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Zheng HZ, Dai W, Xu MH, Lin YY, Zhu XL, Long H, Tong LL, Xu XG. Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses. Genes (Basel) 2024; 15:940. [PMID: 39062719 PMCID: PMC11275416 DOI: 10.3390/genes15070940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.
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Affiliation(s)
- Hao-Zhi Zheng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Wei Dai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Meng-Han Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Yu-Ye Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Xing-Li Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Hui Long
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Li-Li Tong
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing 210038, China;
| | - Xiao-Gang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
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Wang J, Kan J, Wang J, Yan X, Li Y, Soe T, Tembrock LR, Xing G, Li S, Wu Z, Jia M. The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history. FRONTIERS IN PLANT SCIENCE 2024; 15:1404071. [PMID: 38887455 PMCID: PMC11181306 DOI: 10.3389/fpls.2024.1404071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Backgrounds Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated. Methods We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes. Results The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved. Conclusion This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.
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Affiliation(s)
- Jie Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junhu Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xinlin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yi Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Thida Soe
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Zhiqiang Wu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Minlong Jia
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Huang J, Hu X, Zhou Y, Peng YJ, Liu Z. Phylogeny, Genetic Diversity and Population Structure of Fritillaria cirrhosa and Its Relatives Based on Chloroplast Genome Data. Genes (Basel) 2024; 15:730. [PMID: 38927666 PMCID: PMC11202927 DOI: 10.3390/genes15060730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years and are under priority protection in China. Despite their medicinal and protective value, research on their phylogeny, genetic diversity, and divergence remains limited. Here, we investigate the chloroplast genome variation architecture of 46 samples of F. cirrhosa and its relatives collected from various regions, encompassing the majority of wild populations across diverse geographical areas. The results indicate abundant variations in 46 accessions including 1659 single-nucleotide polymorphisms and 440 indels. Six variable markers (psbJ, ndhD, ycf1, ndhG, trnT-trnL, and rpl32-trnL) were identified. Phylogenetic and network analysis, population structure analysis, and principal component analysis showed that the 46 accessions formed five clades with significant divergence, which were related to their geographical distribution. The regions spanning from the southern Hengduan Mountains to the Qinghai-Tibet Plateau exhibited the highest levels of genetic diversity. F. cirrhosa and its relatives may have suffered a genetic bottleneck and have a relatively low genetic diversity level. Moreover, geographical barriers and discrete patches may have accelerated population divergence. The study offers novel perspectives on the phylogeny, genetic diversity, and population structure of F. cirrhosa and its relatives, information that can inform conservation and utilization strategies in the future.
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Affiliation(s)
- Jiao Huang
- College of Life Science, Leshan Normal University, Leshan 614000, China
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Chi X, Chen R, Zhang F, Chen S. Comparative plastomes of species from Phrymaceae and Mazaceae: insights into adaptive evolution, codon usage bias, and phylogenetic relationships. Genome 2023; 66:281-294. [PMID: 37159948 DOI: 10.1139/gen-2023-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The phylogeny of the species from Phrymaceae and Mazaceae has undergone many adjustments and changes in recent years. Moreover, there is little plastome information on the Phrymaceae. In this study, we compared the plastomes of six species from the Phrymaceae and 10 species from the Mazaceae. The gene order, contents, and orientation of the 16 plastomes were found to be highly similar. A total of 13 highly variable regions were identified among the 16 species. An accelerated rate of substitution was found in the protein-coding genes, particularly cemA and matK. The combination of effective number of codons, parity rule 2, and neutrality plots revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported {Mazaceae [(Phrymaceae + Wightiaceae) + (Paulowniaceae + Orobanchaceae)]} relationships in the Lamiales. Our findings can provide useful information to analyze the phylogeny and molecular evolution within the Phrymaceae and Mazaceae.
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Affiliation(s)
- Xiaofeng Chi
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Ronglian Chen
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Faqi Zhang
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Shilong Chen
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
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Li E, Liu K, Deng R, Gao Y, Liu X, Dong W, Zhang Z. Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae). BMC PLANT BIOLOGY 2023; 23:32. [PMID: 36639619 PMCID: PMC9840334 DOI: 10.1186/s12870-023-04034-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 01/02/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon. RESULTS The 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon. CONCLUSION Our study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.
