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Zhang J, Huang H, Qu C, Meng X, Meng F, Yao X, Wu J, Guo X, Han B, Xing S. Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.). PLANTA 2021; 255:26. [PMID: 34940902 DOI: 10.1007/s00425-021-03812-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The Albizia julibrissin chloroplasts have a classical chloroplast genome structure, containing 93 coding genes and 34 non-coding genes. Our research provides basic data for plant phylogenetic evolutionary studies. There is limited genomic information available for the important Chinese herb Albizia julibrissin Durazz. In this study, we constructed the chloroplast (Cp) genome of A. julibrissin. The length of the assembled Cp genome was 175,922 bp consisting of four conserved regions: a 5145 bp small single-copy (SSC) region, a 91,323 bp large single-copy (LSC) region, and two identical length-inverted repeat (IR) regions (39,725 bp). This Cp genome included 34 non-coding RNAs and 93 unique genes, the former contains 30 transfer and 4 ribosomal RNA genes. Gene annotation indicated some of the coding genes (82) in the A. julibrissin Cp genome classified in the Leguminosae family, with some to other related families (11). The results show that low GC content (36.9%) and codon bias towards A- or T-terminal codons may affect the frequency of gene codon usage. The sequence analysis identified 30 forward, 18 palindrome, and 1 reverse repeat > 30 bp length, and 149 simple sequence repeats (SSR). Fifty-five RNA editing sites in the Cp of A. julibrissin were predicted, most of which are C-to-U conversions. Analysis of the reverse repeat expansion or contraction and divergence area between several species, including A. julibrissin, was performed. The phylogenetic tree revealed that A. julibrissin was most closely related to Albizia odoratissima and Albizia bracteata, followed by Samanea saman, forming an evolutionary branch with Mimosa pudica and Leucaena trichandra. The research results are helpful for breeding and genetic improvement of A. julibrissin, and also provide valuable information for understanding the evolution of this plant.
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Affiliation(s)
- Jing Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Huizhen Huang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, 421008, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-Aging, Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Minneapolis, 55108, USA
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaoyan Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Bangxing Han
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, West Anhui University, Lu'an, 237012, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, 230012, China.
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102
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Dong S, Ying Z, Yu S, Wang Q, Liao G, Ge Y, Cheng R. Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships. BMC Genomics 2021; 22:880. [PMID: 34872502 PMCID: PMC8647421 DOI: 10.1186/s12864-021-08193-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. RESULTS The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. CONCLUSIONS Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.
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Affiliation(s)
- Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zhiqi Ying
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shuisheng Yu
- The Administration Bureau of Zhejiang Jiulongshan National Nature Reserve, Suichang, Zhejiang Province, People's Republic of China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Guanghui Liao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China.
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103
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Li DM, Li J, Wang DR, Xu YC, Zhu GF. Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). BMC PLANT BIOLOGY 2021; 21:558. [PMID: 34814832 PMCID: PMC8611967 DOI: 10.1186/s12870-021-03315-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/03/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. RESULTS Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda 'Red Leaf', Kaempferia rotunda 'Silver Diamonds' and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630-163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172-88,632 bp), a small single copy (SSC, 15,393-15,917 bp) and a pair of inverted repeats (IRs, 29,673-29,833 bp). The genomes contain 111-113 different genes, including 79 protein coding genes, 28-30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + "the Kaempferia clade" consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. CONCLUSIONS Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dai-Rong Wang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ye-Chun Xu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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104
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Luo Y, He J, Lyu R, Xiao J, Li W, Yao M, Pei L, Cheng J, Li J, Xie L. Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae. Front Genet 2021; 12:730495. [PMID: 34804117 PMCID: PMC8600051 DOI: 10.3389/fgene.2021.730495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/20/2021] [Indexed: 02/01/2023] Open
Abstract
The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion.
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Affiliation(s)
- Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Wenhe Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jinyu Li
- Beijing Institute of Landscape Architecture, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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105
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Xie C, An W, Liu S, Huang Y, Yang Z, Lin J, Zheng X. Comparative genomic study on the complete plastomes of four officinal Ardisia species in China. Sci Rep 2021; 11:22239. [PMID: 34782652 PMCID: PMC8594775 DOI: 10.1038/s41598-021-01561-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/21/2021] [Indexed: 11/23/2022] Open
Abstract
Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China. However, ambiguous species delineation and genetic information limit the development and utilization of this genus. In this study, the chloroplast genomes of four Ardisia species, namely A. gigantifolia Stapf, A. crenata Sims, A. villosa Roxb. and A. mamillata Hance, were sequenced, annotated, and analyzed comparatively. All the four chloroplast genomes possess a typical quadripartite structure, and each of the genomes is about 156 Kb in size. The structure and gene content of the Ardisia plastomes were conservative and showed low sequence divergence. Furthermore, we identified five mutation hotspots as candidate DNA barcodes for Ardisia, namely, trnT-psbD, ndhF-rpl32, rpl32-ccsA, ccsA-ndhD and ycf1. Phylogenetic analysis based on the whole-chloroplast genomes data showed that Ardisia was sister to Tapeinosperma Hook. f. In addition, the results revealed a great topological profile of Ardisia's with strong support values, which matches their geographical distribution patterns. Summarily, our results provide useful information for investigations on taxonomic differences, molecular identification, and phylogenetic relationships of Ardisia plants.
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Affiliation(s)
- Chunzhu Xie
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Wenli An
- grid.411866.c0000 0000 8848 7685School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Shanshan Liu
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Yuying Huang
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Zerui Yang
- grid.411866.c0000 0000 8848 7685School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Ji Lin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong, China.
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong, China.
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106
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Feng Y, Xiang X, Akhter D, Pan R, Fu Z, Jin X. Mitochondrial Phylogenomics of Fagales Provides Insights Into Plant Mitogenome Mosaic Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:762195. [PMID: 34733309 PMCID: PMC8558628 DOI: 10.3389/fpls.2021.762195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 09/17/2021] [Indexed: 05/13/2023]
Abstract
Fagales are an order of woody plants and comprise more than 1,100 species, most of which produce economically important timbers, nuts, and fruits. Their nuclear and plastid genomes are well-sequenced and provided valuable resources to study their phylogeny, breeding, resistance, etc. However, little is known about the mitochondrial genomes (mitogenomes), which hinder a full understanding of their genome evolution. In this study, we assembled complete mitogenomes of 23 species, covering five of the seven families of Fagales. These mitogenomes had similar gene sets but varied 2.4 times in size. The mitochondrial genes were highly conserved, and their capacity in phylogeny was challenging. The mitogenomic structure was extremely dynamic, and synteny among species was poor. Further analyses of the Fagales mitogenomes revealed extremely mosaic characteristics, with horizontal transfer (HGT)-like sequences from almost all seed plant taxa and even mitoviruses. The largest mitogenome, Carpinus cordata, did not have large amounts of specific sequences but instead contained a high proportion of sequences homologous to other Fagales. Independent and unequal transfers of third-party DNA, including nuclear genome and other resources, may partially account for the HGT-like fragments and unbalanced size expansions observed in Fagales mitogenomes. Supporting this, a mitochondrial plasmid-like of nuclear origin was found in Carpinus. Overall, we deciphered the last genetic materials of Fagales, and our large-scale analyses provide new insights into plant mitogenome evolution and size variation.
