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Almerekova S, Yermagambetova M, Ivaschenko A, Turuspekov Y, Abugalieva S. Comparative Analysis of Plastome Sequences of Seven Tulipa L. (Liliaceae Juss.) Species from Section Kolpakowskianae Raamsd. Ex Zonn and Veldk. Int J Mol Sci 2024; 25:7874. [PMID: 39063115 PMCID: PMC11277319 DOI: 10.3390/ijms25147874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Tulipa L. is a genus of significant economic, environmental, and cultural importance in several parts of the world. The exact number of species in the genus remains uncertain due to inherent taxonomic challenges. We utilized next-generation sequencing technology to sequence and assemble the plastid genomes of seven Tulipa species collected in Kazakhstan and conducted a comparative analysis. The total number of annotated genes was 136 in all seven studied Tulipa species, 114 of which were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Nine regions (petD, ndhH, ycf2-ycf3, ndhA, rpl16, clpP, ndhD-ndhF, rpoC2, and ycf1) demonstrated significant nucleotide variability, suggesting their potential as molecular markers. A total of 1388 SSRs were identified in the seven Tulipa plastomes, with mononucleotide repeats being the most abundant (60.09%), followed by dinucleotide (34.44%), tetranucleotide (3.90%), trinucleotide (1.08%), pentanucleotide (0.22%), and hexanucleotide (0.29%). The Ka/Ks values of the protein-coding genes ranged from 0 to 3.9286, with the majority showing values <1. Phylogenetic analysis based on a complete plastid genome and protein-coding gene sequences divided the species into three major clades corresponding to their subgenera. The results obtained in this study may contribute to understanding the phylogenetic relationships and molecular taxonomy of Tulipa species.
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Affiliation(s)
- Shyryn Almerekova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Moldir Yermagambetova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
| | | | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (M.Y.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
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Zheng HZ, Dai W, Xu MH, Lin YY, Zhu XL, Long H, Tong LL, Xu XG. Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses. Genes (Basel) 2024; 15:940. [PMID: 39062719 PMCID: PMC11275416 DOI: 10.3390/genes15070940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.
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Affiliation(s)
- Hao-Zhi Zheng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Wei Dai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Meng-Han Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Yu-Ye Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Xing-Li Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Hui Long
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Li-Li Tong
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing 210038, China;
| | - Xiao-Gang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
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Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
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Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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Gao C, Li T, Zhao X, Wu C, Zhang Q, Zhao X, Wu M, Lian Y, Li Z. Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis. BMC PLANT BIOLOGY 2023; 23:318. [PMID: 37316771 DOI: 10.1186/s12870-023-04338-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND The genus Rosa (Rosaceae) contains approximately 200 species, most of which have high ecological and economic values. Chloroplast genome sequences are important for studying species differentiation, phylogeny, and RNA editing. RESULTS In this study, the chloroplast genomes of three Rosa species, Rosa hybrida, Rosa acicularis, and Rosa rubiginosa, were assembled and compared with other reported Rosa chloroplast genomes. To investigate the RNA editing sites in R. hybrida (commercial rose cultivar), we mapped RNA-sequencing data to the chloroplast genome and analyzed their post-transcriptional features. Rosa chloroplast genomes presented a quadripartite structure and had highly conserved gene order and gene content. We identified four mutation hotspots (ycf3-trnS, trnT-trnL, psbE-petL, and ycf1) as candidate molecular markers for differentiation in the Rosa species. Additionally, 22 chloroplast genomic fragments with a total length of 6,192 bp and > 90% sequence similarity with their counterparts were identified in the mitochondrial genome, representing 3.96% of the chloroplast genome. Phylogenetic analysis including all sections and all subgenera revealed that the earliest divergence in the chloroplast phylogeny roughly distinguished species of sections Pimpinellifoliae and Rosa and subgenera Hulthemia. Moreover, DNA- and RNA-sequencing data revealed 19 RNA editing sites, including three synonymous and 16 nonsynonymous, in the chloroplast genome of R. hybrida that were distributed among 13 genes. CONCLUSIONS The genome structure and gene content of Rosa chloroplast genomes are similar across various species. Phylogenetic analysis based on the Rosa chloroplast genomes has high resolution. Additionally, a total of 19 RNA editing sites were validated by RNA-Seq mapping in R. hybrida. The results provide valuable information for RNA editing and evolutionary studies of Rosa and a basis for further studies on genomic breeding of Rosa species.
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Affiliation(s)
- Chengwen Gao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China.
| | - Teng Li
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
- School of Public Health, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Xia Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Chuanhong Wu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Qian Zhang
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Xiangzhong Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Mingxuan Wu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Yihong Lian
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Zhiqiang Li
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China.
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Ma D, Ding Q, Zhao Z, Han X, Zheng HL. Chloroplast genome analysis of three Acanthus species reveal the adaptation of mangrove to intertidal habitats. Gene 2023; 873:147479. [PMID: 37182557 DOI: 10.1016/j.gene.2023.147479] [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: 03/04/2023] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
Acanthus is a distinctive genus that covers three species with different ecological niches including Acanthus mollis (arid terrestrial), Acanthus leucostachyus (damp forest) and Acanthus ilicifolius (coastal intertidal). It is an intriguing question how these species evolved from terrestrial to coastal intertidal. In the present study, we assembled chloroplast genomes of A. ilicifolius, A. leucostachyus and A. mollis, which exhibited typical quadripartite structures. The sizes were 150,758, 154,686 and 150,339 bp that comprised a large single copy (LSC, 82,963, 86,461 and 82,612 bp), a small single copy (SSC, 17,191, 17,511 and 17,019 bp), and a pair of inverted repeats (IRs, 25,302, 25,357 and 25,354 bp), respectively. Gene annotation revealed that A. ilicifolius, A. leucostachyus and A. mollis contained 113, 112 and 108 unique genes, each of which contained 79, 79 and 74 protein-coding genes, 30, 29 and 30 tRNAs, and 4 rRNA genes, respectively. Differential gene analysis revealed plenty of ndhs gene deletions in the terrestrial plant A. mollis. Nucleotide diversity analysis showed that the psbK, ycf1, ndhG, and rpl22 have the highest nucleotide variability. Compared to A. leucostachyus and A. mollis, seven genes in A. ilicifolius underwent positive selection. Among them, the atpF gene showed a strong positive selection throughout terrestrial to marine evolution and was important for adaptation to coastal intertidal habitats. Phylogenetic analysis indicated that A. ilicifolius has a closer genetic relationship with A. leucostachyus than A. mollis which further confirmed the evolutionary direction of Acanthus going from terrestrial to coastal intertidal zones.
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Affiliation(s)
- Dongna Ma
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiansu Ding
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Zhizhu Zhao
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Han
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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Zhang SD, Yan K, Ling LZ. Characterization and phylogenetic analyses of ten complete plastomes of Spiraea species. BMC Genomics 2023; 24:137. [PMID: 36944915 PMCID: PMC10029230 DOI: 10.1186/s12864-023-09242-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Spiraea is a genus of deciduous shrubs that contains 80-120 species, is mainly distributed in the Northern Hemisphere and has diversified in East Asia. Spiraea species are cultivated as ornamental plants and some are used in traditional herbal medicine. Based on morphological characteristics and genetic markers, phylogenetic classification exhibits low discriminatory power. RESULTS In present study, we assembled and characterized the chloroplast (cp) genomes of ten Spiraea species and comparatively analysed with five reported cp genomes of this genus. The cp genomes of the fifteen Spiraea species, ranging from 155,904 to 158,637 bp in length, were very conserved and no structural rearrangements occurred. A total of 85 protein-coding genes (PCGs), 37 tRNAs and 8 rRNAs were annotated. We also examined 1,010 simple sequence repeat (SSR) loci, most of which had A/T base preference. Comparative analysis of cp genome demonstrated that single copy and non-coding regions were more divergent than the inverted repeats (IRs) and coding regions and six mutational hotspots were detected. Selection pressure analysis showed that all PCGs were under purifying selection. Phylogenetic analysis based on the complete cp genome data showed that Spiraea formed a monophyletic group and was further divided into two major clades. Infrageneric classification in each clade was supported with a high resolution value. Moreover, the phylogenetic trees based on each individual mutational hotspot segment and their combined dataset also consisted of two major clades, but most of the phylogenetic relationships of interspecies were not well supported. CONCLUSIONS Although the cp genomes of Spiraea species exhibited high conservation in genome structure, gene content and order, a large number of polymorphism sites and several mutation hotspots were identified in whole cp genomes, which might be sufficiently used as molecular markers to distinguish Spiraea species. Phylogenetic analysis based on the complete cp genome indicated that infrageneric classification in two major clades was supported with high resolution values. Therefore, the cp genome data of the genus Spiraea will be effective in resolving the phylogeny in this genus.
