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Wang T, Liu Y, Zou K, Guan M, Wu Y, Hu Y, Yu H, Du J, Wu D. The Analysis, Description, and Examination of the Maize LAC Gene Family's Reaction to Abiotic and Biotic Stress. Genes (Basel) 2024; 15:749. [PMID: 38927685 PMCID: PMC11202975 DOI: 10.3390/genes15060749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Laccase (LAC) is a diverse group of genes found throughout the plant genome essential for plant growth and the response to stress by converting monolignin into intricate lignin formations. However, a comprehensive investigation of maize laccase has not yet been documented. A bioinformatics approach was utilized in this research to conduct a thorough examination of maize (Zea mays L.), resulting in the identification and categorization of 22 laccase genes (ZmLAC) into six subfamilies. The gene structure and motifs of each subgroup were largely consistent. The distribution of the 22 LAC genes was uneven among the maize chromosomes, with the exception of chromosome 9. The differentiation of the genes was based on fragment replication, and the differentiation time was about 33.37 million years ago. ZmLAC proteins are primarily acidic proteins. There are 18 cis-acting elements in the promoter sequences of the maize LAC gene family associated with growth and development, stress, hormones, light response, and stress response. The analysis of tissue-specific expression revealed a high expression of the maize LAC gene family prior to the V9 stage, with minimal expression at post-V9. Upon reviewing the RNA-seq information from the publicly available transcriptome, it was discovered that ZmLAC5, ZmLAC10, and ZmLAC17 exhibited significant expression levels when exposed to various biotic and abiotic stress factors, suggesting their crucial involvement in stress responses and potential value for further research. This study offers an understanding of the functions of the LAC genes in maize's response to biotic and abiotic stress, along with a theoretical basis for comprehending the molecular processes at play.
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Affiliation(s)
- Tonghan Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (T.W.); (K.Z.); (Y.W.); (Y.H.); (H.Y.); (J.D.)
| | - Yang Liu
- College of Resource and Environment, Anhui Science and Technology University, Fengyang 233100, China; (Y.L.); (M.G.)
| | - Kunliang Zou
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (T.W.); (K.Z.); (Y.W.); (Y.H.); (H.Y.); (J.D.)
| | - Minhui Guan
- College of Resource and Environment, Anhui Science and Technology University, Fengyang 233100, China; (Y.L.); (M.G.)
| | - Yutong Wu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (T.W.); (K.Z.); (Y.W.); (Y.H.); (H.Y.); (J.D.)
| | - Ying Hu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (T.W.); (K.Z.); (Y.W.); (Y.H.); (H.Y.); (J.D.)
| | - Haibing Yu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (T.W.); (K.Z.); (Y.W.); (Y.H.); (H.Y.); (J.D.)
| | - Junli Du
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (T.W.); (K.Z.); (Y.W.); (Y.H.); (H.Y.); (J.D.)
| | - Degong Wu
- College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China; (T.W.); (K.Z.); (Y.W.); (Y.H.); (H.Y.); (J.D.)
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Xu X, Wu M, Gou G, Wei T, Yang D, Dai Z. The complete chloroplast genome of Dendrocalamus liboensis Hsueh & D. Z. Li 1985 and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:158-162. [PMID: 38274849 PMCID: PMC10810639 DOI: 10.1080/23802359.2024.2306204] [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: 08/09/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Dendrocalamus liboensis Hsueh & D. Z. Li 1985 is a unique member of the Bambusoideae subfamily found in Guizhou, China. The species has both economic importance and ornamental value. This study represents the first report of the sequencing and assembly of the complete chloroplast genome of D. liboensis. The total length of the genome was 139,483 bp, with a conventional quadripartite framework consisting of a large single-copy (LSC) region (83,001 bp in length), a small single-copy (SSC) region (12,896 bp in length), and two inverted repeats (IR) regions (both 21,793 bp in length). Overall, the D. liboensis chloroplast genome contained 128 functional genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis showed that D. liboensis closely resembled D. sapidus, with both found on a strongly supported branch of the phylogenetic tree.
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Affiliation(s)
- Xue Xu
- College of Life Sciences/Institute of Agro-bioengineering, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education), Guizhou University, Guiyang, China
| | - Mingli Wu
- College of Life Sciences/Institute of Agro-bioengineering, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education), Guizhou University, Guiyang, China
| | - Guangqian Gou
- College of Life Sciences/Institute of Agro-bioengineering, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education), Guizhou University, Guiyang, China
| | | | | | - Zhaoxia Dai
- College of Forestry, Guizhou University, Guiyang, China
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Shim D, Jeon SH, Kim JC, Yoon DK. Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha ( Camellia sinensis var. sinensis)" Using Complete Chloroplast Genome Sequences. Curr Issues Mol Biol 2024; 46:1091-1106. [PMID: 38392187 PMCID: PMC10888334 DOI: 10.3390/cimb46020069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Wild teas are valuable genetic resources for studying evolution and breeding. Here, we report the complete chloroplast genome of the ancient Korean tea 'Hadong Cheon-nyeon Cha' (C. sinensis var. sinensis), which is known as the oldest tea tree in Korea. This study determined seven Camellia sinensis var. sinenesis, including Hadong Cheon-nyeon Cha (HCNC) chloroplast genome sequences, using Illumina sequencing technology via de novo assembly. The chloroplast genome sizes ranged from 157,019 to 157,114 bp and were organized into quadripartite regions with the typical chloroplast genomes. Further, differences in SNPs and InDels were detected across the seven chloroplast genomes through variance analysis. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These genomic resources provide evolutionary insight into Korean tea plant cultivars and lay the foundation for a better understanding of the ancient Korean tea plant HCNC.