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Affiliation(s)
- Yanlei Feng
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- College of Agriculture and Biotechnology, Institute of Crop Science, Zhejiang University, Hangzhou, China
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaoguo Xiang
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Delara Akhter
- College of Agriculture and Biotechnology, Institute of Crop Science, Zhejiang University, Hangzhou, China
- Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Ronghui Pan
- College of Agriculture and Biotechnology, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Zhixi Fu
- College of Life Science, Sichuan Normal University, Chengdu, China
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China
| | - Xiaohua Jin
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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107
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The complete chloroplast genome sequence of Rubus hirsutus Thunb. and a comparative analysis within Rubus species. Genetica 2021; 149:299-311. [PMID: 34546501 DOI: 10.1007/s10709-021-00131-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/18/2021] [Indexed: 11/27/2022]
Abstract
Rubus hirsutus is a type of tonifying kidney-essence herb that belongs to the Rosaceae family, and has been commonly used to treat multiple diseases, such as polyuria, impotence, and infertility. In this study, we determined the complete chloroplast sequence of R. hirsutus and conduced a comparative analysis within the genus Rubus. The assembled chloroplast (cp.) genome is 156,380 bp in length with a GC content of 37.0% and shares a conserved quadripartite structure within the other cp. genomes in this genus. A total of 132 unique genes were annotated in the cp. genome of R. hirsutus, which contained 87 protein-coding genes, 37 tRNAs, and eight rRNAs. Seventeen duplicated genes were identified in the inverted repeats region. Furthermore, 70 simple sequence repeats and 35 long repeats were detected in total in the R. hirsutus chloroplast genome. Eight mutational hotspots were identified in the cp. genome of this species with higher nucleotide variations in non-coding regions than those of coding regions. Furthermore, the gene order, codon usage, and repeat sequence distribution were highly consistent in Rubus according to the results of a comparative analysis. A phylogenetic analysis indicated that there was a sister relationship between R. hirsutus and R. chingii. Overall, the complete chloroplast genome of R. hirsutus and the comparative analysis will help to further the evolutionary study, conservation, phylogenetic reconstruction, and development of molecular barcodes for the genus Rubus.
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108
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Yang J, Choi MJ, Kim SH, Choi HJ, Kim SC. Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles ( Hosta; Asparagaceae) in East Asia. PLANTS 2021; 10:plants10101980. [PMID: 34685791 PMCID: PMC8538707 DOI: 10.3390/plants10101980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/23/2022]
Abstract
The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Ulleung-do & Dok-do, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Mi-Jung Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea;
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea;
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea;
- Correspondence: (H.-J.C.); (S.-C.K.); Tel.: +82-55-213-3457 (H.-J.C.); +82-31-299-4499 (S.-C.K.)
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea;
- Correspondence: (H.-J.C.); (S.-C.K.); Tel.: +82-55-213-3457 (H.-J.C.); +82-31-299-4499 (S.-C.K.)
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109
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Edera AA, Small I, Milone DH, Sanchez-Puerta MV. Deepred-Mt: Deep representation learning for predicting C-to-U RNA editing in plant mitochondria. Comput Biol Med 2021; 136:104682. [PMID: 34343887 DOI: 10.1016/j.compbiomed.2021.104682] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
In land plant mitochondria, C-to-U RNA editing converts cytidines into uridines at highly specific RNA positions called editing sites. This editing step is essential for the correct functioning of mitochondrial proteins. When using sequence homology information, edited positions can be computationally predicted with high precision. However, predictions based on the sequence contexts of such edited positions often result in lower precision, which is limiting further advances on novel genetic engineering techniques for RNA regulation. Here, a deep convolutional neural network called Deepred-Mt is proposed. It predicts C-to-U editing events based on the 40 nucleotides flanking a given cytidine. Unlike existing methods, Deepred-Mt was optimized by using editing extent information, novel strategies of data augmentation, and a large-scale training dataset, constructed with deep RNA sequencing data of 21 plant mitochondrial genomes. In comparison to predictive methods based on sequence homology, Deepred-Mt attains significantly better predictive performance, in terms of average precision as well as F1 score. In addition, our approach is able to recognize well-known sequence motifs linked to RNA editing, and shows that the local RNA structure surrounding editing sites may be a relevant factor regulating their editing. These results demonstrate that Deepred-Mt is an effective tool for predicting C-to-U RNA editing in plant mitochondria. Source code, datasets, and detailed use cases are freely available at https://github.com/aedera/deepredmt.
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Affiliation(s)
- Alejandro A Edera
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL/CONICET, Ciudad Universitaria, Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL/CONICET, Ciudad Universitaria, Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina.
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina.
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Habib S, Dong S, Liu Y, Liao W, Zhang S. The complete mitochondrial genome of Cycas debaoensis revealed unexpected static evolution in gymnosperm species. PLoS One 2021; 16:e0255091. [PMID: 34293066 PMCID: PMC8297867 DOI: 10.1371/journal.pone.0255091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/11/2021] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial genomes of vascular plants are well known for their liability in architecture evolution. However, the evolutionary features of mitogenomes at intra-generic level are seldom studied in vascular plants, especially among gymnosperms. Here we present the complete mitogenome of Cycas debaoensis, an endemic cycad species to the Guangxi region in southern China. In addition to assemblage of draft mitochondrial genome, we test the conservation of gene content and mitogenomic stability by comparing it to the previously published mitogenome of Cycas taitungensis. Furthermore, we explored the factors such as structural rearrangements and nuclear surveillance of double-strand break repair (DSBR) proteins in Cycas in comparison to other vascular plant groups. The C. debaoensis mitogenome is 413,715 bp in size and encodes 69 unique genes, including 40 protein coding genes, 26 tRNAs, and 3 rRNA genes, similar to that of C. taitungensis. Cycas mitogenomes maintained the ancestral intron content of seed plants (26 introns), which is reduced in other lineages of gymnosperms, such as Ginkgo biloba, Taxus cuspidata and Welwitschia mirabilis due to selective pressure or retroprocessing events. C. debaoensis mitogenome holds 1,569 repeated sequences (> 50 bp), which partially account for fairly large intron size (1200 bp in average) of Cycas mitogenome. The comparison of RNA-editing sites revealed 267 shared non-silent editing site among predicted vs. empirically observed editing events. Another 33 silent editing sites from empirical data increase the total number of editing sites in Cycas debaoensis mitochondrial protein coding genes to 300. Our study revealed unexpected conserved evolution between the two Cycas species. Furthermore, we found strict collinearity of the gene order along with the identical set of genomic content in Cycas mt genomes. The stability of Cycas mt genomes is surprising despite the existence of large number of repeats. This structural stability may be related to the relative expansion of three DSBR protein families (i.e., RecA, OSB, and RecG) in Cycas nuclear genome, which inhibit the homologous recombinations, by monitoring the accuracy of mitochondrial chromosome repair.
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Affiliation(s)
- Sadaf Habib
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Shanshan Dong
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Yang Liu
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Wenbo Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shouzhou Zhang
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
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111
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Zhu B, Hu L, Qian F, Gao Z, Gan C, Liu Z, Du X, Wang H. Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species. PLoS One 2021; 16:e0254109. [PMID: 34237086 PMCID: PMC8266105 DOI: 10.1371/journal.pone.0254109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/20/2021] [Indexed: 11/18/2022] Open
Abstract
Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with “subunits of ATP synthase” (atpB), “subunits of NADH-dehydrogenase” (ndhG and ndhE), and “self-replication” (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species.