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Affiliation(s)
- Shu-Dong Zhang
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China
| | - Kai Yan
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China.
| | - Li-Zhen Ling
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China.
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Gao Y, Liu K, Li E, Wang Y, Xu C, Zhao L, Dong W. Dynamic evolution of the plastome in the Elm family (Ulmaceae). PLANTA 2022; 257:14. [PMID: 36526857 DOI: 10.1007/s00425-022-04045-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
This study compared the plastomes of Ulmaceae allowing analyses of the dynamic evolution, including genome structure, codon usage bias, repeat sequences, molecular mutation rates, and phylogenetic inferences. Ulmaceae is a small family in the order Rosales. This family consists of seven genera, including Ulmus, Zelkova, Planera, Hemiptelea, Phyllostylon, Ampelocera, and Holoptelea. Ulmaceae is an interesting lineage from plant biogeographic, systematic, evolutionary, and paleobotanic perspectives. It is also a good model to investigate the evolution of the plastomes in woody plants. In this study, we sequenced and assembled the complete plastomes of the six Ulmaceae genera to compare genomic structures and reveal the molecular evolutionary patterns. The size of the quadripartite plastomes ranged from 158,290 bp to 161,886 bp. The genomes contained 131 genes, including 87 coding genes, 36 tRNA, and 8 rRNA. The gene number, gene content, and genomic structure were highly consistent among the Ulmaceae genera. Nine variable regions including ndhA intron, ndhF-rpl32, ycf1, psbK-trnS, rps16-trnQ, trnT-trnL, trnT-psbD, trnS-trnG, and rpl32-trnL, were identified in Ulmaceae plastomes according to the nucleotide diversity values. Condon usage was biased among the genes and showed consistent trends in the seven genera. Molecular evolution analyses revealed that most of the genes and all gene groups were under widespread purifying selection. Twelve genes (ccsA, matK, psbH, psbK, rbcL, rpl22, rpl32, rpoA, rps12, rps15, rps16, and ycf2) were under positive selection. Phylogenetic analyses supported that Ulmaceae should be divided into two main clades, such as the temperate clade, including Ulmus, Zelkova, Planera, and Hemiptelea and the tropical clade, including Phyllostylon, Ampelocera and Holoptelea. This study reports the structure and evolutionary characteristics of the Elm family. These new genomic data will benefit assessments of genomic evolution and provide information to elucidate the phylogenetic relationships among Ulmaceae species.
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Affiliation(s)
- Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Enzhe Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liangcheng Zhao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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Wang X, Xu KW, Lee SY, Wu J, Li Q, Chen BJ. Characterization of the chloroplast genome and phylogenetic analysis of Ceratopteris pteridoides (Pteridaceae). GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Li Y, Zhang L, Wang T, Zhang C, Wang R, Zhang D, Xie Y, Zhou N, Wang W, Zhang H, Hu B, Li W, Zhao Q, Wang L, Wu X. The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses. JOURNAL OF PLANT RESEARCH 2022; 135:723-737. [PMID: 36260182 DOI: 10.1007/s10265-022-01417-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
We sequenced and analyzed the complete chloroplast genomes of Lilium amoenum, Lilium souliei, and Nomocharis forrestii in detail, including the first sequence and structural comparison of Nomocharis forrestii. We found that the lengths and nucleotide composition of the three chloroplast genes showed little variation. The chloroplast genomes of the three Lilium species contain 87 protein coding genes (PCGs), 38 tRNAs, and 8 rRNA genes. The only difference is that Nomocharis forrestii had an additional infA pseudogene. In the sequence analysis of the Lilium chloroplast genomes, 216 SSRs, 143 pairs of long repeats, 571 SNPs, and 202 indels were detected. In addition, we identified seven hypervariable regions that can be used as potential molecular markers and DNA barcodes of Lilium through complete sequence alignment. The phylogenetic tree was constructed from the three chloroplast genome sequences of Lilium obtained here and 40 chloroplast genome sequences from the NCBI database (including 35 Lilium species, 4 Fritillaria species, and one species of Smilax). The analysis showed that the species clustering of the genus Lilium essentially conformed to the classical morphological classification system of Comber, but differences in the classification of individual species remained. In our report, we support the reclassification of Lilium henryi and Lilium rosthorniiy in the genus Lilium. In general, this study not only provides genome data for three Lilium species, but also provides a comparative analysis of the Lilium chloroplast genomes. These advances will help to identify Lilium species, clarify the phylogenetic analysis of the Lilium genus, and help to solve and improve the disputes and deficiencies in the traditional morphological classification.
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Affiliation(s)
- Yuan Li
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - LiNa Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - TianXi Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - ChaoChao Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - RuiJia Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - Da Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - YuQi Xie
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - NingNing Zhou
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - WeiZhen Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - HuiMin Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - Bin Hu
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - WenHan Li
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - QingQing Zhao
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - LiHua Wang
- Flower Research Institute, Yunnan Agriculture Academy of Science, Panlong District, Kunming, 650025, Yunnan, China.
| | - XueWei Wu
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China.
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Wen Y, Qin Y, Shao B, Li J, Ma C, Liu Y, Yang B, Jin X. The extremely reduced, diverged and reconfigured plastomes of the largest mycoheterotrophic orchid lineage. BMC PLANT BIOLOGY 2022; 22:448. [PMID: 36123622 PMCID: PMC9487142 DOI: 10.1186/s12870-022-03836-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/09/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Plastomes of heterotrophic plants have been greatly altered in structure and gene content, owing to the relaxation of selection on photosynthesis-related genes. The orchid tribe Gastrodieae is the largest and probably the oldest mycoheterotrophic clade of the extant family Orchidaceae. To characterize plastome evolution across members of this key important mycoheterotrophic lineage, we sequenced and analyzed the plastomes of eleven Gastrodieae members, including representative species of two genera, as well as members of the sister group Nervilieae. RESULTS The plastomes of Gastrodieae members contain 20 protein-coding, four rRNA and five tRNA genes. Evolutionary analysis indicated that all rrn genes were transferred laterally and together, forming an rrn block in the plastomes of Gastrodieae. The plastome GC content of Gastrodia species ranged from 23.10% (G. flexistyla) to 25.79% (G. javanica). The plastome of Didymoplexis pallens contains two copies each of ycf1 and ycf2. The synonymous and nonsynonymous substitution rates were very high in the plastomes of Gastrodieae among mycoheterotrophic species in Orchidaceae and varied between genes. CONCLUSIONS The plastomes of Gastrodieae are greatly reduced and characterized by low GC content, rrn block formation, lineage-specific reconfiguration and gene content, which might be positively selected. Overall, the plastomes of Gastrodieae not only serve as an excellent model for illustrating the evolution of plastomes but also provide new insights into plastome evolution in parasitic plants.