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Affiliation(s)
- Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Rongyan Deng
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xinyu Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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Gao Y, Liu K, Li E, Wang Y, Xu C, Zhao L, Dong W. Dynamic evolution of the plastome in the Elm family (Ulmaceae). PLANTA 2022; 257:14. [PMID: 36526857 DOI: 10.1007/s00425-022-04045-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
This study compared the plastomes of Ulmaceae allowing analyses of the dynamic evolution, including genome structure, codon usage bias, repeat sequences, molecular mutation rates, and phylogenetic inferences. Ulmaceae is a small family in the order Rosales. This family consists of seven genera, including Ulmus, Zelkova, Planera, Hemiptelea, Phyllostylon, Ampelocera, and Holoptelea. Ulmaceae is an interesting lineage from plant biogeographic, systematic, evolutionary, and paleobotanic perspectives. It is also a good model to investigate the evolution of the plastomes in woody plants. In this study, we sequenced and assembled the complete plastomes of the six Ulmaceae genera to compare genomic structures and reveal the molecular evolutionary patterns. The size of the quadripartite plastomes ranged from 158,290 bp to 161,886 bp. The genomes contained 131 genes, including 87 coding genes, 36 tRNA, and 8 rRNA. The gene number, gene content, and genomic structure were highly consistent among the Ulmaceae genera. Nine variable regions including ndhA intron, ndhF-rpl32, ycf1, psbK-trnS, rps16-trnQ, trnT-trnL, trnT-psbD, trnS-trnG, and rpl32-trnL, were identified in Ulmaceae plastomes according to the nucleotide diversity values. Condon usage was biased among the genes and showed consistent trends in the seven genera. Molecular evolution analyses revealed that most of the genes and all gene groups were under widespread purifying selection. Twelve genes (ccsA, matK, psbH, psbK, rbcL, rpl22, rpl32, rpoA, rps12, rps15, rps16, and ycf2) were under positive selection. Phylogenetic analyses supported that Ulmaceae should be divided into two main clades, such as the temperate clade, including Ulmus, Zelkova, Planera, and Hemiptelea and the tropical clade, including Phyllostylon, Ampelocera and Holoptelea. This study reports the structure and evolutionary characteristics of the Elm family. These new genomic data will benefit assessments of genomic evolution and provide information to elucidate the phylogenetic relationships among Ulmaceae species.
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Affiliation(s)
- Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Enzhe Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liangcheng Zhao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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Zhang H, Zhang X, Sun Y, Landis JB, Li L, Hu G, Sun J, Tiamiyu BB, Kuang T, Deng T, Sun H, Wang H. Plastome phylogenomics and biogeography of the subfam. Polygonoideae (Polygonaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:893201. [PMID: 36275552 PMCID: PMC9581148 DOI: 10.3389/fpls.2022.893201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Polygonaceae has a complex taxonomic history, although a few studies using plastid or nuclear DNA fragments have explored relationships within this family, intrafamilial relationships remain controversial. Here, we newly sequenced and annotated 17 plastomes representing 12 genera within Polygonaceae. Combined with previously published data, a total of 49 plastomes representing 22/46 Polygonaceae genera and 16/20 Polygonoideae genera were collected to infer the phylogeny of Polygonaceae, with an emphasis on Polygonoideae. Plastome comparisons revealed high conservation within Polygonoideae in structure and gene order. Phylogenetic analyses using both Maximum Likelihood and Bayesian methods revealed two major clades and seven tribes within Polygonoideae. BEAST and S-DIVA analyses suggested a Paleocene origin of Polygonoideae in Asia. While most genera of Polygonoideae originated and further diversified in Asia, a few genera experienced multiple long-distance dispersal events from Eurasia to North America after the Miocene, with a few dispersal events to the Southern Hemisphere also being detected. Both ancient vicariance and long-distance events have played important roles in shaping the current distribution pattern of Polygonoideae.