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Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Lijuan Hu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Zuomin Gao
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Chenchen Gan
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Zhaochao Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
- * E-mail:
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Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution. PLANTS 2021; 10:plants10061229. [PMID: 34204211 PMCID: PMC8234754 DOI: 10.3390/plants10061229] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
This study presents for the first time the complete chloroplast genomes of four medicinal species in the Capparaceae family belonging to two different genera, Cadaba and Maerua (i.e., C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia), to investigate their evolutionary process and to infer their phylogenetic positions. The four species are considered important medicinal plants, and are used in the treatment of many diseases. In the genus Cadaba, the chloroplast genome ranges from 156,481 bp to 156,560 bp, while that of Maerua ranges from 155,685 bp to 155,436 bp. The chloroplast genome of C. farinosa, M. crassifolia and M. oblongifolia contains 138 genes, while that of C. glandulosa contains 137 genes, comprising 81 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Out of the total genes, 116–117 are unique, while the remaining 19 are replicated in inverted repeat regions. The psbG gene, which encodes for subunit K of NADH dehydrogenase, is absent in C. glandulosa. A total of 249 microsatellites were found in the chloroplast genome of C. farinosa, 251 in C. glandulosa, 227 in M. crassifolia and 233 in M. oblongifolia, the majority of which are mononucleotides A/T found in the intergenic spacer. Comparative analysis revealed variable hotspot regions (atpF, rpoC2, rps19 and ycf1), which can be used as molecular markers for species authentication and as regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. The monophyly of Capparaceae and other families under Brassicales, as well as the phylogenetic positions of the studied species, are highly supported by all the relationships in the phylogenetic tree. The cp genomes reported in this study will provide resources for studying the genetic diversity of Capparaceae, as well as resolving phylogenetic relationships within the family.
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Liu S, Feng S, Huang Y, An W, Yang Z, Xie C, Zheng X. Characterization of the Complete Chloroplast Genome of Buddleja Lindleyana. J AOAC Int 2021; 105:202-210. [PMID: 33944934 DOI: 10.1093/jaoacint/qsab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/25/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Buddleja lindleyana Fort., which belongs to the Loganiaceae with a distribution throughout the tropics, is widely used as an ornamental plant in China. Buddleja contains several morphologically similar species, which need to be identified by molecular identification. But there is little molecular research on the genus Buddleja. OBJECTIVE Using molecular biology techniques to sequence and analyze the complete chloroplast (cp) genome of B. lindleyana. METHODS According to next-generation sequencing to sequence the genome data, a series of bioinformatics software were used to assembly and analysis the molecular structure of cp genome of B. lindleyana. RESULTS The complete cp genome of B. lindleyana is a circular 154,487-bp-long molecule with a GC content of 38.1%. It has a familiar quadripartite structure, including a large single-copy region (LSC; 85,489 bp), a small single-copy region (SSC; 17,898bp) and a pair of inverted repeats (IRs; 25,550 bp). A total of 133 genes were identified in the genome, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 2 pseudogenes. CONCLUSIONS These results suggested that B. lindelyana cp genome could be used as a potential genomic resource to resolve the phylogenetic positions and relationships of Loganiaceae, and will offer valuable information for future research in the identification of Buddleja species and will conduce to genomic investigations of these species.
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Affiliation(s)
- Shanshan Liu
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Shiyin Feng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405
| | - Yuying Huang
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Wenli An
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Zerui Yang
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Chunzhu Xie
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Xiasheng Zheng
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
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Alzahrani D, Albokhari E, Yaradua S, Abba A. Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships. Saudi J Biol Sci 2021; 28:2476-2490. [PMID: 33911961 PMCID: PMC8071925 DOI: 10.1016/j.sjbs.2021.01.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/17/2021] [Accepted: 01/21/2021] [Indexed: 11/29/2022] Open
Abstract
This current study presents, for the first time, the complete chloroplast genome of two Cleomaceae species: Dipterygium glaucum and Cleome chrysantha in order to evaluate the evolutionary relationship. The cp genome is 158,576 bp in length with 35.74% GC content in D. glaucum and 158,111 bp with 35.96% GC in C. chrysantha. Inverted repeats IR 26,209 bp, 26,251 bp each, LSC of 87,738 bp, 87,184 bp and SSC of 18,420 bp, 18,425 bp respectively. There are 136 genes in the genome, which includes 80 protein coding genes, 31 tRNA genes and four rRNA genes were observed in both chloroplast genomes. 117 genes are unique while the remaining 19 genes are duplicated in IR regions. The analysis of repeats shows that the cp genome includes all types of repeats with more frequent occurrences of palindromic; Also, this analysis indicates that the total number of simple sequence repeats (SSR) were 323 in D. glaucum, and 313 in C. chrysantha, of which the majority of the SSRs in these plastid genomes were mononucleotide repeats A/T which are located in the intergenic spacer. Moreover, the comparative analysis of the four cp sequences revealed four hotspot genes (atpF, rpoC2, rps19, and ycf1), these variable regions could be used as molecular makers for the species authentication as well as resources for inferring phylogenetic relationships of the species. All the relationships in the phylogenetic tree are with high support, this indicate that the complete chloroplast genome is a useful data for inferring phylogenetic relationship within the Cleomaceae and other families. The simple sequence repeats identified will be useful for identification, genetic diversity, and other evolutionary studies of the species. This study reported the first cp genome of the genus Dipterygium and Cleome. The finding of this study will be beneficial for biological disciplines such as evolutionary and genetic diversity studies of the species within the core Cleomaceae.
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Affiliation(s)
- Dhafer Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Enas Albokhari
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Biological Sciences, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Samaila Yaradua
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
| | - Abidina Abba
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Biological Sciences, Faculty of Sciences, Federal University Lokoja, Kogi State, Nigeria
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116
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Cheng Y, He X, Priyadarshani SVGN, Wang Y, Ye L, Shi C, Ye K, Zhou Q, Luo Z, Deng F, Cao L, Zheng P, Aslam M, Qin Y. Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca. BMC Genomics 2021; 22:167. [PMID: 33750312 PMCID: PMC7941912 DOI: 10.1186/s12864-021-07490-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/26/2021] [Indexed: 01/30/2023] Open
Abstract
Background Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored. Results The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes. Conclusions In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07490-9.
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Affiliation(s)
- Yan Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoxue He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - S V G N Priyadarshani
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yu Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Ye
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chao Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kangzhuo Ye
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiao Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ziqiang Luo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fang Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ling Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ping Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mohammad Aslam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
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de Santana Lopes A, Gomes Pacheco T, Nascimento da Silva O, do Nascimento Vieira L, Guerra MP, Pacca Luna Mattar E, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Plastid genome evolution in Amazonian açaí palm (Euterpe oleracea Mart.) and Atlantic forest açaí palm (Euterpe edulis Mart.). PLANT MOLECULAR BIOLOGY 2021; 105:559-574. [PMID: 33386578 DOI: 10.1007/s11103-020-01109-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Odyone Nascimento da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Wang Y, Zhao B, Lu Z, Shi Y, Li J. The complete chloroplast genome provides insight into the polymorphism and adaptive evolution of Garcinia paucinervis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1879676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Yifei Wang
- Department of Pharmacognosy, College of Pharmacy, Guilin Medical University, Guilin, China
| | - Bo Zhao
- Department of Pharmacognosy, College of Pharmacy, Guilin Medical University, Guilin, China
| | - Zhaocen Lu
- Department of Characteristic Economic Plant Research Center, Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Department of Characteristic Economic Plant Research Center, Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Jingjian Li
- Department of Pharmacognosy, College of Pharmacy, Guilin Medical University, Guilin, China
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119
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Dong F, Lin Z, Lin J, Ming R, Zhang W. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. PLANTS 2021; 10:plants10020283. [PMID: 33540810 PMCID: PMC7912957 DOI: 10.3390/plants10020283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023]
Abstract
Rambutan (Nephelium lappaceum L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.