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Affiliation(s)
- Yingying Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Ying Qin
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, Guangxi, China
| | - Bingyi Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jianwu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan, 666303, China
| | - Chongbo Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yan Liu
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, 541006, Guangxi, China.
| | - Boyun Yang
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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11
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Yu J, Xia M, Wang Y, Chi X, Xu H, Chen S, Zhang F. Short and long reads chloroplast genome assemblies and phylogenomics of Artemisia tangutica (Asteraceae). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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12
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Ulaszewski B, Meger J, Mishra B, Thines M, Burczyk J. Complete Chloroplast Genomes of Fagus sylvatica L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs. Genes (Basel) 2021; 12:1357. [PMID: 34573338 PMCID: PMC8468245 DOI: 10.3390/genes12091357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022] Open
Abstract
Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of Fagus sylvatica, an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution. Our results confirm the hypothesis of a low cpDNA diversity in European beech. The chloroplast genome size was remarkably stable (158,428 ± 37 bp). The polymorphic markers, 12 microsatellites (SSR), four SNPs and one indel, were found only in the single copy regions, while inverted repeat regions were monomorphic both in terms of length and sequence, suggesting highly efficient suppression of mutation. The within-individual analysis of polymorphisms showed >9k of markers which were proportionally present in gene and non-gene areas. However, an investigation of the frequency of alternate alleles revealed that the source of this diversity originated likely from nuclear-encoded plastome remnants (NUPTs). Phylogeographic and Mantel correlation analysis based on the complete chloroplast genomes exhibited clustering of individuals according to geographic distance in the first distance class, suggesting that the novel markers and in particular the cpSSRs could provide a more detailed picture of beech population structure in Central Europe.
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Affiliation(s)
- Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
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13
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Complete plastomes of six species of Wikstroemia (Thymelaeaceae) reveal paraphyly with the monotypic genus Stellera. Sci Rep 2021; 11:13608. [PMID: 34193929 PMCID: PMC8245458 DOI: 10.1038/s41598-021-93057-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/18/2021] [Indexed: 12/05/2022] Open
Abstract
Wikstroemia (Thymelaeaceae) is a diverse genus that extends from Asia to Australia and has been recorded on the Hawaiian Islands. Despite its medicinal properties and resource utilization in pulp production, genetic studies of the species in this important genus have been neglected. In this study, the plastome sequences of six species of Wikstroemia were sequenced and analysed. The plastomes ranged in size between 172,610 bp (W. micrantha) and 173,697 bp (W. alternifolia) and exhibited a typical genome structure consisting of a pair of inverted repeat (IR) regions separated by a large single-copy (LSC) region and a small single-copy (SSC) region. The six plastomes were similar in the 138 or 139 genes predicted, which consisted of 92 or 93 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC contents were identical (36.7%). Comparative genomic analyses were conducted with the inclusion of two additional published species of Wikstroemia in which the sequence divergence and expansion of IRs in the plastomes were determined. When compared to the coding sequences (CDSs) of Aquilaria sinensis, five genes, namely, rpl2, rps7, rps18, ycf1 and ycf2, indicated positive selection in W. capitata. The plastome-based phylogenetic analysis inferred that Wikstroemia in its current state is paraphyletic to Stellera chamaejasme, while the ITS-based tree analyses could not properly resolve the phylogenetic relationship between Stellera and Wikstroemia. This finding rekindled interest in the proposal to synonymize Stellera with Wikstroemia, which was previously proposed but rejected due to taxonomic conflicts. Nevertheless, this study provides valuable genomic information to aid in the taxonomic implications and phylogenomic reconstruction of Thymelaeaceae.
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14
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Xu G, Xu W. Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis. PROTOPLASMA 2021; 258:559-571. [PMID: 33230625 DOI: 10.1007/s00709-020-01585-y] [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: 05/18/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
As a basalmost family of Vitaceae, Chinese wild Vitis species offer key insights into the demographic history of grapes. In this study, we obtained 10 complete chloroplast (cp) genomes from Chinese wild-growing Vitis species based on our whole genome re-sequencing data. These chloroplast genomes ranged from 160,838 to 232,020 bp in size and exhibited typical quadripartite structures. Comparative analyses revealed that inverted repeat (IR) regions are especially abundant and contribute to cp genome arrangements. Phylogenetic analysis of the whole Vitis cp genomes supported three clearly partitioned main origins, in keeping with their geographic distributions, among which East Asian species from China were found to be sister species with Eurasian Vitis species but exhibited significant divergence from the North American group. Two well-supported subgroups were observed within the Chinese wild-growing Vitis species. Among these species, Vitis piasezkii and Vitis betulifolia were closely related species, exhibiting a support rate of 100%. The molecular clock-based divergence time suggested that the earliest split subspecies was Vitis pseudoreticulata, which further indicated that the origin and initial gene pool are located in southern China (the habitat of V. pseudoreticulata is located in the region). Coincidentally, the divergence time was during the Pleistocene period (2.6-0.1 Ma). Due to glacial/interglacial temperature fluctuations, cold-adapted subspecies, e.g., Vitis amurensis, could re-colonize new habitats. Our results may help to elucidate the adaptive radiation of Chinese wild Vitis species in different environments.
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Affiliation(s)
- Guangya Xu
- School of Agronomy, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China
| | - Weirong Xu
- School of Food & Wine, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China.
- Chinese Wine Industry Technology Institute, Yinchuan, 750021, China.
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15
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Liu S, Wang Z, Su Y, Wang T. Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences. BMC PLANT BIOLOGY 2021; 21:31. [PMID: 33413107 PMCID: PMC7792340 DOI: 10.1186/s12870-020-02800-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/16/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Comparative chloroplast genomics could shed light on the major evolutionary events that established plastomic diversity among closely related species. The Polypodiaceae family is one of the most species-rich and underexplored groups of extant ferns. It is generally recognized that the plastomes of Polypodiaceae are highly notable in terms of their organizational stability. Hence, no research has yet been conducted on genomic structural variation in the Polypodiaceae. RESULTS The complete plastome sequences of Neolepisorus fortunei, Neolepisorus ovatus, and Phymatosorus cuspidatus were determined based on next-generation sequencing. Together with published plastomes, a comparative analysis of the fine structure of Polypodiaceae plastomes was carried out. The results indicated that the plastomes of Polypodiaceae are not as conservative as previously assumed. The size of the plastomes varies greatly in the Polypodiaceae, and the large insertion fragments present in the genome could be the main factor affecting the genome length. The plastome of Selliguea yakushimensis exhibits prominent features including not only a large-scale IR expansion exceeding several kb but also a unique inversion. Furthermore, gene contents, SSRs, dispersed repeats, and mutational hotspot regions were identified in the plastomes of the Polypodiaceae. Although dispersed repeats are not abundant in the plastomes of Polypodiaceae, we found that the large insertions that occur in different species are mobile and are always adjacent to repeated hotspot regions. CONCLUSIONS Our results reveal that the plastomes of Polypodiaceae are dynamic molecules, rather than constituting static genomes as previously thought. The dispersed repeats flanking insertion sequences contribute to the repair mechanism induced by double-strand breaks and are probably a major driver of structural evolution in the plastomes of Polypodiaceae.
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Affiliation(s)
- Shanshan Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, Guangdong, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China.
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16
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The ambiguity of the basic terms related to eukaryotes and the more consistent etymology based on eukaryotic signatures in Asgard archaea. Biosystems 2020; 197:104178. [DOI: 10.1016/j.biosystems.2020.104178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 11/23/2022]
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17
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Gao C, Wu C, Zhang Q, Zhao X, Wu M, Chen R, Zhao Y, Li Z. Characterization of Chloroplast Genomes From Two Salvia Medicinal Plants and Gene Transfer Among Their Mitochondrial and Chloroplast Genomes. Front Genet 2020; 11:574962. [PMID: 33193683 PMCID: PMC7642825 DOI: 10.3389/fgene.2020.574962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Salvia species have been widely used as medicinal plants and have played an important role in the treatment and recovery of individuals with COVID-19. In this study, we reported two newly identified whole chloroplast genome sequences of Salvia medicinal plants (Salvia yangii and Salvia miltiorrhiza f. alba) and compared them with those of seven other reported Salvia chloroplast genomes. These were proven to be highly similar in terms of overall size, genome structure, gene content, and gene order. We identified 10 mutation hot spots (trnK-rps16, atpH-atpI, psaA-ycf3, ndhC-trnV, ndhF, rpl32-trnL, ndhG-ndhI, rps15-ycf1, ycf1a, and ycf1b) as candidate DNA barcodes for Salvia. Additionally, we observed the transfer of nine large-sized chloroplast genome fragments, with a total size of 49,895 bp (accounting for 32.97% of the chloroplast genome), into the mitochondrial genome as they shared >97% sequence similarity. Phylogenetic analyses of the whole chloroplast genome provided a high resolution of Salvia. This study will pave the way for the identification and breeding of Salvia medicinal plants and further phylogenetic evolutionary research on them as well.