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Affiliation(s)
- Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jacob B. Landis
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jiao Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bashir B. Tiamiyu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianhui Kuang
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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Zuo (左胜) S, Guo (郭新异) X, Mandáková T, Edginton M, Al-Shehbaz IA, Lysak MA. Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution. PLANT PHYSIOLOGY 2022; 190:403-420. [PMID: 35670733 PMCID: PMC9434143 DOI: 10.1093/plphys/kiac268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/09/2022] [Indexed: 05/20/2023]
Abstract
Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted in the extant c. 17 genera and 60 species endemic to Australia and New Zealand (10 species). As postpolyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. In Microlepidieae, different extents of homoeologous recombination between the two parental subgenomes generated clades marked by slow ("cold") versus fast ("hot") genome diploidization. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, we analyzed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. The four recovered intra-tribal clades mirror the varied diploidization of Microlepidieae genomes, suggesting that the intrinsic genomic features underlying the extent of diploidization are shared among genera and species within one clade. Nevertheless, even congeneric species may exert considerable morphological disparity (e.g. in fruit shape), whereas some species within different clades experience extensive morphological convergence despite the different pace of their genome diploidization. We showed that faster genome diploidization is positively associated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, our results confirm the potential of Microlepidieae as a promising subject for the analysis of postpolyploid genome diploidization in Brassicaceae.
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Affiliation(s)
| | | | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Mark Edginton
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Toowong, QLD 4066, Australia
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Wang Y, Wang J, Chen Y, Liu S, Zhao Y, Chen N. Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10024. [PMID: 36011659 PMCID: PMC9408514 DOI: 10.3390/ijerph191610024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
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Affiliation(s)
- Yichao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongfang Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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Chen C, Xia X, Peng J, Wang D. Comparative Analyses of Six Complete Chloroplast Genomes from the Genus Cupressus and Juniperus (Cupressaceae). Gene 2022; 837:146696. [PMID: 35738448 DOI: 10.1016/j.gene.2022.146696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/05/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022]
Abstract
Cupressaceae is a conifer family distributed around the world. Cupressus and Juniperus are the main genera of the Cupressaceae family and have important medicinal value. This leads to confusion between Cupressus and Juniperus due to similar morphologies. Here, the complete cp genomes of two Cupressus (C. duclouxiana and C. funebri) and four Juniperus (J. chinensis, J. gaussenii J. pingii and J. procumbens) were sequenced. The results revealed that the length of the cp genomes ranged from 126,996 bp to 129,959 bp, with 119 genes comprising 82 protein-coding genes, 33 transfer RNAs and 4 ribosomal RNAs. All chloroplast genomes of Cupressus and Juniperus lost whole IR regions, which is consistent with gymnosperm cp genome studies. In addition, the number of SSRs per species ranged from 54 to 73 and was dominated by mononucleotide repeats. In the six cp genomes of Cupressus and Juniperus, five highly divergent regions, including accD, accD-rpl2, ycf1, ycf2 and rrn23-rrn4.5, can be used as DNA barcodes of interspecific relationships and potential genetic markers. We compared the gene selection pressures (C. chengiana as reference species), and 6 genes underwent positive selection, the majority of which were related to photosynthesis. Phylogenetic results showed that the monophyly of Cupressus and Juniperus supported most bootstrap support. Cupressus funebris and J. chinensis were resolved to be early diverging species within Cupressus and Juniperus, and the two genera were sister groups to each other. This research revealed a new understanding of the structural pluralism and phylogenetic relationships of Cupressaceae cp genomes. These results will facilitate comprehension of the complexity and diversity of conifer cp genomes. SIGNIFICANCE:: Phylogenetic relationships among Cupressus, Juniperus, and their closest relatives are controversial, and generic delimitations have been in flux for the past decade. To address relationships and attempt to produce a more robust classification, we sequenced 6 new plastid genomes (plastomes) from the two variously described genera in this complex (Cupressus and Juniperus) and compared them with additional plastomes from diverse members of Cupressaceae. Our study corroborated the accD of Cupressophytes have a tendency to expand in size and strongly supported a sister relationship between Cupressus and Juniperus. The disparity in these results could be traced to the facts that the chloroplast genome is uniparentally inherited, also the usage of the whole chloroplast genome for this research is of a better advantage compared to usage of selected genes or portion of the plastome. The complete CP genomic data will provide useful information for studying genetic diversity and species identification, which is important for the overarching goal of biodiversity conservation.