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Affiliation(s)
- Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Zhicong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
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120
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Alzahrani DA. Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis. PLANTS 2021; 10:plants10020270. [PMID: 33573201 PMCID: PMC7911161 DOI: 10.3390/plants10020270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 12/30/2022]
Abstract
Abutilon fruticosum is one of the endemic plants with high medicinal and economic value in Saudi Arabia and belongs to the family Malvaceae. However, the plastome sequence and phylogenetic position have not been reported until this study. In this research, the complete chloroplast genome of A. fruticosum was sequenced and assembled, and comparative and phylogenetic analyses within the Malvaceae family were conducted. The chloroplast genome (cp genome) has a circular and quadripartite structure with a total length of 160,357 bp and contains 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). The repeat analyses indicate that all the types of repeats (palindromic, complement, forward and reverse) were present in the genome, with palindromic occurring more frequently. A total number of 212 microsatellites were identified in the plastome, of which the majority are mononucleotides. Comparative analyses with other species of Malvaceae indicate a high level of resemblance in gene content and structural organization and a significant level of variation in the position of genes in single copy and inverted repeat borders. The analyses also reveal variable hotspots in the genomes that can serve as barcodes and tools for inferring phylogenetic relationships in the family: the regions include trnH-psbA, trnK-rps16, psbI-trnS, atpH-atpI, trnT-trnL, matK, ycf1 and ndhH. Phylogenetic analysis indicates that A. fruticosum is closely related to Althaea officinalis, which disagrees with the previous systematic position of the species. This study provides insights into the systematic position of A. fruticosum and valuable resources for further phylogenetic and evolutionary studies of the species and the Malvaceae family to resolve ambiguous issues within the taxa.
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Affiliation(s)
- Dhafer A Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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Yang J, Chiang YC, Hsu TW, Kim SH, Pak JH, Kim SC. Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan. Sci Rep 2021; 11:1152. [PMID: 33441744 PMCID: PMC7806662 DOI: 10.1038/s41598-020-80143-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Genus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Tsai-Wen Hsu
- Taiwan Endemic Species Research Institute, 1 Mingshen East Road, Chichi Township, Nantou, 55244, Taiwan
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Jae-Hong Pak
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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122
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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.
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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.
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Yang Q, Fu GF, Wu ZQ, Li L, Zhao JL, Li QJ. Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China. FRONTIERS IN PLANT SCIENCE 2021; 12:774482. [PMID: 35082807 PMCID: PMC8784687 DOI: 10.3389/fpls.2021.774482] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/08/2021] [Indexed: 05/11/2023]
Abstract
Chloroplasts are critical to plant survival and adaptive evolution. The comparison of chloroplast genomes could provide insight into the adaptive evolution of closely related species. To identify potential adaptive evolution in the chloroplast genomes of four montane Zingiberaceae taxa (Cautleya, Roscoea, Rhynchanthus, and Pommereschea) that inhabit distinct habitats in the mountains of Yunnan, China, the nucleotide sequences of 13 complete chloroplast genomes, including five newly sequenced species, were characterized and compared. The five newly sequenced chloroplast genomes (162,878-163,831 bp) possessed typical quadripartite structures, which included a large single copy (LSC) region, a small single copy (SSC) region, and a pair of inverted repeat regions (IRa and IRb), and even though the structure was highly conserved among the 13 taxa, one of the rps19 genes was absent in Cautleya, possibly due to expansion of the LSC region. Positive selection of rpoA and ycf2 suggests that these montane species have experienced adaptive evolution to habitats with different sunlight intensities and that adaptation related to the chloroplast genome has played an important role in the evolution of Zingiberaceae taxa.
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Affiliation(s)
- Qian Yang
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Gao-Fei Fu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhi-Qiang Wu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Li Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- *Correspondence: Jian-Li Zhao,
| | - Qing-Jun Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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Abstract
Computers are able to systematically exploit RNA-seq data allowing us to efficiently detect RNA editing sites in a genome-wide scale. This chapter introduces a very flexible computational framework for detecting RNA editing sites in plant organelles. This framework comprises three major steps: RNA-seq data processing, RNA read alignment, and RNA editing site detection. Each step is discussed in sufficient detail to be implemented by the reader. As a study case, the framework will be used with publicly available sequencing data to detect C-to-U RNA editing sites in the coding sequences of the mitochondrial genome of Nicotiana tabacum.
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Affiliation(s)
- Alejandro A Edera
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown, Argentina.
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
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Chloroplast genome evolution in the Dracunculus clade (Aroideae, Araceae). Genomics 2020; 113:183-192. [PMID: 33326831 DOI: 10.1016/j.ygeno.2020.12.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/19/2020] [Accepted: 12/10/2020] [Indexed: 01/04/2023]
Abstract
Chloroplast (cp) genomes are considered important for the study of lineage-specific molecular evolution, population genetics, and phylogenetics. Our aim here was to elucidate the molecular evolution in cp genomes of species in the Dracunculus clade (Aroideae, Araceae). We report de novo assembled cp genomes for eight species from eight genera and also retrieved cp genomes of four species from the National Center for Biotechnology Information (NCBI). The cp genomes varied in size from 162,424 bp to 176,835 bp. Large Single Copy (LSC) region ranged in size from 87,141 bp to 95,475 bp; Small Single Copy (SSC) from 14,338 bp to 23,981 bp; and Inverted Repeats (IRa and IRb) from 25,131 bp to 32,708 bp. The expansion in inverted repeats led to duplication of ycf1 genes in four species. The genera showed high similarity in gene content and yielded 113 unique genes (79 protein-coding, 4 rRNA, and 30 tRNA genes). Codon usage, amino acid frequency, RNA editing sites, microsatellites repeats, transition and transversion substitutions, and synonymous and non-synonymous substitutions were also similar across the clade. A previous study reported deletion of ycf1, accD, psbE, trnL-CAA, and trnG-GCC genes in four Amorphophallus species. Our study supports conservative structure of cp genomes in the Dracunculus clade including Amorphophallus species and does not support gene deletion mentioned above. We also report suitable polymorphic loci based on comparative analyses of Dracunculus clade species, which could be useful for phylogenetic inference. Overall, the current study broad our knowledge about the molecular evolution of chloroplast genome in aroids.