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Affiliation(s)
- Chengwen Gao
- Laboratory of Medical Biology, Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | | | | | | | | | | | | | - Zhiqiang Li
- Laboratory of Medical Biology, Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
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18
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Amar MH. ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica. J Genet Eng Biotechnol 2020; 18:42. [PMID: 32797323 PMCID: PMC7427673 DOI: 10.1186/s43141-020-00057-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/04/2020] [Indexed: 11/10/2022]
Abstract
Background Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. Results Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap’s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. Conclusion To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.
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Affiliation(s)
- Mohamed Hamdy Amar
- Egyptian Deserts Gene Bank, Desert Research Center, B.O.P, Cairo, 11753, Egypt.
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19
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Cui H, Ding Z, Zhu Q, Wu Y, Gao P. Population structure and genetic diversity of watermelon ( Citrullus lanatus) based on SNP of chloroplast genome. 3 Biotech 2020; 10:374. [PMID: 32832334 DOI: 10.1007/s13205-020-02372-5] [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: 04/28/2020] [Accepted: 07/31/2020] [Indexed: 11/28/2022] Open
Abstract
Citrullus amarus (citronmelon) is an important crop with resistance to many diseases. The chloroplast genome is important in studying the genetic evolution of plants. The C. amarus chloroplast genome was first reported in this study using a novel assembly method based on whole genome sequencing. We identified 82 SNP sites in chloroplast genome with 313 watermelon materials. The 82 SNPs could effectively divide the natural watermelon population into four groups: C. lanatus subsp. lanatus, C. lanatus subsp. mucosospermus, C. lanatus subsp. vulgaris (ecologically from the Americas) and C. lanatus subsp. vulgaris (ecologically from Asia), with decreasing genetic diversity (π) (6.6 × 10-5, 2.4 × 10-5, 9.8 × 10-6 and 5.41 × 10-6, respectively). The single fruit weight, soluble solids, fruit color and 1000-seed weight of C. lanatus subsp. lanatus were significantly different from those of the other three groups. These results indicate that the complete chloroplast genome can be used in studying population genetics of watermelon, which is helpful for classification among intra species subgroups and identification of core germplasm resources.
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Affiliation(s)
- Haonan Cui
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, 150030 Heilongjiang China
| | - Zhuo Ding
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, 150030 Heilongjiang China
| | - Qianglong Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Yue Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, 150030 Heilongjiang China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, 150030 Heilongjiang China
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20
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Pinevich AV. Chloroplast history clarified by the criterion of light-harvesting complex. Biosystems 2020; 196:104173. [PMID: 32534171 DOI: 10.1016/j.biosystems.2020.104173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 01/13/2023]
Abstract
Bacterial essence of mitochondria and chloroplasts was initially proclaimed in general outline. Later, the remarkable insight gave way to an elaborate hypothesis. Finally, it took shape of a theory confirmed by molecular biology data. In particular, the rrn operon, which is the key phylogeny marker, locates chloroplasts on the tree of Cyanobacteria. Chloroplast ancestry and diversity can be also traced with the rpoС and psbA genes, rbc operon, and other molecular criteria of prime importance. Another criterion, also highly reliable, is light-harvesting complex (LHC). LHC pigment and protein moieties specify light acclimation strategies in evolutionary retrospect and modern biosphere. The onset of symbiosis between eukaryotic host and pre-chloroplast, as well as further mutual adjustment of partners depended on physiological competence of LHC. In this review, the criterion of LHC is applied to the origin and diversity of chloroplasts. In particular, ancient cyanobacterium possessing tandem antenna (encoded by the cbp genes and the pbp genes, correspondingly), and defined as a prochlorophyte, is argued to be chloroplast ancestor.
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Affiliation(s)
- Alexander V Pinevich
- St. Petersburg State University, Department of Microbiology, St. Petersburg, Russia.
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21
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Zhang GJ, Dong R, Lan LN, Li SF, Gao WJ, Niu HX. Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants. Int J Mol Sci 2020; 21:ijms21030707. [PMID: 31973163 PMCID: PMC7037861 DOI: 10.3390/ijms21030707] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 11/16/2022] Open
Abstract
The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.
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Affiliation(s)
- Guo-Jun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
| | - Hong-Xing Niu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
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Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution. Gene 2020; 732:144355. [PMID: 31935501 DOI: 10.1016/j.gene.2020.144355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/13/2023]
Abstract
Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.
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Zhang T, Xing Y, Xu L, Bao G, Zhan Z, Yang Y, Wang J, Li S, Zhang D, Kang T. Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae. Chin Med 2019; 14:53. [PMID: 31798674 PMCID: PMC6883693 DOI: 10.1186/s13020-019-0274-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/04/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Baitouweng is a traditional Chinese medicine with a long history of different applications. Although referred to as a single medicine, Baitouweng is actually comprised of many closely related species. It is therefore critically important to identify the different species that are utilized in these medicinal applications. Knowledge about their phylogenetic relationships can be derived from their chloroplast genomes and may provide additional insights into development of molecular markers. METHODS Genomic DNA was extracted from six species of Pulsatilla and then sequenced on an Illumina HiSeq 4000. Sequences were assembled into contigs by SOAPdenovo 2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the cp genomes of the six species were analyzed and compared with closely related species. Additionally, phylogenetic trees were constructed, based on single nucleotide polymorphisms (SNPs) and 51 shared protein-coding gene sequences in the cp genome among all 31 species via maximum likelihood. RESULTS The size of cp genomes of P. chinensis (Bge.) Regel, P. chinensis (Bge.) Regel var. kissii (Mandl) S. H. Li et Y. H. Huang, P. cernua (Thunb.) Bercht. et Opiz f. plumbea J. X. Ji et Y. T. zhao, P. dahurica (Fisch.) Spreng, P. turczaninovii Kryl. et Serg, and P. cernua (Thunb.) Bercht. et Opiz. were 163,851 bp, 163,756 bp, 162,481 bp, 162,450 bp, 162,795 bp, and 162,924 bp, respectively. Each species included two inverted repeat regions, a small single-copy region, and a large single-copy region. A total of 134 genes were annotated, including 90 protein-coding genes, 36 tRNAs, and eight rRNAs across all species. In simple sequence repeat analysis, only P. dahurica was found to contain hexanucleotide repeats. A total of 26, 39, 32, 37, 32 and 43 large repeat sequences were identified in the genic regions of the six Pulsatilla species. Nucleotide diversity analysis revealed that the rpl36 gene and ccsA-ndhD region have the highest Pi value. In addition, two phylogenetic trees of the cp genomes were constructed, which laced all Pulsatilla species into one branch within Ranunculaceae. CONCLUSIONS We identified and analyzed the cp genome features of six species of P. Miller, with implications for species identification and phylogenetic analysis.