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Affiliation(s)
- Can Chen
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
| | - Xi Xia
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
| | - Jingyu Peng
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
| | - Dawei Wang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
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11
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Sun J, Wang S, Wang Y, Wang R, Liu K, Li E, Qiao P, Shi L, Dong W, Huang L, Guo L. Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies ( Arnebia, Boraginaceae) in China. FRONTIERS IN PLANT SCIENCE 2022; 13:920826. [PMID: 35755641 PMCID: PMC9218939 DOI: 10.3389/fpls.2022.920826] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/11/2022] [Indexed: 05/03/2023]
Abstract
Arnebiae Radix is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of Arnebia in China, and the two species Arnebia euchroma and Arnebia guttata are the source plants of Arnebiae Radix according to the Chinese Pharmacopoeia. Molecular markers that permit species identification and facilitate studies of the genetic diversity and divergence of the wild populations of these two source plants have not yet been developed. Here, we sequenced the chloroplast genomes of 56 samples of five Arnebia species using genome skimming methods. The Arnebia chloroplast genomes exhibited quadripartite structures with lengths from 149,539 and 152,040 bp. Three variable markers (rps16-trnQ, ndhF-rpl32, and ycf1b) were identified, and these markers exhibited more variable sites than universal chloroplast markers. The phylogenetic relationships among the five Arnebia species were completely resolved using the whole chloroplast genome sequences. Arnebia arose during the Oligocene and diversified in the middle Miocene; this coincided with two geological events during the late Oligocene and early Miocene: warming and the progressive uplift of Tianshan and the Himalayas. Our analyses revealed that A. euchroma and A. guttata have high levels of genetic diversity and comprise two and three subclades, respectively. The two clades of A. euchroma exhibited significant genetic differences and diverged at 10.18 Ma in the middle Miocene. Three clades of A. guttata diverged in the Pleistocene. The results provided new insight into evolutionary history of Arnebia species and promoted the conservation and exploitation of A. euchroma and A. guttata.
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Affiliation(s)
- Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ruishan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ping Qiao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linyuan Shi
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Shang C, Li E, Yu Z, Lian M, Chen Z, Liu K, Xu L, Tong Z, Wang M, Dong W. Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.873100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole chloroplast genome of 12 genotypes of B. sinensis from different geographical locations, covering most wild populations. The B. sinensis chloroplast genome size ranged from 158,959 to 159,045 base pairs (bp) and displayed a typical circular quadripartite structure. Comparative analyses of 12 B. sinensis chloroplast genome revealed 33 polymorphic simple sequence repeats (SSRs), 105 polymorphic single nucleotide polymorphisms (SNPs), and 55 indels. Phylogenetic analysis showed that the 12 genotypes were grouped into 2 branches, which is consistent with the geographical distribution (Eastern clade and Western clade). Divergence time estimates showed that the two clades were divergent from 0.6 Ma in the late Pleistocene. Ex situ conservation is essential for this species. In this study, we identified SNPs, indels, and microsatellites of B. sinensis by comparative analyses of chloroplast genomes and determined genetic variation between populations using these genomic markers. Chloroplast genomic resources are also important for further domestication, population genetic, and phylogenetic analysis, possibly in combination with molecular markers of mitochondrial and/or nuclear genomes.
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13
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Hu G, Wu Y, Guo C, Lu D, Dong N, Chen B, Qiao Y, Zhang Y, Pan Q. Haplotype Analysis of Chloroplast Genomes for Jujube Breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:841767. [PMID: 35360311 PMCID: PMC8961131 DOI: 10.3389/fpls.2022.841767] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/11/2022] [Indexed: 05/31/2023]
Abstract
Jujube (family Rhamnaceae) is an important economic fruit tree in China. In this study, we reported 26 chloroplast (cp) sequences of jujube using Illumina paired-end sequencing. The sequence length of cp genome was 161, 367-161, 849 bp, which was composed of a large single-copy region (89053-89437 bp) and a small single-copy region (19356-19362 bp) separated by a pair of reverse repeat regions (26478-26533 bp). Each cp genome encodes the same 130 genes, including 112 unique genes, being quite conserved in genome structure and gene sequence. A total of 118 single base substitutions (SNPs) and 130 InDels were detected in 65 jujube accessions. Phylogenetic and haplotype network construction methods were used to analyze the origin and evolution of jujube and its sour-tasting relatives. We detected 32 effective haplotypes, consisting of 20 unique jujube haplotypes and 9 unique sour-jujube haplotypes. Compared with sour-jujube, jujube showed greater haplotype diversity at the chloroplast DNA level. To cultivate crisp and sweet fruit varieties featuring strong resistance, by combining the characteristics of sour-jujube and cultivated jujube, three hybrid combinations were suggested for reciprocal crosses: "Dongzao" × "Jingzao39," "Dongzao" × "Jingzao60," "Dongzao" × "Jingzao28." This study provides the basis for jujube species' identification and breeding, and lays the foundation for future research.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuping Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qinghua Pan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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14