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Bautista MAC, Zheng Y, Hu Z, Deng Y, Chen T. Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae). PLANTS (BASEL, SWITZERLAND) 2020; 9:E1671. [PMID: 33260641 PMCID: PMC7760935 DOI: 10.3390/plants9121671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 12/30/2022]
Abstract
Bougainvillea (Nyctaginaceae) is a popular ornamental plant group primarily grown for its striking colorful bracts. However, despite its established horticultural value, limited genomic resources and molecular studies have been reported for this genus. Thus, to address this existing gap, complete chloroplast genomes of four species (Bougainvillea glabra, Bougainvillea peruviana, Bougainvillea pachyphylla, Bougainvillea praecox) and one Bougainvillea cultivar were sequenced and characterized. The Bougainvillea cp genomes range from 153,966 bp to 154,541 bp in length, comprising a large single-copy region (85,159 bp-85,708 bp) and a small single-copy region (18,014 bp-18,078 bp) separated by a pair of inverted repeats (25,377-25,427 bp). All sequenced plastomes have 131 annotated genes, including 86 protein-coding, eight rRNA, and 37 tRNA genes. These five newly sequenced Bougainvillea cp genomes were compared to the Bougainvillea spectabilis cp genome deposited in GeBank. The results showed that all cp genomes have highly similar structures, contents, and organization. They all exhibit quadripartite structures and all have the same numbers of genes and introns. Codon usage, RNA editing sites, and repeat analyses also revealed highly similar results for the six cp genomes. The amino acid leucine has the highest proportion and almost all favored synonymous codons have either an A or U ending. Likewise, out of the 42 predicted RNA sites, most conversions were from serine (S) to leucine (L). The majority of the simple sequence repeats detected were A/T mononucleotides, making the cp genomes A/T-rich. The contractions and expansions of the IR boundaries were very minimal as well, hence contributing very little to the differences in genome size. In addition, sequence variation analyses showed that Bougainvillea cp genomes share nearly identical genomic profiles though several potential barcodes, such as ycf1, ndhF, and rpoA were identified. Higher variation was observed in both B. peruviana and B. pachyphylla cp sequences based on SNPs and indels analysis. Phylogenetic reconstructions further showed that these two species appear to be the basal taxa of Bougainvillea. The rarely cultivated and wild species of Bougainvillea (B. pachyphylla, B. peruviana, B. praecox) diverged earlier than the commonly cultivated species and cultivar (B. spectabilis, B. glabra, B. cv.). Overall, the results of this study provide additional genetic resources that can aid in further phylogenetic and evolutionary studies in Bougainvillea. Moreover, genetic information from this study is potentially useful in identifying Bougainvillea species and cultivars, which is essential for both taxonomic and plant breeding studies.
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Affiliation(s)
- Mary Ann C. Bautista
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China;
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zheng
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China;
| | - Zhangli Hu
- School of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518060, China;
| | - Yunfei Deng
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Chen
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China;
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
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Li J, Ye GY, Liu HL, Wang ZH. Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae. PLoS One 2020; 15:e0242591. [PMID: 33237925 PMCID: PMC7688171 DOI: 10.1371/journal.pone.0242591] [Citation(s) in RCA: 6] [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: 09/22/2020] [Accepted: 11/06/2020] [Indexed: 11/29/2022] Open
Abstract
Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.
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Affiliation(s)
- Jie Li
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guang-ying Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hai-lin Liu
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zai-hua Wang
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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128
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Ren T, Li ZX, Xie DF, Gui LJ, Peng C, Wen J, He XJ. Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships. BMC PLANT BIOLOGY 2020; 20:519. [PMID: 33187470 PMCID: PMC7663912 DOI: 10.1186/s12870-020-02696-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/12/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. RESULTS Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. CONCLUSION The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.
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Affiliation(s)
- Ting Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zi-Xuan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ling-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang Peng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jun Wen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Yang J, Takayama K, Youn JS, Pak JH, Kim SC. Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea. Genes (Basel) 2020; 11:E1338. [PMID: 33198274 PMCID: PMC7697516 DOI: 10.3390/genes11111338] [Citation(s) in RCA: 12] [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: 10/16/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
Beech trees of the genus Fagus (Fagaceae) are monoecious and distributed in the Northern Hemisphere. They represent an important component of mixed broad-leaved evergreen-deciduous forests and are an economically important source of timber. Despite their ecological and economical importance, however, little is known regarding the overall plastome evolution among Fagus species in East Asia. In particular, the taxonomic position and status of F. multinervis, a beech species endemic to Ulleung Island of Korea, remains unclear even today. Therefore, in this study, we characterized four newly completed plastomes of East Asian Fagus species (one accession each of F. crenata and F. multinervis and two accessions of F. japonica). Moreover, we performed phylogenomic analyses comparing these four plastomes with F. sylvatica (European beech) plastome. The four plastomes were highly conserved, and their size ranged from 158,163 to 158,348 base pair (bp). The overall GC content was 37.1%, and the sequence similarity ranged from 99.8% to 99.99%. Codon usage patterns were similar among species, and 7 of 77 common protein-coding genes were under positive selection. Furthermore, we identified five highly variable hotspot regions of the Fagus plastomes (ccsA/ndhD, ndhD/psaC, ndhF/rpl32, trnS-GCU/trnG-UCC, and ycf1). Phylogenetic analysis revealed the monophyly of Fagus as well as early divergence of the subgenus Fagus and monophyletic Engleriana. Finally, phylogenetic results supported the taxonomic distinction of F. multinervis from its close relatives F. engleriana and F. japonica. However, the sister species and geographic origin of F. multinervis on Ulleung Island could not be determined.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan;
| | - Jin-Suk Youn
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Jae-Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Gyeonggi-do, Suwon 16419, Korea
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Mwanzia VM, He DX, Gichira AW, Li Y, Ngarega BK, Karichu MJ, Kamau PW, Li ZZ. The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots. PLANT DIVERSITY 2020; 42:334-342. [PMID: 33134616 PMCID: PMC7584794 DOI: 10.1016/j.pld.2020.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 06/02/2023]
Abstract
Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences. However, due to extensive similarity between species in this genus, morphological characters are generally inadequate for taxonomic classification. Currently, molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited. One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome. Here, we sequenced and analyzed the plastomes of five Aponogeton species collected from China, Zambia, and Kenya, and subsequently screened these plastomes for divergent DNA hotspots. The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp. The Large and the Small Single Copies are separated by two Inverted Repeats. One hundred and thirteen unique genes were identified including 79 protein-coding, 30 tRNA, and four rRNA genes. We found that the most abundant repeats in all but one species were mononucleotide repeats (A/T) and that there were 23 potential RNA ending sites. Interestingly, a ~3 kb inversion, which includes the accD gene, was detected within the Asian species of Aponogeton. The inversion may be related to more frequent exchanges between this region and the nuclear genome. Furthermore, we detected mutational hotspot sites among the five Aponogeton species. Three of these hotspots are intergenic spacer regions (accD-psaI, rbcL-accD and trnH-GUG-psbA) that might be suitable for use as barcodes to resolve intra-generic relationships. We also identified four highly variable protein-coding genes (ccsA, rpl22, rps16 and ycf1) may be used as barcodes to resolve the higher-level phylogenies. Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton.
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Affiliation(s)
- Virginia M. Mwanzia
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ding-Xuan He
- School of Biological and Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Andrew W. Gichira
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yan Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Boniface K. Ngarega
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Mwihaki J. Karichu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | | | - Zhi-Zhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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131
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Tan W, Gao H, Jiang W, Zhang H, Yu X, Liu E, Tian X. The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes. Sci Rep 2020; 10:16309. [PMID: 33005000 PMCID: PMC7529812 DOI: 10.1038/s41598-020-73392-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
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Affiliation(s)
- Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Weiling Jiang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Huanyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Erwei Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
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132
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Park S, Park S. Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima. Sci Rep 2020; 10:16288. [PMID: 33004955 PMCID: PMC7529770 DOI: 10.1038/s41598-020-73397-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/14/2020] [Indexed: 11/09/2022] Open
Abstract
Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.,Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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133
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Zheng P, Wang D, Huang Y, Chen H, Du H, Tu J. Detection and Analysis of C-to-U RNA Editing in Rice Mitochondria-Encoded ORFs. PLANTS 2020; 9:plants9101277. [PMID: 32998293 PMCID: PMC7600565 DOI: 10.3390/plants9101277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/30/2020] [Accepted: 09/27/2020] [Indexed: 01/05/2023]
Abstract
Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA modification and is almost omnipresent in plant chloroplasts and mitochondria. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alterations needs to be investigated further. Here, by means of Sanger sequencing and publicly available RNA-seq data, we identified a total of 569 C-to-U editing sites in rice mitochondria-encoded open reading frames (ORFs), 85.41% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, based on the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 569 C-to-U RNA editing sites in their biological context. More precise information about C-to-U editing sites in rice mitochondria-encoded ORFs will facilitate our investigation on the function of C-to-U editing events in rice and also provide a valid benchmark from rice for the analysis of mitochondria C-to-U editing in other plant species.
