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Qin J, Ma Y, Liu Y, Wang Y. Phylogenomic analysis and dynamic evolution of chloroplast genomes of Clematis nannophylla. Sci Rep 2024; 14:15109. [PMID: 38956388 PMCID: PMC11220099 DOI: 10.1038/s41598-024-65154-6] [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: 02/22/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Clematis nannophylla is a perennial shrub of Clematis with ecological, ornamental, and medicinal value, distributed in the arid and semi-arid areas of northwest China. This study successfully determined the chloroplast (cp) genome of C. nannophylla, reconstructing a phylogenetic tree of Clematis. This cp genome is 159,801 bp in length and has a typical tetrad structure, including a large single-copy, a small single-copy, and a pair of reverse repeats (IRa and IRb). It contains 133 unique genes, including 89 protein-coding, 36 tRNA, and 8 rRNA genes. Additionally, 66 simple repeat sequences, 50 dispersed repeats, and 24 tandem repeats were found; many of the dispersed and tandem repeats were between 20-30 bp and 10-20 bp, respectively, and the abundant repeats were located in the large single copy region. The cp genome was relatively conserved, especially in the IR region, where no inversion or rearrangement was observed, further revealing that the coding regions were more conserved than the noncoding regions. Phylogenetic analysis showed that C. nannophylla is more closely related to C. fruticosa and C. songorica. Our analysis provides reference data for molecular marker development, phylogenetic analysis, population studies, and cp genome processes to better utilise C. nannophylla.
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Affiliation(s)
- Jinping Qin
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China
| | - Yushou Ma
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China
| | - Ying Liu
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China.
| | - Yanlong Wang
- College of Animal Husbandry and Veterinary Science, Qinghai University, Xining, 810016, Qinghai, China.
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Xu N, Du X, Zhang XX, Yang HL. The complete chloroplast genome of Salix lindleyana (salicaceae), a plateau plant species. Mitochondrial DNA B Resour 2023; 8:877-881. [PMID: 37614527 PMCID: PMC10443960 DOI: 10.1080/23802359.2023.2246675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023] Open
Abstract
Salix lindleyana Wallich ex Andersson 1851 is a species of genus Salix which mainly grows on mountains above 3000 m at sea level in Qinghai-Tibetan Plateau (including the Himalayas and Hengduan Mountains). To determine its phylogenetic position within Salix, we reconstructed S. lindleyana complete chloroplast (cp) genome sequence by de novo assembly using whole-genome sequencing data. The completed chloroplast genome was 155,304 bp, with a total GC content of 36.7%. It had a very typical tetrad structure, including a large single-copy (LSC) region of 84,539 bp, a small single-copy (SSC) region of 16,161 bp, and two inverted repeats (IR) regions of 27,302 bp. A total of 132 functional genes were distributed in the chloroplast genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that S. lindleyana was clustered with Salix dasyclados Wimmer 1849 and Salix variegata Franchet 1887. The complete chloroplast genome of S. lindleyana provides potential genetic resources for further phylogenetic studies.
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Affiliation(s)
- Nan Xu
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xin Du
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiu-Xing Zhang
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hai-Ling Yang
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Wang SB, Liu YQ, Zhang L, Li R, Huang Y. The complete chloroplast genome of Primula amethystina subsp . argutidens (Primulaceae). Mitochondrial DNA B Resour 2023; 8:737-741. [PMID: 37435317 PMCID: PMC10332233 DOI: 10.1080/23802359.2023.2231108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Primula amethystina subsp. argutidens (Franchet) W. W. Smith & H. R. Fletcher (1942) is a blooming plant of the family Primulaceae. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of P. amethystina subsp. argutidens. The cp genome of P. amethystina subsp. argutidens is 151,560 bp in length with a GC content of 37%. The assembled genome has a typical quadripartite structure, containing a large single-copy (LSC) region of 83,516 bp, a small single-copy (SSC) region of 17,692 bp, and a pair of inverted repeat (IR) regions of 25,176 bp. The cp genome contains 115 unique genes, including 81 protein-coding genes, four rRNA genes, and 30 tRNA genes. Phylogenetic analysis showed that P. amethystina subsp. argutidens was closely related to P. amethystina.