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Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae). BIOMED RESEARCH INTERNATIONAL 2022; 2022:5364094. [PMID: 35252450 PMCID: PMC8893999 DOI: 10.1155/2022/5364094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/11/2022] [Indexed: 01/21/2023]
Abstract
The genus Styrax L. consists of approximately 130 species distributed in the Americas, eastern Asia, and the Mediterranean region. The phylogeny and evolutionary history of this genus are not clear. Knowledge of the phylogenetic relationships and the method for species identification will be critical for the evolution of this genus. In this study, we sequenced the chloroplast genome of 17 Styrax samples and added 17 additional chloroplast genome sequences from GenBank. The data were used to investigate chloroplast genome evolution, infer phylogenetic relationships, and access the species identification rate within Styrax. The Styrax chloroplast genome contains typical quadripartite structures, ranging from 157,641 bp to 159,333 bp. The chloroplast genome contains 114 unique genes. The P distance among the Styrax species ranged from 0.0003 to 0.00611. Seventeen small inversions and SSR sites were discovered in the Styrax chloroplast genome. By comparing with the chloroplast genome sequences, six mutation hotspots were identified, and the markers ycf1b and trnT-trnL were identified as the best Styrax-specific DNA barcodes. The specific barcodes and superbarcode exhibited higher discriminatory power than universal barcodes. Chloroplast phylogenomic results improved the resolution of the phylogenetic relationships of Styrax compared to previous analyses.
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15
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Jamal A, Wen J, Ma ZY, Ahmed I, Abdullah, Chen LQ, Nie ZL, Liu XQ. Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification. Front Genet 2021; 12:709996. [PMID: 34917123 PMCID: PMC8670589 DOI: 10.3389/fgene.2021.709996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.
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Affiliation(s)
- Abbas Jamal
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Long-Qing Chen
- Southwest Engineering Technology and Research Center of Landscape Architecture, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
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16
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Luo C, Huang W, Sun H, Yer H, Li X, Li Y, Yan B, Wang Q, Wen Y, Huang M, Huang H. Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications. BMC Genomics 2021; 22:571. [PMID: 34303345 PMCID: PMC8310579 DOI: 10.1186/s12864-021-07807-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Impatiens L. is a genus of complex taxonomy that belongs to the family Balsaminaceae (Ericales) and contains approximately 1000 species. The genus is well known for its economic, medicinal, ornamental, and horticultural value. However, knowledge about its germplasm identification, molecular phylogeny, and chloroplast genomics is limited, and taxonomic uncertainties still exist due to overlapping morphological features and insufficient genomic resources. RESULTS We sequenced the chloroplast genomes of six different species (Impatiens chlorosepala, Impatiens fanjingshanica, Impatiens guizhouensis, Impatiens linearisepala, Impatiens loulanensis, and Impatiens stenosepala) in the karst area of China and compared them with those of six previously published Balsaminaceae species. We contrasted genomic features and repeat sequences, assessed sequence divergence and constructed phylogenetic relationships. Except for those of I. alpicola, I. pritzelii and I. glandulifera, the complete chloroplast genomes ranging in size from 151,366 bp (I. alpicola) to 154,189 bp (Hydrocera triflora) encoded 115 distinct genes [81 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) genes]. Moreover, the characteristics of the long repeat sequences and simple sequence repeats (SSRs) were determined. psbK-psbI, trnT-GGU-psbD, rpl36-rps8, rpoB-trnC-GCA, trnK-UUU-rps16, trnQ-UUG, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, and ycf4-cemA were identified as divergence hotspot regions and thus might be suitable for species identification and phylogenetic studies. Additionally, the phylogenetic relationships based on Maximum likelihood (ML) and Bayesian inference (BI) of the whole chloroplast genomes showed that the chloroplast genome structure of I. guizhouensis represents the ancestral state of the Balsaminaceae family. CONCLUSION Our study provided detailed information about nucleotide diversity hotspots and the types of repeats, which can be used to develop molecular markers applicable to Balsaminaceae species. We also reconstructed and analyzed the relationships of some Impatiens species and assessed their taxonomic statuses based on the complete chloroplast genomes. Together, the findings of the current study might provide valuable genomic resources for systematic evolution of the Balsaminaceae species.