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Affiliation(s)
- Tingting Zhang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
- Liaoning Quality Monitoring and Technology Service Center for Chinese Materia Medica Raw Materials, Dalian, China
| | - Guihua Bao
- School of Mongol Medicine, Inner Mongolia University for Nationalities, Tongliao, China
| | - Zhilai Zhan
- Traditional Chinese Medicine Resource Center, Chinese Academy of Traditional Chinese Medicine, Beijing, China
| | - Yanyun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Jiahao Wang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Shengnan Li
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Dachuan Zhang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Tingguo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
- Liaoning Quality Monitoring and Technology Service Center for Chinese Materia Medica Raw Materials, Dalian, China
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Li YX, Li ZH, Schuiteman A, Chase MW, Li JW, Huang WC, Hidayat A, Wu SS, Jin XH. Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes. Mol Phylogenet Evol 2019; 139:106540. [DOI: 10.1016/j.ympev.2019.106540] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/05/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
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Yang Y, Zhang Y, Chen Y, Gul J, Zhang J, Liu Q, Chen Q. Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species. PeerJ 2019; 7:e7713. [PMID: 31579601 PMCID: PMC6756139 DOI: 10.7717/peerj.7713] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022] Open
Abstract
As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.
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Affiliation(s)
- Yong Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Ying Zhang
- Life Sciences and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Juma Gul
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Qiang Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Qing Chen
- Bawangling National Nature Reserve, Changjiang, Hainan Province, China
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Chang ACG, Chen T, Li N, Duan J. Perspectives on Endosymbiosis in Coralloid Roots: Association of Cycads and Cyanobacteria. Front Microbiol 2019; 10:1888. [PMID: 31474965 PMCID: PMC6702271 DOI: 10.3389/fmicb.2019.01888] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Past endosymbiotic events allowed photosynthetic organisms to flourish and evolve in terrestrial areas. The precursor of chloroplasts was an ancient photosynthetic cyanobacterium. Presently, cyanobacteria are still capable of establishing successful symbioses in a wide range of hosts. One particular host plant among the gymnosperms is cycads (Order Cycadales) in which a special type of root system, referred to as coralloid roots, develops to house symbiotic cyanobacteria. A number of studies have explained coralloid root formation and cyanobiont invasion but the questions on mechanisms of this host-microbe association remains vague. Most researches focus on diversity of symbionts in coralloid roots but equally important is to explore the underlying mechanisms of cycads-Nostoc symbiosis as well. Besides providing an overview of relevant areas presently known about this association and citing putative genes involved in cycad-cyanobacteria symbioses, this paper aims to identify the limitations that hamper attempts to get to the root of the matter and suggests future research directions that may prove useful.
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Affiliation(s)
- Aimee Caye G. Chang
- University of Chinese Academy of Sciences, Beijing, China
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Chen
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Nan Li
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Duan
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Moore KR, Magnabosco C, Momper L, Gold DA, Bosak T, Fournier GP. An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids. Front Microbiol 2019; 10:1612. [PMID: 31354692 PMCID: PMC6640209 DOI: 10.3389/fmicb.2019.01612] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/27/2019] [Indexed: 01/16/2023] Open
Abstract
The phylum Cyanobacteria includes free-living bacteria and plastids, the descendants of cyanobacteria that were engulfed by the ancestral lineage of the major photosynthetic eukaryotic group Archaeplastida. Endosymbiotic events that followed this primary endosymbiosis spread plastids across diverse eukaryotic groups. The remnants of the ancestral cyanobacterial genome present in all modern plastids, enable the placement of plastids within Cyanobacteria using sequence-based phylogenetic analyses. To date, such phylogenetic studies have produced conflicting results and two competing hypotheses: (1) plastids diverge relatively recently in cyanobacterial evolution and are most closely related to nitrogen-fixing cyanobacteria, or (2) plastids diverge early in the evolutionary history of cyanobacteria, before the divergence of most cyanobacterial lineages. Here, we use phylogenetic analysis of ribosomal proteins from an expanded data set of cyanobacterial and representative plastid genomes to infer a deep placement for the divergence of the plastid ancestor lineage. We recover plastids as sister to Gloeomargarita and show that the group diverges from other cyanobacterial groups before Pseudanabaena, a previously unreported placement. The tree topologies and phylogenetic distances in our study have implications for future molecular clock studies that aim to model accurate divergence times, especially with respect to groups containing fossil calibrations. The newly sequenced cyanobacterial groups included here will also enable the use of novel cyanobacterial microfossil calibrations.
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Affiliation(s)
- Kelsey R Moore
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Cara Magnabosco
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States
| | - Lily Momper
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - David A Gold
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species. Int J Mol Sci 2019; 20:ijms20051045. [PMID: 30823362 PMCID: PMC6429227 DOI: 10.3390/ijms20051045] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 11/16/2022] Open
Abstract
Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.
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Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome. FORESTS 2019. [DOI: 10.3390/f10020087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Acer truncatum Bunge is a particular forest tree species found in the north of China. Due to the recent discovery that its seeds contain a considerable amount of nervonic acid, this species has received more and more attention. However, there have been no reports of the genome in this species. In this study, we report on the Acer truncatum genome sequence produced by genome survey sequencing. In total, we obtained 61.90 Gbp of high-quality data, representing approximately 116x coverage of the Acer truncatum genome. The genomic characteristics of Acer truncatum include a genome size of 529.88 Mbp, a heterozygosis rate of 1.06% and a repeat rate of 48.8%. A total of 392,961 high-quality genomic SSR markers were developed and a graphical map of the annotated circular chloroplast genome was generated. Thus far, this is the first report of de novo whole genome sequencing and assembly of Acer truncatum. We believe that this genome sequence dataset may provide a new resource for future genomic analysis and molecular breeding studies of Acer truncatum.
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Gurusamy R, Lee EM, Nam GH, Lee B, Park S. The complete chloroplast genome of monocot plant, Maianthemum dilatatum. Mitochondrial DNA B Resour 2018; 3:1185-1186. [PMID: 33474458 PMCID: PMC7799983 DOI: 10.1080/23802359.2018.1524723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/31/2018] [Indexed: 12/01/2022] Open
Abstract
The complete chloroplast genome sequence of Maianthemum dilatatum is sequenced and analyzed. The chloroplast genome is 156,921 bp, with 36.7% GC content. A pair of inverted repeats of 26,468 bp is separated by a large single-copy region (85,554 bp) and a small single-copy region (18,431 bp). It encodes 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Of 132 individual genes, 19 genes are duplicated in the IR regions, while 14 genes are encoded with one intron and three genes with two introns.
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Affiliation(s)
- Raman Gurusamy
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Gi Heum Nam
- Plant Resources Division, National Institute of Biological Resources of Korea, Incheon, Republic of Korea
| | - Byoungyoon Lee
- Plant Resources Division, National Institute of Biological Resources of Korea, Incheon, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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31
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Singh H. Desiccation and radiation stress tolerance in cyanobacteria. J Basic Microbiol 2018; 58:813-826. [PMID: 30080267 DOI: 10.1002/jobm.201800216] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/29/2018] [Accepted: 07/16/2018] [Indexed: 11/10/2022]
Abstract
Cyanobacteria are among the oldest living organisms on this planet, existing since more than 3 billion years. They are ideal organisms for investigating biological processes such as photosynthesis, respiration, circadian rhythm, photoregulation of gene expression, developmental gene rearrangements, and specialized cell differentiation. They are nearly ubiquitous in distribution, have colonized a wide range of ecosystems including soil, air, dry rock, and aquatic systems, and even occupy extreme niches that are inaccessible to other organisms. Such wide ecological distribution reflects their capacity to acclimate to extreme environments. They show great adaptive abilities and have survived various adverse physiological growth conditions like desiccation, high temperatures, extreme pH, cold, osmosis, salt, light, nitrogen, and high salinity. Their ancient origin and surviving through numerous stresses during evolution indicates their remarkable capabilities to survive and prevail under different environmental and man-made stresses. It has been hypothesized that similar and overlap stress response mechanisms help them to survive different stresses. It has been stated that responses against stresses like radiation has been accidental-exhibited because of similar response against desiccation stress, which has prevailed more during evolution. These overlaps and similarities in stress responses have been instrumental in making these organisms a large class of biological entities today. Present review discuss about stress tolerance in cyanobacteria against two extreme stresses - desiccation and gamma radiation. It also discuss the commonality and underlying molecular mechanisms in these two stress responses.