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Affiliation(s)
- Shu-Bao Wang
- School of Life Sciences, Yunnan Normal University, Kunming, PR China
| | - Yun-Qi Liu
- School of Life Sciences, Yunnan Normal University, Kunming, PR China
| | - Li Zhang
- School of Life Sciences, Yunnan Normal University, Kunming, PR China
| | - Rui Li
- School of Life Sciences, Yunnan Normal University, Kunming, PR China
| | - Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, PR China
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Weng L, Jiang Y, Wang Y, Zhang X, Zhou P, Wu M, Li H, Sun H, Chen S. Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae). BMC PLANT BIOLOGY 2023; 23:284. [PMID: 37246219 DOI: 10.1186/s12870-023-04271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade. RESULTS These 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599-31,486 bp) separated by a large single-copy region (LSC: 82,048-94,046 bp) and a small single-copy region (SSC: 16,343-17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL-accD, ycf4-cemA, petA-psbJ, ycf1-ndhF, ndhF-rpl32 and ycf1, and it was found that ndhF-rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes. CONCLUSION The Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF-rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.
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Affiliation(s)
- Long Weng
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yunhui Jiang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yong Wang
- Yunnan Institute of Forest Inventory and Planning, Kunming, 650051, China
| | - Xuemei Zhang
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Ping Zhou
- College of Basic Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Mei Wu
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Hongzhe Li
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shaotian Chen
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
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Zhang H, Si Y, Zhao R, Sheng Q, Zhu Z. Complete chloroplast genome and phylogenetic relationship of Nymphaea nouchali (Nymphaeaceae), a rare species of water lily in China. Gene 2023; 858:147139. [PMID: 36621658 DOI: 10.1016/j.gene.2022.147139] [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: 07/29/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023]
Abstract
Nymphaea nouchali is a native species of Chinese water lily with important ornamental, economical, and medicinal purposes. However, due to the serious disturbance by alien biological invasion and human factors, N. nouchali is in an endangered state in China and urgently needs to be protected. Here, we reported the complete chloroplast genome of N. nouchali for the first time, and we found that its plastome is 159 978 bp long, comprising large and small single copies and two inverted repeats (90 001, 19 603, and 50 374 bp, respectively), indicating a typical tetrad structure. In total, 130 genes were identified, including 85 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. Additionally, 136 simple sequence repeat sites were identified, composed mainly of single nucleotide (46.32%) and trinucleotide (47.05%) sequences. Five highly variable sites (psaI, rps19, ndhF, rps15, and ycf1) with a high Pi value were identified as potential molecular markers. Phylogenetic analysis showed that N. nouchali and N. ampla are closely related, and further validated previous water lily classification results based on morphological characteristics, which divided water lilies into five subgenera: Nymphaea, Brachyceras, Anecphya, Hydrocallis, and Lotos. These results are valuable for the identification and the formulation of protection strategies of N. nouchali, as well as contributing to understanding the evolutionary relationships among Nymphaeaceae species.
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Affiliation(s)
- Huihui Zhang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Yu Si
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Runan Zhao
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Sheng
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Zunling Zhu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; College of Art & Design, Nanjing Forestry University, Nanjing 210037, China.