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Affiliation(s)
- Chao Luo
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
- Department of Landscape Architecture and Plant Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Wulue Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Huayu Sun
- Department of Landscape Architecture and Plant Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Huseyin Yer
- Department of Landscape Architecture and Plant Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Xinyi Li
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Yang Li
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Bo Yan
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Qiong Wang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Yonghui Wen
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Meijuan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China.
| | - Haiquan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China.
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Dong W, Xu C, Liu Y, Shi J, Li W, Suo Z. Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae). BMC Genomics 2021; 22:434. [PMID: 34107868 PMCID: PMC8191006 DOI: 10.1186/s12864-021-07769-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 06/03/2021] [Indexed: 12/04/2022] Open
Abstract
Background Crape myrtles, belonging to the genus Lagerstroemia L., have beautiful paniculate inflorescences and are cultivated as important ornamental tree species for landscaping and gardening. However, the phylogenetic relationships within Lagerstroemia have remained unresolved likely caused by limited sampling and the insufficient number of informative sites used in previous studies. Results In this study, we sequenced 20 Lagerstroemia chloroplast genomes and combined with 15 existing chloroplast genomes from the genus to investigate the phylogenetic relationships and divergence times within Lagerstroemia. The phylogenetic results indicated that this genus is a monophyletic group containing four clades. Our dating analysis suggested that Lagerstroemia originated in the late Paleocene (~ 60 Ma) and started to diversify in the middle Miocene. The diversification of most species occurred during the Pleistocene. Four variable loci, trnD-trnY-trnE, rrn16-trnI, ndhF-rpl32-trnL and ycf1, were discovered in the Lagerstroemia chloroplast genomes. Conclusions The chloroplast genome information was successfully utilized for molecular characterization of diverse crape myrtle samples. Our results are valuable for the global genetic diversity assessment, conservation and utilization of Lagerstroemia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07769-x.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, 100083, Beijing, China.
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jipu Shi
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Wenying Li
- Institute of Forestry New Technologies, Chinese Academy of Forestry, 100091, Beijing, China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
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Dong W, Liu Y, Xu C, Gao Y, Yuan Q, Suo Z, Zhang Z, Sun J. Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae). BMC Genomics 2021; 22:293. [PMID: 33888057 PMCID: PMC8060999 DOI: 10.1186/s12864-021-07590-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 04/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes. RESULTS The Distylium chloroplast genome size was 159,041-159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. CONCLUSIONS The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Qingjun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Alimba CG, Adewumi OO, Binuyo OM, Odeigah PGC. Wild black rats (Rattus rattus Linnaeus, 1758) as zoomonitor of genotoxicity and systemic toxicity induced by hazardous emissions from Abule Egba unsanitary landfill, Lagos, Nigeria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10603-10621. [PMID: 33098559 DOI: 10.1007/s11356-020-11325-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
Wild black rats (Rattus rattus) inhabiting Abule Egba landfill (AEL) were used as zoomonitor to assess health risk associated with exposure to hazardous chemicals from landfills. Twenty five R. rattus (16♂ and 9♀) captured within AEL and 15 (9♂ and 6♀) (control) caught from Iyano Ipaja (10 km away from AEL) were examined for bone marrow micronucleated polychromatic erythrocytes (MNPCE) and polychromatic erythrocytes/normochromatic erythrocytes (PCE/NCE) ratio, abnormal sperm morphology, alterations in hematological indices and erythrocyte morphology, and histopathology of the viscera using standard protocols. There was significant (p < 0.05) increase in MNPCE but decrease PCE/NCE ratio in bone marrow cells of exposed rats than the reference site. MNPCE was insignificantly higher in male than females. Cauda epididymal sperms from exposed rats showed significant high frequency of teratozoospermia. Erythrocyte count, hemoglobin concentrations, percentage hematocrits, mean corpuscular hemoglobin concentrations, leucocyte count, and lymphocytes decreased while mean corpuscular volume, neutrophils, and mean corpuscular hemoglobin increased in the exposed rats compared to the control. Also, abnormal erythrocyte morphology: acanthocytes, codocytes (target cells), schizocytes, and tear drops significantly increased in the exposed rats. Marginal sexual dimorphism was observed between males and females in the incidence of hematological indices. Histopathological lesions including interstitial edema, hemorrhage, lymphoid depletion, cellular infiltrations, proliferation of the alveolar pneumocytes, necrosis, tissue degeneration, and reduced germinal epithelium were observed in the testes, liver, lungs, heart, kidney, and spleen from the exposed rats compared to the control. Some physicochemicals and metals analyzed in leachates from the landfill are capable of inducing genome instability and systemic toxicity in the exposed rats. Rattus rattus exposed to hazardous chemicals from AEL harbored somatic and germ cell mutations, and tissue damage compared to the control rats. We suggest that R. rattus are useful sentinel for genotoxicity and system toxicity assessment of landfill-polluted sites.Graphical abstract.