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Affiliation(s)
- Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed-to-be) University, Vile Parle (W), Mumbai, India
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Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis. Genes (Basel) 2017; 8:genes8090212. [PMID: 28925932 PMCID: PMC5615346 DOI: 10.3390/genes8090212] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 12/23/2022] Open
Abstract
Clusterbean (Cyamopsis tetragonoloba L.), also known as guar, belongs to the family Leguminosae, and is an annual herbaceous legume. Guar is the main source of galactomannan for gas mining industries. In the present study, the draft chloroplast genome of clusterbean was generated and compared to some of the previously reported legume chloroplast genomes. The chloroplast genome of clusterbean is 152,530 bp in length, with a quadripartite structure consisting of large single copy (LSC) and small single copy (SSC) of 83,025 bp and 17,879 bp in size, respectively, and a pair of inverted repeats (IRs) of 25,790 bp in size. The chloroplast genome contains 114 unique genes, which includes 78 protein coding genes, 30 tRNAs, 4 rRNAs genes, and 2 pseudogenes. It also harbors a 50 kb inversion, typical of the Leguminosae family. The IR region of the clusterbean chloroplast genome has undergone an expansion, and hence, the whole rps19 gene is included in the IR, as compared to other legume plastid genomes. A total of 220 simple sequence repeats (SSRs) were detected in the clusterbean plastid genome. The analysis of the clusterbean plastid genome will provide useful insights for evolutionary, molecular and genetic engineering studies.
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Li Y, Xu W, Zou W, Jiang D, Liu X. Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species. BOTANICAL STUDIES 2017; 58:37. [PMID: 28905330 PMCID: PMC5597560 DOI: 10.1186/s40529-017-0192-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/20/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Phoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus. RESULTS We sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies. CONCLUSION This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.
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Affiliation(s)
- Yingang Li
- Zhejiang Academy of Forestry, Hangzhou, 310023 China
| | - Wuqin Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Wentao Zou
- Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520 China
| | - Dongyue Jiang
- Zhejiang Academy of Forestry, Hangzhou, 310023 China
| | - Xinhong Liu
- Zhejiang Academy of Forestry, Hangzhou, 310023 China
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Du YP, Bi Y, Yang FP, Zhang MF, Chen XQ, Xue J, Zhang XH. Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses. Sci Rep 2017; 7:5751. [PMID: 28720853 PMCID: PMC5515919 DOI: 10.1038/s41598-017-06210-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/08/2017] [Indexed: 12/19/2022] Open
Abstract
Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this study, we present the use of complete chloroplast genomes to explore the phylogeny of this genus. We sequenced nine Lilium chloroplast genomes and retrieved seven published chloroplast genomes for comparative and phylogenetic analyses. The genomes ranged from 151,655 bp to 153,235 bp in length and had a typical quadripartite structure with a conserved genome arrangement and moderate divergence. A comparison of sixteen Lilium chloroplast genomes revealed ten mutation hotspots. Single nucleotide polymorphisms (SNPs) for any two Lilium chloroplast genomes ranged from 8 to 1,178 and provided robust data for phylogeny. Except for some of the shortest internodes, phylogenetic relationships of the Lilium species inferred from the chloroplast genome obtained high support, indicating that chloroplast genome data will be useful to help resolve the deeper branches of phylogeny.
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Affiliation(s)
- Yun-Peng Du
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yu Bi
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- School of Horticulture, Jilin Agricultural University, Changchun, Jilin Province, 130000, China
| | - Feng-Ping Yang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ming-Fang Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xu-Qing Chen
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jing Xue
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiu-Hai Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology; Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Reinecke DL, Zarka A, Leu S, Boussiba S. Cloning, molecular characterization, and phylogeny of two evolutionary distinct glutamine synthetase isoforms in the green microalga Haematococcus pluvialis (Chlorophyceae). JOURNAL OF PHYCOLOGY 2016; 52:961-972. [PMID: 27402429 DOI: 10.1111/jpy.12444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/19/2016] [Indexed: 06/06/2023]
Abstract
Haematococcus pluvialis (Chlorophyta) is a widely used microalga of great economic potential, yet its molecular genetics and evolution are largely unknown. We present new detailed molecular and phylogenetic analysis of two glutamine synthetase (GS) enzymes and genes (gln) under the Astaxanthin-inducing conditions of light- and nitrogen-stress. Structure analysis identified key residues and confirmed two decameric GS2 holoenzymes, a cytoplasmic enzyme, termed GS2c , and a plastidic form, termed GS2p , due to chloroplast-transit peptides at its N-terminus. Gene expression analysis showed dissociation of mRNA, protein, and enzyme activity levels for both GS2 under different growth conditions, indicating the strong post-transcriptional regulation. Data-mining identified novel and specified published gln genes from Prasinophyceae, Chlorophyta, Trebouxiophyceae, Charophyceae, Bryophyta, Lycopodiophyta, Spermatophyta, and Rhodophyta. Phylogenetic analysis found homologues to the cytosolic GS2c of H. pluvialis in all other photo- and non-photosynthetic Eukaryota. The chloroplastic GS2p was restricted to Chlorophyta, Bryophyta, some Proteobacteria and Fungii; no homologues were identified in Spermatophyta or other Eukaryota. This indicates two independent prokaryotic donors for these two gln genes in H. pluvialis. Combined phylogenetic analysis of GS, chl-b synthase, elongation factor, and light harvesting complex homologues project a newly refined model of Viridiplantae evolution. Herein, a GS1 evolved into the cytosolic GS2c and was passed on to all Eukaryota. Later, the chloroplastic GS2p entered the Archaeplastida lineage via a horizontal gene transfer at the divergence of Chlorophyta and Rhodophyta lineages. GS2p persisted in Chlorophyta and Bryophyta, but was lost during Spermatophyta evolution. These data suggest the revision of GS classification and nomenclature, and extend our understanding of the photosynthetic Eukaryota evolution.
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Affiliation(s)
- Diana L Reinecke
- Food and Bioprocess Engineering Group, Wageningen University, P.O. Box 8129, 6700 EV, Wageningen, the Netherlands
| | - Aliza Zarka
- Microalgal Biotechnology Lab, Blaustein Institutes of Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 84990, Israel
| | - Stefan Leu
- Microalgal Biotechnology Lab, Blaustein Institutes of Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 84990, Israel
| | - Sammy Boussiba
- Microalgal Biotechnology Lab, Blaustein Institutes of Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 84990, Israel
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Liu F, Xu Y, Han G, Zhou L, Ali A, Zhu S, Li X. Molecular Evolution and Genetic Variation of G2-Like Transcription Factor Genes in Maize. PLoS One 2016; 11:e0161763. [PMID: 27560803 PMCID: PMC4999087 DOI: 10.1371/journal.pone.0161763] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/11/2016] [Indexed: 12/29/2022] Open
Abstract
The productivity of maize (Zea mays L.) depends on the development of chloroplasts, and G2-like transcription factors play a central role in regulating chloroplast development. In this study, we identified 59 G2-like genes in the B73 maize genome and systematically analyzed these genes at the molecular and evolutionary levels. Based on gene structure character, motif compositions and phylogenetic analysis, maize G2-like genes (ZmG1- ZmG59) were divided into seven groups (I-VII). By synteny analysis, 18 collinear gene pairs and strongly conserved microsyntny among regions hosting G2-like genes across maize and sorghum were found. Here, we showed that the vast majority of ZmG gene duplications resulted from whole genome duplication events rather than tandem duplications. After gene duplication events, some ZmG genes were silenced. The functions of G2-like genes were multifarious and most genes that are expressed in green tissues may relate to maize photosynthesis. The qRT-PCR showed that the expression of these genes was sensitive to low temperature and drought. Furthermore, we analyzed differences of ZmGs specific to cultivars in temperate and tropical regions at the population level. Interestingly, the single nucleotide polymorphism (SNP) analysis revealed that nucleotide polymorphism associated with different temperature zones. Above all, G2-like genes were highly conserved during evolution, but polymorphism could be caused due to a different geographical location. Moreover, G2-like genes might be related to cold and drought stresses.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Yunjian Xu
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Guomin Han
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Lingyan Zhou
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Asif Ali
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Suwen Zhu
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
- * E-mail:
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Feng YL, Wicke S, Li JW, Han Y, Lin CS, Li DZ, Zhou TT, Huang WC, Huang LQ, Jin XH. Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species. Genome Biol Evol 2016; 8:2164-75. [PMID: 27412609 PMCID: PMC4987110 DOI: 10.1093/gbe/evw144] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 11/13/2022] Open
Abstract
The plastid genome (plastome) of heterotrophic plants like mycoheterotrophs and parasites shows massive gene losses in consequence to the relaxation of functional constraints on photosynthesis. To understand the patterns of this convergent plastome reduction syndrome in heterotrophic plants, we studied 12 closely related orchids of three different lifeforms from the tribe Neottieae (Orchidaceae). We employ a comparative genomics approach to examine structural and selectional changes in plastomes within Neottieae. Both leafy and leafless heterotrophic species have functionally reduced plastid genome. Our analyses show that genes for the NAD(P)H dehydrogenase complex, the photosystems, and the RNA polymerase have been lost functionally multiple times independently. The physical reduction proceeds in a highly lineage-specific manner, accompanied by structural reconfigurations such as inversions or modifications of the large inverted repeats. Despite significant but minor selectional changes, all retained genes continue to evolve under purifying selection. All leafless Neottia species, including both visibly green and nongreen members, are fully mycoheterotrophic, likely evolved from leafy and partially mycoheterotrophic species. The plastomes of Neottieae span many stages of plastome degradation, including the longest plastome of a mycoheterotroph, providing invaluable insights into the mechanisms of plastome evolution along the transition from autotrophy to full mycoheterotrophy.
