [PMID: 33457836 PMCID: PMC7781995 DOI: 10.1080/23802359.2020.1778566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Litsea elongata (Nees) J. D. Hooker is an economically important timber and medicine tree. In this study, the complete plastid genome of L. elongata was assembled and analyzed. The plastid genome mapped a 154,027 bp circular DNA molecule with a GC content of 39.2%, consisting of a large single-copy region (LSC) of 93,688 bp, a small single-copy region (SSC) of 18,851 bp, and two inverted repeat regions (IRa and Irb) of 20,744 bp. A total of 127 genes were detected in the plastid genome, including eight ribosomal RNA (rRNA) genes, 36 transfer RNA (tRNA) genes, and 83 protein-coding genes. Phylogenomic analysis based on 39 complete plastomes of Laureae in the family Lauraceae supports the close relationships among L. coreana, L. elongata, L. japonica, and L. pierrei.
Collapse
Affiliation(s)
- Chao Liu
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on Yungui Plateau, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Huanhuan Chen
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on Yungui Plateau, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Lihong Han
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on Yungui Plateau, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Lizhou Tang
- Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on Yungui Plateau, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| |
Collapse
|
28
|
Atypical Lindenane-Type Sesquiterpenes from Lindera myrrha. Molecules 2020; 25:molecules25081830. [PMID: 32316243 PMCID: PMC7221893 DOI: 10.3390/molecules25081830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 12/20/2022] Open
Abstract
Two new lindenane sesquiterpenes were obtained from the roots of Lindera myrrha. These compounds were structurally elucidated by HRMS data, extensive NMR analyses, and comparison between experimental and theoretical 13C-NMR data. Myrrhalindenane A is the first monomeric seco-d lindenane displaying a non-rearranged, cyclohexanic C-ring. Myrrhalindenane B is the second occurrence of an angular lindenane-sesquiterpene related to a C6-C7 lactonization.
Collapse
|
29
|
Carrion ADA, Hinsinger DD, Strijk JS. Genomics of the critically endangered monotypic genus Sinopora: the plastome of S. hongkongensis (Lauraceae). Mitochondrial DNA B Resour 2020; 5:379-381. [PMID: 33366565 PMCID: PMC7748805 DOI: 10.1080/23802359.2019.1703590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sinopora hongkongensis is a critically endangered endemic tree species restricted to Hong Kong. Here we report its plastome sequence. The S. hongkongensis plastome was 158,612 bp in length, with a large single-copy (LSC) region of 89,405 bp and a small single-copy (SSC) region of 18,205 bp, separated by two inverted repeat (IR) regions of 25,498 bp. It contained 126 genes, including 89 coding genes, 29 tRNA genes, and 8 rRNA genes. The overall GC content was 39.0%, and 43.0%, 37.7%, and 34.0%, in the IRs, LSC, and SSC regions, respectively. A phylogenetic analysis combining a subset of Lauraceae plastomes with closely related outgroup families confirms the placement of S. hongkongensis in Lauraceae and explores relationships with other genera in the family.
Collapse
Affiliation(s)
- Angelo Damian Armijos Carrion
- Biodiversity Genomics Team, Plant Ecophysiology and Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Damien Daniel Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology and Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | - Joeri Sergej Strijk
- Biodiversity Genomics Team, Plant Ecophysiology and Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, China
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Tian X, Ye J, Song Y. Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae. PeerJ 2019; 7:e7662. [PMID: 31608166 PMCID: PMC6786250 DOI: 10.7717/peerj.7662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/12/2019] [Indexed: 01/02/2023] Open
Abstract
Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate.