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6
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Characterization of the Plastid Genome of the Vulnerable Endemic Indosasa lipoensis and Phylogenetic Analysis. DIVERSITY 2023. [DOI: 10.3390/d15020197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Indosasa lipoensis, an ornamental garden plant, belongs to the Indosasa genus of the subfamily Bambooaceae within Poaceae. Indosasa lipoensis is endangered and requires protection owing to its relatively narrow distribution area. Chloroplast (cp) genome offers a novel awareness of the evolutionary and genetic variation of higher plants. Herein, we assembled and elucidated the complete cp genome of I. lipoensis, and compared it with four previously published cp genomes from this genus. The I. lipoensis cp genome was 139,655 bp in size, with a typical quadripartite structure, encompassing a large single-copy region (LSC, 83,256 bp), a small single-copy region (SSC, 12,809 bp), and a pair of inverted repeat regions (IR, 21,795 bp). The cp genome consisted of 130 genes with 84 protein-coding genes (CDS), 38 tRNA genes, and 8 rRNA genes. The plastomes were highly conservative, compared to other bamboo species, and exhibited similar patterns of codon usage, number of repeat sequences, and expansion and contraction of the IR boundary. Five hypervariable hotspots were identified as potential DNA barcodes, namely rbcL, petA, petB, trnL-UAG, and ndhE-ndhI, respectively. Phylogenetic analysis based on the complete cp genomes revealed, with high resolution, that I. lipoensis and I. gigantea were most closely related. Overall, these results provided valuable characterization for the future conservation, genetic evaluation, and the breeding of I. lipoensis.
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Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 2022; 612:283-291. [PMID: 36477129 PMCID: PMC9729109 DOI: 10.1038/s41586-022-05453-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
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Affiliation(s)
- Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Binia De Cahsan
- Section for Molecular Ecology and Evolution, The Globe Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian S Michelsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karina K Sand
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, Grenoble, France
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Astrid M A Schmidt
- Nordic Foundation for Development and Ecology (NORDECO), Copenhagen, Denmark
- DIS Study Abroad in Scandinavia, University of Copenhagen, Copenhagen, Denmark
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Alexey S Tesakov
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Ian Snowball
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - John C Gosse
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Yucheng Wang
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Ana Prohaska
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeppe Å Kristensen
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
- Geological Survey of Denmark and Greenland, (GEUS), Copenhagen, Denmark
| | - Morten Bjerager
- Department of Geophysics and Sedimentary Basins, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- University of Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL, Paris, France
| | - Marc Macias-Fauria
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alan J Hidy
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Collins
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolaj K Larsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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Ren W, Jiang Z, Zhang M, Kong L, Zhang H, Liu Y, Fu Q, Ma W. The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements. FRONTIERS IN PLANT SCIENCE 2022; 13:987443. [PMID: 36092427 PMCID: PMC9459086 DOI: 10.3389/fpls.2022.987443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Salix floderusii is a rare alpine tree species in the Salix genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of S. floderusii for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The S. floderusii cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of S. floderusii and Salix caprea were shorter than those of Salix cinerea, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the rpl22 coding region, psbM/trnD-GUC non-coding region, petA/psbJ non-coding region, and ycf1 coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future Salix species. In addition, phylogenetic analysis indicated that the cp genome of S. floderusii is sister to Salix cupularis and belongs to the Subgenus Vetrix. Genes (Sf-trnI, Sf-PpsbA, aadA, Sf-TpsbA, Sf-trnA) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene aadA. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the aadA gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent S. floderusii cp transformation systems and developing strategies for the genetic improvement of S. floderusii.