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Affiliation(s)
- Yan-Lei Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Germany
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan, China
| | - Yu Han
- Nanchang University, Jiangxi, China
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - De-Zhu Li
- Key Laboratory of Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ting-Ting Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Chang Huang
- Chenshan Shanghai Botanical Garden, Shanghai, Songjiang, China
| | - Lu-Qi Huang
- National Resource Centre for Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Walter J, Lynch F, Battchikova N, Aro EM, Gollan PJ. Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3997-4008. [PMID: 27012282 PMCID: PMC4915528 DOI: 10.1093/jxb/erw112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Calcium is integral to the perception, communication and adjustment of cellular responses to environmental changes. However, the role of Ca(2+) in fine-tuning cellular responses of wild-type cyanobacteria under favourable growth conditions has not been examined. In this study, extracellular Ca(2+) has been altered, and changes in the whole transcriptome of Anabaena sp. PCC 7120 have been evaluated under conditions replete of carbon and combined nitrogen. Ca(2+) induced differential expression of many genes driving primary cellular metabolism, with transcriptional regulation of carbon- and nitrogen-related processes responding with opposing trends. However, physiological effects of these transcriptional responses on biomass accumulation, biomass composition, and photosynthetic activity over the 24h period following Ca(2+) adjustment were found to be minor. It is well known that intracellular carbon:nitrogen balance is integral to optimal cell growth and that Ca(2+) plays an important role in the response of heterocystous cyanobacteria to combined-nitrogen deprivation. This work adds to the current knowledge by demonstrating a signalling role of Ca(2+) for making sensitive transcriptional adjustments required for optimal growth under non-limiting conditions.
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Affiliation(s)
- Julia Walter
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Fiona Lynch
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Peter J Gollan
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
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Yi DK, Choi K, Joo M, Yang JC, Mustafina FU, Han JS, Son DC, Chang KS, Shin CH, Lee YM. The complete chloroplast genome sequence of Abies nephrolepis (Pinaceae: Abietoideae). JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2016. [DOI: 10.1016/j.japb.2016.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Zhu W, Liu T, Liu C, Zhou F, Lai XE, Hu D, Chen J, Huang S. The complete chloroplast genome sequence of Cunninghamia lanceolata. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:405-406. [PMID: 26730645 DOI: 10.3109/19401736.2015.1127366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We determined the complete chloroplast genome sequence of Cunninghamia lanceolata (GenBank accession: NC_021437.1) in this study. The total length of the chloroplast genome is 135 334 bp. The GC content is 35%. A total of 119 genes are successfully annotated, including 35 tRNA (20 tRNA species), 3 rRNA (3 rRNA species) and 81 protein-coding genes (81 PCG species). Twelve protein-coding genes (rps16, ycf3, rpoC1, atpF, rps12, ndhB, rpl2, rpl16, petD, petB, ndhA, rps15) contain one or two introns. A maximum likelihood phylogenetic analysis showed that this newly characterized Cunninghamia lanceolata chloroplast genome will provide essential data for further study on phylogenetic resolution, biodiversity for the genus Cunninghamia and Taxodiacea.
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Affiliation(s)
- Wenjuan Zhu
- a Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm & College of Forestry and Landscape Architecture , South China Agricultural University , Guangzhou , China
| | - Taiyi Liu
- a Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm & College of Forestry and Landscape Architecture , South China Agricultural University , Guangzhou , China
| | - Chunxin Liu
- a Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm & College of Forestry and Landscape Architecture , South China Agricultural University , Guangzhou , China
| | - Feng Zhou
- b College of Life Sciences , Guangzhou , China
| | - Xu En Lai
- c Longshan Forestry Farm of Lechang City , Lechang , China
| | - Dehuo Hu
- d Guangzhou Academy of Forestry , Guangzhou , China
| | - Jiehu Chen
- e Science Corporation of Gene , GuangZhou , China
| | - Shaowei Huang
- a Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm & College of Forestry and Landscape Architecture , South China Agricultural University , Guangzhou , China
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Choi KS, Chung MG, Park S. The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions. FRONTIERS IN PLANT SCIENCE 2016. [PMID: 27047524 DOI: 10.3359/fpls.2016.00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of Veronica nakaiana and the related species Veronica persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica, and V. sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51, and 53 in V. nakaiana, V. persica, and V. sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating Veroniceae phylogenetic relationships.
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Affiliation(s)
- Kyoung Su Choi
- Department of Life Sciences, Yeungnam University Gyeongsan, South Korea
| | - Myong Gi Chung
- Department of Biology, The Research Institute of Natural Science, Gyeongsang National University Jinju, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University Gyeongsan, South Korea
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42
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Choi KS, Chung MG, Park S. The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions. FRONTIERS IN PLANT SCIENCE 2016; 7:355. [PMID: 27047524 PMCID: PMC4804161 DOI: 10.3389/fpls.2016.00355] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of Veronica nakaiana and the related species Veronica persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica, and V. sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51, and 53 in V. nakaiana, V. persica, and V. sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating Veroniceae phylogenetic relationships.
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Affiliation(s)
- Kyoung Su Choi
- Department of Life Sciences, Yeungnam UniversityGyeongsan, South Korea
| | - Myong Gi Chung
- Department of Biology, The Research Institute of Natural Science, Gyeongsang National UniversityJinju, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam UniversityGyeongsan, South Korea
- *Correspondence: SeonJoo Park
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43
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Delmont TO, Eren AM, Vineis JH, Post AF. Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica. Front Microbiol 2015; 6:1090. [PMID: 26579075 PMCID: PMC4620155 DOI: 10.3389/fmicb.2015.01090] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/22/2015] [Indexed: 11/30/2022] Open
Abstract
Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface.