Collapse
Affiliation(s)
- Xiangyu Tian
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Junwei Ye
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna, Yunnan, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| |
Collapse
|
32
|
Zhou T, Ruhsam M, Wang J, Zhu H, Li W, Zhang X, Xu Y, Xu F, Wang X. The Complete Chloroplast Genome of Euphrasia regelii, Pseudogenization of ndh Genes and the Phylogenetic Relationships Within Orobanchaceae. Front Genet 2019; 10:444. [PMID: 31156705 PMCID: PMC6528182 DOI: 10.3389/fgene.2019.00444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/29/2019] [Indexed: 12/31/2022] Open
Abstract
Euphrasia (Orobanchaceae) is a genus which is widely distributed in temperate regions of the southern and northern hemisphere. The taxonomy of Euphrasia is still controversial due to the similarity of morphological characters and a lack of genomic resources. Here, we present the first complete chloroplast (cp) genome of this taxonomically challenging genus. The cp genome of Euphrasia regelii consists of 153,026 bp, including a large single-copy region (83,893 bp), a small single-copy region (15,801 bp) and two inverted repeats (26,666 bp). There are 105 unique genes, including 71 protein-coding genes, 30 tRNA and 4 rRNA genes. Although the structure and gene order is comparable to the one in other angiosperm cp genomes, genes encoding the NAD(P)H dehydrogenase complex are widely pseudogenized due to mutations resulting in frameshifts, and stop codon positions. We detected 36 dispersed repeats, 7 tandem repeats and 65 simple sequence repeat loci in the E. regelii plastome. Comparative analyses indicated that the cp genome of E. regelii is more conserved compared to other hemiparasitic taxa in the Pedicularideae and Buchnereae. No structural rearrangements or loss of genes were detected. Our analyses suggested that three genes (clpP, ycf2 and rps14) were under positive selection and other genes under purifying selection. Phylogenetic analysis of monophyletic Orobanchaceae based on 45 plastomes indicated a close relationship between E. regelii and Neobartsia inaequalis. In addition, autotrophic lineages occupied the earliest diverging branches in our phylogeny, suggesting that autotrophy is the ancestral trait in this parasitic family.
Collapse
Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jian Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Honghong Zhu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Wenli Li
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi’an, China
| | - Yucan Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fusheng Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| |
Collapse
|
33
|
Thode VA, Lohmann LG. Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:796. [PMID: 31275342 PMCID: PMC6594259 DOI: 10.3389/fpls.2019.00796] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/03/2019] [Indexed: 05/13/2023]
Abstract
Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of Amphilophium (Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of Anemopaegma prostratum. We explored the structure and content of the assembled plastomes and performed comparative analyses within Amphilophium and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among Amphilophium, showing significant differences in length (155,262-164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between rps19 and rpl2 genes, within petD, or within petB). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of A. prostratum is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the petB gene. Amphilophium plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for Amphilophium and Anemopaegma prostratum. The differences in structure detected within Amphilophium plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.
Collapse
|
34
|
Liao Q, Ye T, Song Y. Complete chloroplast genome sequence of a subtropical tree, Parasassafras confertiflorum (Lauranceae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:1216-1217. [PMID: 33474469 PMCID: PMC7799558 DOI: 10.1080/23802359.2018.1532331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasassafras confertiflorum (Meisn.) D.G. Long is the single tree species of the genus Parasassafras D.G. Long in the family Lauraceae. To better determine its phylogenetic location with respect to the related Lauraceae species, the complete chloroplast genome of P. confertiflorum was sequenced. The whole plastome is 152,555 bp in length, consisting of a pair of inverted repeat (IR) regions of 20,079 bp, one large single copy (LSC) region of 93,604 bp, and one small single copy (SSC) region of 18,793 bp. The genome contains 127 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 36 transfer RNA genes. The overall GC content of the whole plastome is 39.1%. Further, maximum likelihoodphylogenetic analyses were conducted using 34 complete plastomes of the Lauraceae, which support close relationships between P. confertiflorum and Actinodaphne trichocarpa, Lindera benzoin, L. latifolia, L. metcalfiana, L. robusta, and Neolitsea sericea rather than Laurus nobilis or Sinosassafras flavinervium.
Collapse
Affiliation(s)
- Qiong Liao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Tinghong Ye
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Science, Yezin, Nay Pyi Taw, Myanmar
| |
Collapse
|