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Affiliation(s)
- Peng Zheng
- Zhejiang Provincial Key Laboratory of Crop Germplasm Resources, Institute of Crop Science, Zhejiang University, No. 866, Yu-Hang-Tang Road, Hangzhou 310058, China; (P.Z.); (Y.H.); (H.C.)
| | - Dongxin Wang
- College of Life Science and Technology, Guangxi University, Nanning 530004, China;
| | - Yuqing Huang
- Zhejiang Provincial Key Laboratory of Crop Germplasm Resources, Institute of Crop Science, Zhejiang University, No. 866, Yu-Hang-Tang Road, Hangzhou 310058, China; (P.Z.); (Y.H.); (H.C.)
| | - Hao Chen
- Zhejiang Provincial Key Laboratory of Crop Germplasm Resources, Institute of Crop Science, Zhejiang University, No. 866, Yu-Hang-Tang Road, Hangzhou 310058, China; (P.Z.); (Y.H.); (H.C.)
| | - Hao Du
- Zhejiang Provincial Key Laboratory of Crop Germplasm Resources, Institute of Crop Science, Zhejiang University, No. 866, Yu-Hang-Tang Road, Hangzhou 310058, China; (P.Z.); (Y.H.); (H.C.)
- Correspondence: (H.D.); (J.T.)
| | - Jumin Tu
- Zhejiang Provincial Key Laboratory of Crop Germplasm Resources, Institute of Crop Science, Zhejiang University, No. 866, Yu-Hang-Tang Road, Hangzhou 310058, China; (P.Z.); (Y.H.); (H.C.)
- Correspondence: (H.D.); (J.T.)
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134
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Lin Z, Zhou P, Ma X, Deng Y, Liao Z, Li R, Ming R. Comparative analysis of chloroplast genomes in Vasconcellea pubescens A.DC. and Carica papaya L. Sci Rep 2020; 10:15799. [PMID: 32978465 PMCID: PMC7519098 DOI: 10.1038/s41598-020-72769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 08/28/2020] [Indexed: 01/12/2023] Open
Abstract
The chloroplast genome is an integral part of plant genomes in a species along with nuclear and mitochondrial genomes, contributing to adaptation, diversification, and evolution of plant lineages. In the family Caricaceae, only the Carica papaya chloroplast genome and its nuclear and mitochondrial genomes were sequenced, and no chloroplast genome-wide comparison across genera was conducted. Here, we sequenced and assembled the chloroplast genome of Vasconcellea pubescens A.DC. using Oxford Nanopore Technology. The size of the genome is 158,712 bp, smaller than 160,100 bp of the C. papaya chloroplast genome. And two structural haplotypes, LSC_IRa_SSCrc_IRb and LSC_IRa_SSC_IRb, were identified in both V. pubescens and C. papaya chloroplast genomes. The insertion-deletion mutations may play an important role in Ycf1 gene evolution in family Caricaceae. Ycf2 is the only one gene positively selected in the V. pubescens chloroplast genome. In the C. papaya chloroplast genome, there are 46 RNA editing loci with an average RNA editing efficiency of 63%. These findings will improve our understanding of the genomes of these two crops in the family Caricaceae and will contribute to crop improvement.
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Affiliation(s)
- Zhicong Lin
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ping Zhou
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, China
| | - Xinyi Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Youjin Deng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhenyang Liao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ruoyu Li
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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135
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Putintseva YA, Bondar EI, Simonov EP, Sharov VV, Oreshkova NV, Kuzmin DA, Konstantinov YM, Shmakov VN, Belkov VI, Sadovsky MG, Keech O, Krutovsky KV. Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome. BMC Genomics 2020; 21:654. [PMID: 32972367 PMCID: PMC7517811 DOI: 10.1186/s12864-020-07061-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/10/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. RESULTS Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. CONCLUSIONS Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.
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Affiliation(s)
- Yuliya A Putintseva
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
| | - Eugeniya I Bondar
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center", Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Evgeniy P Simonov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, 625003, Russia
| | - Vadim V Sharov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center", Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
- Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - Natalya V Oreshkova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center", Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
- Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Dmitry A Kuzmin
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
- Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - Yuri M Konstantinov
- Laboratory of Plant Genetic Engineering, Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033, Russia
| | - Vladimir N Shmakov
- Laboratory of Plant Genetic Engineering, Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033, Russia
| | - Vadim I Belkov
- Laboratory of Plant Genetic Engineering, Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033, Russia
| | - Michael G Sadovsky
- Institute of Computational Modeling, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Olivier Keech
- Department of Plant Physiology, UPSC, Umeå University, S-90187, Umeå, Sweden
| | - Konstantin V Krutovsky
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research, George-August University of Göttingen, 37075, Göttingen, Germany.
- Laboratory of Population Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia.
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA.
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Pacheco TG, Lopes ADS, Welter JF, Yotoko KSC, Otoni WC, Vieira LDN, Guerra MP, Nodari RO, Balsanelli E, Pedrosa FDO, de Souza EM, Rogalski M. Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features. PLANT MOLECULAR BIOLOGY 2020; 104:21-37. [PMID: 32533420 DOI: 10.1007/s11103-020-01020-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Fátima Welter
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Karla Suemy Clemente Yotoko
- Laboratório de Bioinformática e Evolução, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais, Departamento de Biologia Vegetal, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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137
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Li DM, Ye YJ, Xu YC, Liu JM, Zhu GF. Complete chloroplast genomes of Zingiber montanum and Zingiber zerumbet: Genome structure, comparative and phylogenetic analyses. PLoS One 2020; 15:e0236590. [PMID: 32735595 PMCID: PMC7394419 DOI: 10.1371/journal.pone.0236590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/08/2020] [Indexed: 11/29/2022] Open
Abstract
Zingiber montanum (Z. montanum) and Zingiber zerumbet (Z. zerumbet) are important medicinal and ornamental herbs in the genus Zingiber and family Zingiberaceae. Chloroplast-derived markers are useful for species identification and phylogenetic studies, but further development is warranted for these two Zingiber species. In this study, we report the complete chloroplast genomes of Z. montanum and Z. zerumbet, which had lengths of 164,464 bp and 163,589 bp, respectively. These genomes had typical quadripartite structures with a large single copy (LSC, 87,856-89,161 bp), a small single copy (SSC, 15,803-15,642 bp), and a pair of inverted repeats (IRa and IRb, 29,393-30,449 bp). We identified 111 unique genes in each chloroplast genome, including 79 protein-coding genes, 28 tRNAs and 4 rRNA genes. We analyzed the molecular structures, gene information, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats (SSRs) and long repeats from the two chloroplast genomes. A comparison of the Z. montanum and Z. zerumbet chloroplast genomes detected 489 single-nucleotide polymorphisms (SNPs) and 172 insertions/deletions (indels). Thirteen highly divergent regions, including ycf1, rps19, rps18-rpl20, accD-psaI, psaC-ndhE, psbA-trnK-UUU, trnfM-CAU-rps14, trnE-UUC-trnT-UGU, ccsA-ndhD, psbC-trnS-UGA, start-psbA, petA-psbJ, and rbcL-accD, were identified and might be useful for future species identification and phylogeny in the genus Zingiber. Positive selection was observed for ATP synthase (atpA and atpB), RNA polymerase (rpoA), small subunit ribosomal protein (rps3) and other protein-coding genes (accD, clpP, ycf1, and ycf2) based on the Ka/Ks ratios. Additionally, chloroplast SNP-based phylogeny analyses found that Zingiber was a monophyletic sister branch to Kaempferia and that chloroplast SNPs could be used to identify Zingiber species. The genome resources in our study provide valuable information for the identification and phylogenetic analysis of the genus Zingiber and family Zingiberaceae.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuan-Jun Ye
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ye-Chun Xu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jin-Mei Liu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Mehmood F, Abdullah, Ubaid Z, Shahzadi I, Ahmed I, Waheed MT, Poczai P, Mirza B. Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco ( Nicotiana rustica). PeerJ 2020; 8:e9552. [PMID: 32775052 PMCID: PMC7382938 DOI: 10.7717/peerj.9552] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323-25,369 bp each) separated by a large single-copy (LSC) region (86,510-86,716 bp) and a small single-copy (SSC) region (18,441-18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65-0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.