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Affiliation(s)
- Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhehui Jiang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Meiqi Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Lingyang Kong
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Houliang Zhang
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Yunwei Liu
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Qifeng Fu
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
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Fan Y, Jin Y, Ding M, Tang Y, Cheng J, Zhang K, Zhou M. The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships. FRONTIERS IN PLANT SCIENCE 2021; 12:799904. [PMID: 34975990 PMCID: PMC8715082 DOI: 10.3389/fpls.2021.799904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/18/2021] [Indexed: 05/09/2023]
Abstract
Buckwheat (Fagopyrum genus, Polygonaceae), is an annual or perennial, herbaceous or semi-shrub dicotyledonous plant. There are mainly three cultivated buckwheat species, common buckwheat (Fagopyrum esculentum) is widely cultivated in Asia, Europe, and America, while Tartary buckwheat (F. tataricum) and F. cymosum (also known as F. dibotrys) are mainly cultivated in China. The genus Fagopyrum is taxonomically confusing due to the complex phenotypes of different Fagopyrum species. In this study, the chloroplast (cp) genomes of three Fagopyrum species, F. longistylum, F. leptopodum, F. urophyllum, were sequenced, and five published cp genomes of Fagopyrum were retrieved for comparative analyses. We determined the sequence differentiation, repeated sequences of the cp genomes, and the phylogeny of Fagopyrum species. The eight cp genomes ranged, gene number, gene order, and GC content were presented. Most of variations of Fagopyrum species cp genomes existed in the LSC and SSC regions. Among eight Fagopyrum chloroplast genomes, six variable regions (ndhF-rpl32, trnS-trnG, trnC, trnE-trnT, psbD, and trnV) were detected as promising DNA barcodes. In addition, a total of 66 different SSR (simple sequence repeats) types were found in the eight Fagopyrum species, ranging from 8 to 16 bp. Interestingly, many SSRs showed significant differences especially in some photosystem genes, which provided valuable information for understanding the differences in light adaptation among different Fagopyrum species. Genus Fagopyrum has shown a typical branch that is distinguished from the Rumex, Rheum, and Reynoutria, which supports the unique taxonomic status in Fagopyrum among the Polygonaceae. In addition, phylogenetic analysis based on the cp genomes strongly supported the division of eight Fagopyrum species into two independent evolutionary directions, suggesting that the separation of cymosum group and urophyllum group may be earlier than the flower type differentiation in Fagopyrum plants. The results of the chloroplast-based phylogenetic tree were further supported by the matK and Internal Transcribed Spacer (ITS) sequences of 17 Fagopyrum species, which may help to further anchor the taxonomic status of other members in the urophyllum group in Fagopyrum. This study provides valuable information and high-quality cp genomes for identifying species and evolutionary analysis for future Fagopyrum research.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Guiyang, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ya’nan Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences and Food Engineering, Inner Mongolia MINZU University, Tongliao, China
| | - Mengqi Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Tang
- College of Food Science and Technology, Sichuan Tourism University, Chengdu, China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Complete Chloroplast Genomes of Three Salix Species: Genome Structures and Phylogenetic Analysis. FORESTS 2021. [DOI: 10.3390/f12121681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
High genetic diversity and low differentiation present challenges in taxonomy and systematics of Salix. Chloroplast (cp) genome sequencing is efficient for providing new genomic information and elucidating phylogenetic relationships. Salix spathulifolia Seemen, S. cupularis Rehder, and S. annulifera C.Marquand & Airy Shaw are three shrubby willows spread in high-altitude regions in western China. In this study, the integrated circular cp genomes were sequenced and analyzed, and a phylogeny of Salix was constructed on the basis of the cp genomes. The results of chloroplast assembly and annotation information were used to characterize genome feature and interspecific variation. The phylogenetic position of the three willows was evaluated using phylogenetic analysis. Full-length cp genomes were 155,566–155,680 bp with a typical double-stranded circular quadripartite structure, containing one large single-copy region (LSC, 84,431–4552 bp), one small single-copy region (SSC: 16,206–16,221 bp), and two inverted repeats (IR: 27,453–27,461 bp). The cp genomes encoded 130 genes, including 8 rRNA genes, 37 tRNA genes, and 85 protein-coding genes. The guanine-cytosine (GC) content of the overall genome was 36.7%. Comparison among the three willows’ cp genomes revealed high similarity. Phylogenetic analysis indicated that S. spathulifolia was a basal taxon of clade I, while S. annulifera formed a monophyletic group with S. rorida Laksch.; S. cupularis was sister to S. suchowensis W.C. Cheng and S. psammophila Z. Wang & Chang Y. Yang. The complete chloroplast genomes of the three willows provides an additional sequence-based resource for studying the phylogeny and evolutionary history of Salicaceae.