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Affiliation(s)
- Chibuisi G Alimba
- Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria.
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Technical University of Dortmund, 44139, Dortmund, Germany.
- Department of Cell Biology and Genetics, University of Lagos, Akoka, Lagos, Nigeria.
| | - Olusoji O Adewumi
- Department of Cell Biology and Genetics, University of Lagos, Akoka, Lagos, Nigeria
- Biology Unit, Distance Learning Institute, University of Lagos, Akoka, Lagos State, Nigeria
| | - Olufisayo M Binuyo
- Department of Cell Biology and Genetics, University of Lagos, Akoka, Lagos, Nigeria
- Department of Theriogenology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Peter G C Odeigah
- Department of Cell Biology and Genetics, University of Lagos, Akoka, Lagos, Nigeria
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Liu M, Lu J, Li Y, Zhang L. Complete chloroplast genome of Engelhardtia fenzlii (Juglandaceae). Mitochondrial DNA B Resour 2021; 6:288-289. [PMID: 33553647 PMCID: PMC7850322 DOI: 10.1080/23802359.2020.1863871] [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: 11/18/2022] Open
Abstract
In this study, we successfully assembled and analyzed the chloroplast genome of Engelhardtia fenzlii. The chloroplast genome of E. fenzlii was very similar to those of other Juglandaceae species. The E. fenzlii chloroplast genome is 161,713 bp in length and displays the typical quadripartite structure, which consists of a pair of IR regions (26,016 bp) separated by an LSC region (90,478 bp) and an SSC region (19,203 bp). The chloroplast genome of E. fenzlii contained a total of 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Phylogenetic analysis based on the complete chloroplast genomes showed that Engelhardtia formed a monophyletic clade and E. fenzlii was sister to E. roxburghiana.
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Affiliation(s)
- Mu Liu
- College of Landscape Architecture and Arts, Jiangxi Agricultural University, Nanchang, China
| | - Jinsen Lu
- College of Landscape Architecture and Arts, Jiangxi Agricultural University, Nanchang, China
| | - Yuan Li
- College of Landscape Architecture and Arts, Jiangxi Agricultural University, Nanchang, China
| | - Lvshui Zhang
- College of Landscape Architecture and Arts, Jiangxi Agricultural University, Nanchang, China
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Wang Y, Luo J, Wang M, Ge Y, Guo L. The complete chloroplast genome of the Euphorbia maculata L. (Euphorbiaceae): characterization and phylogeny. Mitochondrial DNA B Resour 2020; 5:3713-3714. [PMID: 33367071 PMCID: PMC7655055 DOI: 10.1080/23802359.2020.1833778] [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: 11/30/2022] Open
Abstract
Euphorbia maculata is an important medicinal plants of the family Euphorbiaceae. The complete chloroplast genome reported here is 162,685 bp in length, including two inverted repeats (IRs) of 26,822 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 90,514 bp and 18,527 bp, respectively. The whole chloroplast genome of E. maculata contains 111 genes, including 77 protein-coding genes, 4 transfer RNA, and 30 ribosome RNA. Phylogenetic analysis indicated that E. maculata is closely related to E. milii and E. tirucalli.
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Affiliation(s)
- Yiheng Wang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Luo
- Natural Resources Bureau of Xishan District of Kunming City, Kunming City, People’s Republic of China
| | - Mengli Wang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yang Ge
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
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