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Affiliation(s)
- Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zartasha Ubaid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iram Shahzadi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Bushra Mirza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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139
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Gomes Pacheco T, Morais da Silva G, de Santana Lopes A, de Oliveira JD, Rogalski JM, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae). PLANTA 2020; 252:17. [PMID: 32666132 DOI: 10.1007/s00425-020-03427-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Complete plastome sequence of Tropaeolum pentaphyllum revealed molecular markers, hotspots of nucleotide polymorphism, RNA editing sites and phylogenetic aspects Tropaeolaceae Juss. ex DC. comprises approximately 95 species across North and South Americas. Tropaeolum pentaphyllum Lam. is an unconventional and endangered species with occurrence in some countries of South America. Although this species presents nutritional, medicinal and ornamental uses, genetic studies involving natural populations or promising genotypes are practically non-existent. Here, we report the nucleotide sequence of T. pentaphyllum plastome. It represents the first complete plastome sequence of the family Tropaeolaceae to be fully sequenced and analyzed in detail. The sequencing data revealed that the T. pentaphyllum plastome is highly similar to the plastomes of other Brassicales. Notwithstanding, our analyses detected some specific features concerning events of IR expansion and structural changes in some genes such as matK, rpoA, and rpoC2. We also detected 251 SSR loci, nine hotspots of nucleotide polymorphism, and two specific RNA editing sites in the plastome of T. pentaphyllum. Moreover, plastid phylogenomic inference indicated a closed relationship between the families Tropaeolaceae and Akaniaceae, which formed a sister group to Moringaceae-Caricaceae. Finally, our data bring new molecular markers and evolutionary features to be applied in the natural population, germplasm collection, and genotype selection aiming conservation, genetic diversity evaluation, and exploitation of this endangered species.
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Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José Daniel de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Marcia Rogalski
- Núcleo de Ciências Biológicas e Ambientais, Instituto Federal do Rio Grande do Sul, Distrito Engenheiro Luiz Englert, Sertão, RS, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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140
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Androsiuk P, Jastrzębski JP, Paukszto Ł, Makowczenko K, Okorski A, Pszczółkowska A, Chwedorzewska KJ, Górecki R, Giełwanowska I. Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species. Sci Rep 2020; 10:11522. [PMID: 32661280 PMCID: PMC7359349 DOI: 10.1038/s41598-020-68563-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/25/2020] [Indexed: 11/08/2022] Open
Abstract
The complete plastome sequences of six species were sequenced to better understand the evolutionary relationships and mutation patterns in the chloroplast genome of the genus Colobanthus. The length of the chloroplast genome sequences of C. acicularis, C. affinis, C. lycopodioides, C. nivicola, C. pulvinatus and C. subulatus ranged from 151,050 to 151,462 bp. The quadripartite circular structure of these genome sequences has the same overall organization and gene content with 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames. A total of 153 repeat sequences were revealed. Forward repeats were dominant, whereas complementary repeats were found only in C. pulvinatus. The mononucleotide SSRs composed of A/T units were most common, and hexanucleotide SSRs were detected least often. Eleven highly variable regions which could be utilized as potential markers for phylogeny reconstruction, species identification or phylogeography were identified within Colobanthus chloroplast genomes. Seventy-three protein-coding genes were used in phylogenetic analyses. Reconstructed phylogeny was consistent with the systematic position of the studied species, and the representatives of the same genus were grouped in one clade. All studied Colobanthus species formed a single group and C. lycopodioides was least similar to the remaining species.
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Affiliation(s)
- Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Karol Makowczenko
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Adam Okorski
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Environmental Management and Agriculture, University of Warmia and Mazury in Olsztyn, ul. Prawocheńskiego 17, 10-720, Olsztyn, Poland
| | - Agnieszka Pszczółkowska
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Environmental Management and Agriculture, University of Warmia and Mazury in Olsztyn, ul. Prawocheńskiego 17, 10-720, Olsztyn, Poland
| | | | - Ryszard Górecki
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Yang J, Kang GH, Pak JH, Kim SC. Characterization and Comparison of Two Complete Plastomes of Rosaceae Species ( Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea. Int J Mol Sci 2020; 21:E4933. [PMID: 32668601 PMCID: PMC7404287 DOI: 10.3390/ijms21144933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
Potentilla dickinsii var. glabrata and Spiraea insularis in the family Rosaceae are species endemic to Ulleung Island, Korea, the latter of which is listed as endangered. In this study, we characterized the complete plastomes of these two species and compared these with previously reported plastomes of other Ulleung Island endemic species of Rosaceae (Cotoneaster wilsonii, Prunus takesimensis, Rubus takesimensis, and Sorbus ulleungensis). The highly conserved complete plastomes of P. dickinsii var. glabrata and S. insularis are 158,637 and 155,524 base pairs with GC contents of 37% and 36.9%, respectively. Comparative phylogenomic analysis identified three highly variable intergenic regions (trnT-UGU/trnL-UAA, rpl32/trnL-UAG, and ndhF/rpl32) and one variable genic region (ycf1). Only 14 of the 75 protein-coding genes have been subject to strong purifying selection. Phylogenetic analysis of 23 representative plastomes within the Rosaceae supported the monophyly of Potentilla and the sister relationship between Potentilla and Fragaria and indicated that S. insularis is sister to a clade containing Cotoneaster, Malus, Pyrus, and Sorbus. The plastome resources generated in this study will contribute to elucidating the plastome evolution of insular endemic Rosaceae on Ulleung Island and also in assessing the genetic consequences of anagenetic speciation for various endemic lineages on the island.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea;
| | - Gi-Ho Kang
- Baekdudaegan National Arboretum, 1501 Chunyang-ro, Chungyang-myeon, Bonghwa-gun, Gyeongsangbuk-do 36209, Korea;
| | - Jae-Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea;
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, Korea
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142
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Transcriptome and complete chloroplast genome of Glycyrrhiza inflata and comparative analyses with the other two licorice species. Genomics 2020; 112:4179-4188. [PMID: 32650098 DOI: 10.1016/j.ygeno.2020.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/04/2020] [Accepted: 07/02/2020] [Indexed: 11/20/2022]
Abstract
In this study, we characterized the transcriptome and chloroplast genome of Glycyrrhiza inflata and performed comparative analyses with G. uralensis and G. glabra. 60,541unigenes were obtained from the transcriptome of G. inflata. The results of function annotation revealed a similar distribution of functional categories among three licorice species. By comparing chloroplast genomes of licorice species, it was demonstrated that the structure and the length of genome as well as gene content and gene order were highly similar. The phylogenetic tree, constructed with the mixed data of transcriptome and chloroplast genome, elucidated that G. inflata and G. glabra had a closer relationship than G. uralensis. Six regions were suggested as potential markers for the identification of three licorice species. In each licorice species, two unigenes were homologous to reference flavonol synthase. For G. inflata, 48 and 21 RNA editing sites were detected by PREP-Cp program and RNA-Seq data mapping, respectively.