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Affiliation(s)
- Tom O. Delmont
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | - A. Murat Eren
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | - Joseph H. Vineis
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | - Anton F. Post
- Coastal Resources Center, Graduate School of Oceanography, University of Rhode IslandNarragansett, RI, USA
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Sanz-Luque E, Chamizo-Ampudia A, Llamas A, Galvan A, Fernandez E. Understanding nitrate assimilation and its regulation in microalgae. FRONTIERS IN PLANT SCIENCE 2015; 6:899. [PMID: 26579149 PMCID: PMC4620153 DOI: 10.3389/fpls.2015.00899] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/09/2015] [Indexed: 05/02/2023]
Abstract
Nitrate assimilation is a key process for nitrogen (N) acquisition in green microalgae. Among Chlorophyte algae, Chlamydomonas reinhardtii has resulted to be a good model system to unravel important facts of this process, and has provided important insights for agriculturally relevant plants. In this work, the recent findings on nitrate transport, nitrate reduction and the regulation of nitrate assimilation are presented in this and several other algae. Latest data have shown nitric oxide (NO) as an important signal molecule in the transcriptional and posttranslational regulation of nitrate reductase and inorganic N transport. Participation of regulatory genes and proteins in positive and negative signaling of the pathway and the mechanisms involved in the regulation of nitrate assimilation, as well as those involved in Molybdenum cofactor synthesis required to nitrate assimilation, are critically reviewed.
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Affiliation(s)
| | | | | | | | - Emilio Fernandez
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
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45
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Lee DG, Kwon J, Eom CY, Kang YM, Roh SW, Lee KB, Choi JS. Directed analysis of cyanobacterial membrane phosphoproteome using stained phosphoproteins and titanium-enriched phosphopeptides. J Microbiol 2015; 53:279-87. [PMID: 25845541 DOI: 10.1007/s12275-015-5021-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/26/2022]
Abstract
Gel-free shotgun phosphoproteomics of unicellular cyanobacterium Synechocystis sp. PCC 6803 has not been reported up to now. The purpose of this study is to develop directed membrane phosphoproteomic method in Synechocystis sp. Total Synechocystis membrane proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and phosphoprotein-stained gel bands were selectively subjected to in-gel trypsin digestion. The phosphorylation sites of the resulting peptides were determined by assigning the neutral loss of [M-H(3)PO(4)] to Ser, Thr, and Tyr residues using nano-liquid chromatography 7 Tesla Fourier transform mass spectrometry. As an initial application, 111 proteins and 33 phosphoproteins were identified containing 11 integral membrane proteins. Identified four unknown phosphoproteins with transmembrane helices were suggested to be involved in membrane migration or transporters based on BLASTP search annotations. The overall distribution of hydrophobic amino acids in pTyr was lower in frequency than that of pSer or pThr. Positively charged amino acids were abundantly revealed in the surrounding amino acids centered on pTyr. A directed shotgun membrane phosphoproteomic strategy provided insight into understanding the fundamental regulatory processes underlying Ser, Thr, and Tyr phosphorylation in multi-layered membranous cyanobacteria.
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Affiliation(s)
- Dong-Gi Lee
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806, Republic of Korea
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Kamikawa R, Tanifuji G, Kawachi M, Miyashita H, Hashimoto T, Inagaki Y. Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. Genome Biol Evol 2015; 7:1133-40. [PMID: 25840416 PMCID: PMC4419806 DOI: 10.1093/gbe/evv060] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Unlike many other photosynthetic dinoflagellates, whose plastids contain a characteristic carotenoid peridinin, members of the genus Lepidodinium are the only known dinoflagellate species possessing green alga-derived plastids. However, the precise origin of Lepidodinium plastids has hitherto remained uncertain. In this study, we completely sequenced the plastid genome of Lepidodinium chlorophorum NIES-1868. Our phylogenetic analyses of 52 plastid-encoded proteins unite L. chlorophorum exclusively with a pedinophyte, Pedinomonas minor, indicating that the green-colored plastids in Lepidodinium spp. were derived from an endosymbiotic pedinophyte or a green alga closely related to pedinophytes. Our genome comparison incorporating the origin of the Lepidodinium plastids strongly suggests that the endosymbiont plastid genome acquired by the ancestral Lepidodinium species has lost genes encoding proteins involved in metabolism and biosynthesis, protein/metabolite transport, and plastid division during the endosymbiosis. We further discuss the commonalities and idiosyncrasies in genome evolution between the L. chlorophorum plastid and other plastids acquired through endosymbiosis of eukaryotic photoautotrophs.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan
| | - Goro Tanifuji
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Masanobu Kawachi
- The National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Hideaki Miyashita
- Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
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Gurusamy R, Lee DH, Park S. The complete chloroplast genome sequence of Dianthus superbus var. longicalycinus. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2015-7. [PMID: 25354144 DOI: 10.3109/19401736.2014.974167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast genome (cpDNA) sequence of Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicine was reported and characterized. The cpDNA of Dianthus superbus var. longicalycinus is 149,539 bp, with 36.3% GC content. A pair of inverted repeats (IRs) of 24,803 bp is separated by a large single-copy region (LSC, 82,805 bp) and a small single-copy region (SSC, 17,128 bp). It encodes 85 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Of 129 individual genes, 13 genes encoded one intron and three genes have two introns.
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Affiliation(s)
| | - Do-Hyung Lee
- b Department of Forest Resources , Yeungnam University , Gyeongsan , Gyeongbuk , Republic of Korea
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48
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Wisecaver JH, Brosnahan ML, Hackett JD. Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates. Genome Biol Evol 2014; 5:2368-81. [PMID: 24259313 PMCID: PMC3879968 DOI: 10.1093/gbe/evt179] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314-1,563 depending on inference method) relative to all other organisms in the analysis (0-782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
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Kim GB, Kwon Y, Yu HJ, Lim KB, Seo JH, Mun JH. The complete chloroplast genome of Phalaenopsis "Tiny Star". Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1300-2. [PMID: 25093401 DOI: 10.3109/19401736.2014.945566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We determined the complete chloroplast DNA sequence of Phalaenopsis "Tiny Star" based on Illumina sequencing. The total length of the chloroplast genome is 148,918 bp long with GC content of 36.7%. It contains 70 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Comparative analysis with the reported orchid chloroplast sequences identified unique InDel variations in the "Tiny Star" chloroplast genome that have potential as genetic markers to investigate the maternal lineage of Phalaenopsis and Doritaenopsis cultivars.
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Affiliation(s)
- Goon-Bo Kim
- a Department of Bioscience and Bioinformatics , Myongji University , Yongin , Korea
| | - Youngeun Kwon
- a Department of Bioscience and Bioinformatics , Myongji University , Yongin , Korea
| | - Hee-Ju Yu
- b Department of Life Science , The Catholic University of Korea , Bucheon , Korea
| | - Ki-Byung Lim
- c Department of Horticultural Science , Kyungpook National University , Daegu , Korea , and
| | | | - Jeong-Hwan Mun
- a Department of Bioscience and Bioinformatics , Myongji University , Yongin , Korea
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50
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Do HDK, Kim JS, Kim JH. A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales). Genome Biol Evol 2014; 6:1699-706. [PMID: 24951560 PMCID: PMC4122936 DOI: 10.1093/gbe/evu138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 454 sequencing system and Sanger sequencing method to trace the evolutionary pattern in the tribe Parideae of the family Melanthiaceae (Liliales). The circular double-stranded cpDNA of P. verticillata (157,379 bp) consists of two inverted repeat regions each of 28,373 bp, a large single copy of 82,726 bp, and a small single copy of 17,907 bp. Gene content and order are generally similar to the previously reported cpDNA sequences within the order Liliales. However, we found that trnI_CAU was triplicated in P. verticillata. In addition, cemA is suspected to be a pseudogene due to the presence of internal stop codons created by poly(A) insertion and single small CA repeats. Such changes were not found in previously examined cpDNAs of the Melanthiaceae or other families of the Liliales, suggesting that such features are unique to the tribe Parideae of Melanthiaceae. The characteristics of P. verticillata cpDNA will provide useful information for uncovering the evolution within Paris and for further research of plastid genome evolution and phylogenetic studies in Liliales.
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Affiliation(s)
- Hoang Dang Khoa Do
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
| | - Jung Sung Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea
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