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Wagner ND, Volf M, Hörandl E. Highly Diverse Shrub Willows ( Salix L.) Share Highly Similar Plastomes. FRONTIERS IN PLANT SCIENCE 2021; 12:662715. [PMID: 34539686 PMCID: PMC8448165 DOI: 10.3389/fpls.2021.662715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/23/2021] [Indexed: 05/23/2023]
Abstract
Plastome phylogenomics is used in a broad range of studies where single markers do not bear enough information. Phylogenetic reconstruction in the genus Salix is difficult due to the lack of informative characters and reticulate evolution. Here, we use a genome skimming approach to reconstruct 41 complete plastomes of 32 Eurasian and North American Salix species representing different lineages, different ploidy levels, and separate geographic regions. We combined our plastomes with published data from Genbank to build a comprehensive phylogeny of 61 samples (50 species) using RAxML (Randomized Axelerated Maximum Likelihood). Additionally, haplotype networks for two observed subclades were calculated, and 72 genes were tested to be under selection. The results revealed a highly conserved structure of the observed plastomes. Within the genus, we observed a variation of 1.68%, most of which separated subg. Salix from the subgeneric Chamaetia/Vetrix clade. Our data generally confirm previous plastid phylogenies, however, within Chamaetia/Vetrix phylogenetic results represented neither taxonomical classifications nor geographical regions. Non-coding DNA regions were responsible for most of the observed variation within subclades and 5.6% of the analyzed genes showed signals of diversifying selection. A comparison of nuclear restriction site associated DNA (RAD) sequencing and plastome data on a subset of 10 species showed discrepancies in topology and resolution. We assume that a combination of (i) a very low mutation rate due to efficient mechanisms preventing mutagenesis, (ii) reticulate evolution, including ancient and ongoing hybridization, and (iii) homoplasy has shaped plastome evolution in willows.
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Affiliation(s)
- Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Goettingen, Göttingen, Germany
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Goettingen, Göttingen, Germany
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12
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Wang ZF, Chang LW, Cao HL. The complete chloroplast genome of Rhododendron kawakamii (Ericaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2538-2540. [PMID: 34377822 PMCID: PMC8330798 DOI: 10.1080/23802359.2021.1959439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Rhododendron kawakamii is endemic in Taiwan island and is a unique and epiphytic species. Here, we report its complete chloroplast genome. The length of the R. kawakamii chloroplast genome is 230,777 bp, with a large single-copy region of 146,155 bp, a small single-copy region of 72,082 bp, and a pair of inverted repeat regions (IRA) of 6,270 bp each. The genome contains 77 protein-coding genes, 29 transfer RNA genes, and four ribosomal RNA genes. In addition, the genome contains 81 simple sequence repeats. Phylogenetic analysis revealed that R. kawakamii is genetically related to R. datiandingense.
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Affiliation(s)
- Zheng-Feng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou.,Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou
| | - Li-Wan Chang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei
| | - Hong-Lin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou.,Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou
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13
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Shrestha B, Gilbert LE, Ruhlman TA, Jansen RK. Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora. Genome Biol Evol 2021; 12:1313-1329. [PMID: 32539116 PMCID: PMC7488351 DOI: 10.1093/gbe/evaa123] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.
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Affiliation(s)
- Bikash Shrestha
- Department of Integrative Biology, University of Texas, Austin
| | - Lawrence E Gilbert
- Faculty of Science, Department of Biological Sciences, Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin.,Faculty of Science, Department of Biological Sciences, Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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Li J, Tang J, Zeng S, Han F, Yuan J, Yu J. Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea. BMC PLANT BIOLOGY 2021; 21:25. [PMID: 33413130 PMCID: PMC7792329 DOI: 10.1186/s12870-020-02793-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/09/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis. RESULTS The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. CONCLUSION Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.
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Affiliation(s)
- Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jianmin Tang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Fang Han
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jing Yuan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716, China.