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143
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Koo HJ, Yang TJ. RNA editing may stabilize membrane-embedded proteins by increasing phydrophobicity: A study of Zanthoxylum piperitum and Z. schinifolium chloroplast NdhG. Gene 2020; 746:144638. [PMID: 32244054 DOI: 10.1016/j.gene.2020.144638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 03/29/2020] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
Most chloroplast genes in Zanthoxylum schinifolium (Korean pepper) and Z. piperitum (Japanese pepper) are subject to neutral or purifying selection (Ka/Ks values < 1); however, NAD(P)H dehydrogenase subunit G (ndhG) has a Ka/Ks value of 1.43, which may indicate positive selection. Here, we modeled the ZsNdhG and ZpNdhG structures by comparing them with the NuoJ subunit of respiratory complex I in Escherichia coli, revealing the locations of four amino acid differences between ZsNdhG and ZpNdhG. As these polymorphisms were located at the end of a membrane-spanning α-helix or in peptide loops external to the membrane, they are not expected to have major effects on the membrane-embedding properties of these proteins. However, we found that C-to-U RNA editing occurred at the ndhG-50 sites of ndhG (uCa to uUa, Ser to Leu) in both species, resulting in changes to an amino acid located in the middle of a membrane-spanning α-helix, which may maintain its hydrophobicity. RNA editing at the ndhG-50 site was conserved in many plant species, and the modeled structures of Anthoceros formosae NdhG and Spirodela polyrhiza NdhB provided further evidence that RNA editing increases the hydrophobicity of membrane-embedded proteins. We also speculate that the polar residues inside membrane-spanning α-helices serve to support the protein structure. This report represents the first RNA-editing site identified in Zanthoxylum and points to the importance of considering RNA editing when identifying positively selected genes based on Ka/Ks values.
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Affiliation(s)
- Hyun Jo Koo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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144
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Mehmood F, Abdullah, Ubaid Z, Bao Y, Poczai P, Mirza B. Comparative Plastomics of Ashwagandha ( Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants. PLANTS (BASEL, SWITZERLAND) 2020; 9:E752. [PMID: 32549379 PMCID: PMC7355740 DOI: 10.3390/plants9060752] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 01/04/2023]
Abstract
Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635-85,765 bp and a small single-copy (SSC) region of 18,457-18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.
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Affiliation(s)
- Furrukh Mehmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
| | - Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
| | - Zartasha Ubaid
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China;
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
| | - Bushra Mirza
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
- Vice Chancellor of Lahore College for Women University, Lahore 54000, Pakistan
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145
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Morales-Briones DF, Kadereit G, Tefarikis DT, Moore MJ, Smith SA, Brockington SF, Timoneda A, Yim WC, Cushman JC, Yang Y. Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l. Syst Biol 2020; 70:219-235. [PMID: 32785686 PMCID: PMC7875436 DOI: 10.1093/sysbio/syaa066] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/01/2020] [Accepted: 09/03/2020] [Indexed: 12/26/2022] Open
Abstract
Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]
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Affiliation(s)
- Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Delphine T Tefarikis
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH 44074-1097, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
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Abdullah, Henriquez CL, Mehmood F, Shahzadi I, Ali Z, Waheed MT, Croat TB, Poczai P, Ahmed I. Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae. PLANTS (BASEL, SWITZERLAND) 2020; 9:E737. [PMID: 32545339 PMCID: PMC7355861 DOI: 10.3390/plants9060737] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 11/17/2022]
Abstract
The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17-18 genes are duplicated in the inverted repeat (IR) regions, comprising 6-7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.
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Affiliation(s)
- Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.); (F.M.); (I.S.); (Z.A.); (M.T.W.)
| | - Claudia L. Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;
| | - Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.); (F.M.); (I.S.); (Z.A.); (M.T.W.)
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
| | - Iram Shahzadi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.); (F.M.); (I.S.); (Z.A.); (M.T.W.)
| | - Zain Ali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.); (F.M.); (I.S.); (Z.A.); (M.T.W.)
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.); (F.M.); (I.S.); (Z.A.); (M.T.W.)
| | - Thomas B. Croat
- Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA;
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan
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147
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Bi C, Lu N, Xu Y, He C, Lu Z. Characterization and Analysis of the Mitochondrial Genome of Common Bean ( Phaseolus vulgaris) by Comparative Genomic Approaches. Int J Mol Sci 2020; 21:E3778. [PMID: 32471098 PMCID: PMC7312688 DOI: 10.3390/ijms21113778] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.
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Affiliation(s)
- Changwei Bi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
| | - Yiqing Xu
- School of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, Jiangsu, China;
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
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148
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Tyagi S, Jung JA, Kim JS, Won SY. Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E568. [PMID: 32365609 PMCID: PMC7285121 DOI: 10.3390/plants9050568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022]
Abstract
Aster spathulifolius, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland A. spathulifolius and compared it with those of the island type and other Aster species. The chloroplast genome of mainland A. spathulifolius is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two A. spathulifolius lines and the other Aster species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All Aster species clustered into a monophyletic group, but the chloroplast genome of mainland A. spathulifolius was more similar to the other Aster species than to that of the island A. spathulifolius. The accD and ndhF genes were detected to be under positive selection within the Aster lineage compared to other related taxa. The complete chloroplast genome of mainland A. spathulifolius presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the Aster genus and the Asteraceae.
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Affiliation(s)
- Swati Tyagi
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea;
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
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149
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Munyao JN, Dong X, Yang JX, Mbandi EM, Wanga VO, Oulo MA, Saina JK, Musili PM, Hu GW. Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E296. [PMID: 32121524 PMCID: PMC7154914 DOI: 10.3390/plants9030296] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022]
Abstract
The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.
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Affiliation(s)
- Jacinta N. Munyao
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Dong
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Yang
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Elijah M. Mbandi
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Vincent O. Wanga
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Millicent A. Oulo
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Josphat K. Saina
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Paul M. Musili
- East Africa Herbarium, National Museums of Kenya, P.O. Box 45166 00100 Nairobi, Kenya;
| | - Guang-Wan Hu
- CAS key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (J.N.M.); (X.D.); (J.-X.Y.); (E.M.M.); (V.O.W.); (M.A.O.); (J.K.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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150
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Mehmood F, Abdullah, Shahzadi I, Ahmed I, Waheed MT, Mirza B. Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae. Genomics 2020; 112:1522-1530. [DOI: 10.1016/j.ygeno.2019.08.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/19/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023]
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