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15
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Mwanzia VM, He DX, Gichira AW, Li Y, Ngarega BK, Karichu MJ, Kamau PW, Li ZZ. The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots. PLANT DIVERSITY 2020; 42:334-342. [PMID: 33134616 PMCID: PMC7584794 DOI: 10.1016/j.pld.2020.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 06/02/2023]
Abstract
Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences. However, due to extensive similarity between species in this genus, morphological characters are generally inadequate for taxonomic classification. Currently, molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited. One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome. Here, we sequenced and analyzed the plastomes of five Aponogeton species collected from China, Zambia, and Kenya, and subsequently screened these plastomes for divergent DNA hotspots. The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp. The Large and the Small Single Copies are separated by two Inverted Repeats. One hundred and thirteen unique genes were identified including 79 protein-coding, 30 tRNA, and four rRNA genes. We found that the most abundant repeats in all but one species were mononucleotide repeats (A/T) and that there were 23 potential RNA ending sites. Interestingly, a ~3 kb inversion, which includes the accD gene, was detected within the Asian species of Aponogeton. The inversion may be related to more frequent exchanges between this region and the nuclear genome. Furthermore, we detected mutational hotspot sites among the five Aponogeton species. Three of these hotspots are intergenic spacer regions (accD-psaI, rbcL-accD and trnH-GUG-psbA) that might be suitable for use as barcodes to resolve intra-generic relationships. We also identified four highly variable protein-coding genes (ccsA, rpl22, rps16 and ycf1) may be used as barcodes to resolve the higher-level phylogenies. Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton.
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Affiliation(s)
- Virginia M. Mwanzia
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ding-Xuan He
- School of Biological and Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Andrew W. Gichira
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yan Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Boniface K. Ngarega
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Mwihaki J. Karichu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | | | - Zhi-Zhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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16
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Zhang L, Chen X, Huang Y. The complete mitochondrial genome of Salix polaris, a specie in harsh arctic environment. Mitochondrial DNA B Resour 2020; 5:3430-3431. [PMID: 33458194 PMCID: PMC7782335 DOI: 10.1080/23802359.2020.1823269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Salix polaris is a dwarf species of the genus Salix which distribute in harsh arctic environment. In this study, we sequenced and assembled whole mitochondrial genome of S. polaris for the first time. The complete mitochondrial genome sequence of this species is a circular molecule of 562920 bp in size, encoding 23 CDS, 21 tRNA genes, and 3 rRNA genes. Mitogenome based phylogenetic tree showed that Salix polaris clustered in the robust clade consist of all Salix species sampled in this study. The complete mitochondrial genome of Salix polaris adds new data into the whole mitochondrial genome of Salix, which is still scarce so far, and we anticipate the accumulation of mitogenome of Salix will facilitate phylogenetic study for this systematic difficult genus.
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Affiliation(s)
- Li Zhang
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, P. R. China
| | - Xiong Chen
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, P. R. China
| | - Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, P. R. China
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17
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Wang L, He N, Li Y, Fang Y, Zhang F. Complete Chloroplast Genome Sequence of Chinese Lacquer Tree ( Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9014873. [PMID: 32071921 PMCID: PMC7011389 DOI: 10.1155/2020/9014873] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/11/2019] [Accepted: 11/25/2019] [Indexed: 11/29/2022]
Abstract
Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.
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Affiliation(s)
- Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Na He
- Xi'an Raw Lacquer and Research Institute, Xi'an 710061, China
| | - Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Feilong Zhang
- Xi'an Raw Lacquer and Research Institute, Xi'an 710061, China
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Li MM, Wang DY, Zhang L, Kang MH, Lu ZQ, Zhu RB, Mao XX, Xi ZX, Tao M. Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics. Int J Mol Sci 2019; 20:ijms20153788. [PMID: 31382526 PMCID: PMC6696080 DOI: 10.3390/ijms20153788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022] Open
Abstract
Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.
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Affiliation(s)
- Meng-Meng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - De-Yan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ming-Hui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhi-Qiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Ren-Bin Zhu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Xing-Xing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhen-Xiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ma Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5190425. [PMID: 31380427 PMCID: PMC6662467 DOI: 10.1155/2019/5190425] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022]
Abstract
Salix wilsonii is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for S. wilsonii based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The S. wilsonii chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the S. wilsonii chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that S. wilsonii was most closely related to S. chaenomeloides and revealed the monophyly of the genus Salix. The complete S. wilsonii chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.
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20
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Zhao YJ, Liu XY, Guo R, Hu KR, Cao Y, Dai F. Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny. BMC Genomics 2019; 20:253. [PMID: 30925896 PMCID: PMC6440167 DOI: 10.1186/s12864-019-5627-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/20/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny. RESULTS Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered. CONCLUSIONS The divergence time of subgenus Vetrix and Salix was about 17.6-16.0 Mya during the period of Middle Miocene Climate Transition (21-14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.
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Affiliation(s)
- You-jie Zhao
- Key Laboratory of Forestry and Ecological Big Data State Forestry Administration, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Xin-yi Liu
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Ran Guo
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Kun-rong Hu
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Yong Cao
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Fei Dai
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
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21
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Huang Y, Chen X, Chen K, Li W, Shi M, Chen J. The complete mitochondrial genome of Salix paraflabellaris, an endemic alpine plant of Yunnan province of China. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1598823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, P. R. China
| | - Xiong Chen
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, P. R. China
| | - Kaiyun Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - Wenqing Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - Mingming Shi
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - Jiahui Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
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22
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Santos V, Almeida C. The complete chloroplast genome sequences of three Spondias species reveal close relationship among the species. Genet Mol Biol 2019; 42:132-138. [PMID: 30856242 PMCID: PMC6428118 DOI: 10.1590/1678-4685-gmb-2017-0265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 06/17/2018] [Indexed: 12/21/2022] Open
Abstract
This study reports the complete chloroplast sequences of three Spondias species. The genome sequences were obtained for Spondias tuberosa, Spondias bahienses, and Spondias mombin using the Illumina sequencing technology by a combination of de novo methods and a reference-guided assembly using Sapindus mukorossi as reference. The genomes of S. tuberosa, S. bahiensis, and S. mombin had 162,036, 162,218, and 162,302 bp, respectively. The coding regions exhibited 130 genes, including 34-35 tRNAs and 4 rRNAs. The results revealed synteny among the genomes, with high conservation in the gene order and content and CG content. The inverted repeat regions (IRA and IRB) and the large and small single copies were very similar among the three genomes. The phylogenomic analysis reported similar topologies as that of previous studies, which used partial chloroplast, wherein S. mombin was the first diverging lineage, while S. tuberosa and S. bahiensis were derived, indicating that the phylogenetic analysis using partial or complete genome produces similar results. In summary, (1) we presented the first complete chloroplast genome for the genus Spondias, (2) phylogenies analyzed using the complete chloroplast genomes revealed a robust phylogenetic topology for Spondias, and (3) gene order, content, and orientation in Spondias are highly conserved.
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Affiliation(s)
- Vanessa Santos
- Universidade Federal de
AlagoasUniversidade Federal de
AlagoasLaboratório de Recursos
GenéticosArapiracaBrazilLaboratório de Recursos Genéticos, Campus
Arapiraca, Universidade Federal de Alagoas, Arapiraca, Brazil
| | - Cícero Almeida
- Universidade Federal de
AlagoasUniversidade Federal de
AlagoasLaboratório de Recursos
GenéticosArapiracaBrazilLaboratório de Recursos Genéticos, Campus
Arapiraca, Universidade Federal de Alagoas, Arapiraca, Brazil
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23
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Wagner ND, Gramlich S, Hörandl E. RAD sequencing resolved phylogenetic relationships in European shrub willows ( Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs. Ecol Evol 2018; 8:8243-8255. [PMID: 30250699 PMCID: PMC6145212 DOI: 10.1002/ece3.4360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 01/03/2023] Open
Abstract
The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic-alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.
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Affiliation(s)
- Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
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