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Affiliation(s)
- Doobo Shim
- Institute of Hadong Green Tea, Hadong 52304, Republic of Korea
| | - Seung Ho Jeon
- Department of Agricultural Life Science, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Jong Cheol Kim
- Institute of Hadong Green Tea, Hadong 52304, Republic of Korea
| | - Dong-Kyung Yoon
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
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Liu DK, Zhou CY, Tu XD, Zhao Z, Chen JL, Gao XY, Xu SW, Zeng MY, Ma L, Ahmad S, Li MH, Lan S, Liu ZJ. Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes. BMC Genomics 2023; 24:749. [PMID: 38057701 DOI: 10.1186/s12864-023-09847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation. RESULTS We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnNGUU-rpl32 > rpoB-trnCGCA > psbK-psbI > psaC-rps15 > trnEUUC-trnTGGU > accD-psaI) and five coding sequences (ycf1 > rps15 > matK > psbK > ccsA) were selected as potential barcodes based on nucleotide diversity and species discrimination analysis, which suggested that the potential barcode ycf1 was most suitable for species discrimination. A total of 47-56 SSRs and 11-14 long repeats (> 20 bp) were identified in Chiloschista plastomes, and they were mostly located in the large single copy intergenic region. Phylogenetic analysis indicated that Chiloschista was monophyletic. It was clustered with Phalaenopsis and formed the basic clade of the subtribe Aeridinae with a moderate support value. The results also showed that seven Chiloschista species were divided into three major clades with full support. CONCLUSION This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.
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Affiliation(s)
- Ding-Kun Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cheng-Yuan Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiong-De Tu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuang Zhao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jin-Liao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu-Yong Gao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shao-Wei Xu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng-Yao Zeng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liang Ma
- Fujian Health College, Fuzhou, 350101, Fujian, China
| | - Sagheer Ahmad
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ming-He Li
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wu H, Li X, Xu X, Zhang Y, Su T. The complete chloroplast genome of Fargesia angustissima T. P. Yi: a panda dietary bamboo species. Mitochondrial DNA B Resour 2023; 8:1183-1186. [PMID: 38188435 PMCID: PMC10769560 DOI: 10.1080/23802359.2023.2275834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/21/2023] [Indexed: 01/09/2024] Open
Abstract
Fargesia angustissima T. P. Yi, categorized into Arundinarieae (Poaceae: Bambusoideae), is a critical species endemic to Minshan Mountain, China. F. angustissima provides shelter and food sources for the giant panda and other endangered animals (e.g. red panda and snub-nosed monkey). This study assembled the complete chloroplast (cp) genome of F. angustissima using the high-throughput sequencing technique. The total cp length was 139,706 bp, containing 130 annotated genes with predicted GC content at 38.87%. The cp genome comprises two single-copy (LSC and SSC) regions, harboring 83,282 bp and 12,830 bp, respectively. The SSC regions were located between two inverted repeats (IR) regions (21,797 bp). Reconstruction of the phylogenetic tree illustrated that F. angustissima clustered F. canaliculata in Fargesia II. The study provides theoretical clues to explore the geographical distribution and species-level identification of the Fargesia genus.
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Affiliation(s)
- Hao Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Xue Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Xianglei Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Yingjian Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, China
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China
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An SM, Kim BY, Kang H, Lee HR, Lee YB, Park YJ, Cheon KS, Kim KA. The complete chloroplast genome sequences of six Hylotelephium species: Comparative genomic analysis and phylogenetic relationships. PLoS One 2023; 18:e0292056. [PMID: 37815995 PMCID: PMC10564136 DOI: 10.1371/journal.pone.0292056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
To evaluate the phylogenetic relationships between Hylotelephium and Orostachys, and to provide important information for further studies, we analyzed the complete chloroplast genomes of six Hylotelephium species and compared the sequences to those of published chloroplast genomes of congeneric species and species of the closely related genus, Orostachys. The total chloroplast genome length of nineteen species, including the six Hylotelephium species analyzed in this study and the thirteen Hylotelephium and Orostachys species analyzed in previous studies, ranged from 150,369 bp (O. minuta) to 151,739 bp (H. spectabile). Their overall GC contents were almost identical (37.7-37.8%). The chloroplast genomes of the nineteen species contained 113 unique genes comprising 79 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Among the annotated genes, fourteen genes contained one intron, and two genes contained two introns. The chloroplast genomes of the nineteen Hylotelephium and Orostachys species had identical structures. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved in the Hylotelephium and Orostachys species. The nucleotide diversity between the Hylotelephium chloroplast genomes was extremely low in all regions, and only one region showed a high Pi value (>0.03). In all nineteen chloroplast genomes, six regions had a high Pi value (>0.03). The phylogenetic analysis showed that the genus delimitation could not be clearly observed even in this study because Hylotelephium formed a paraphyly with subsect. Orostachys of the genus Orostachys. Additionally, the data supported the taxonomic position of Sedum taqeutii, which was treated as a synonym for H. viridescens in previous studies, as an independent taxon.
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Affiliation(s)
- Sung-Mo An
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Halam Kang
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Ha-Rim Lee
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Yoo-Bin Lee
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Yoo-Jung Park
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Kyeong-Sik Cheon
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Kyung-Ah Kim
- Environmental Research Institute, Kangwon National University, Chuncheon, South Korea
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Corvalán LCJ, Sobreiro MB, Carvalho LR, Dias RO, Braga-Ferreira RS, Targueta CP, Silva-Neto CME, Berton BW, Pereira AMS, Diniz-filho JAF, Telles MPC, Nunes R. Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1258794. [PMID: 37822334 PMCID: PMC10562606 DOI: 10.3389/fpls.2023.1258794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
Abstract
Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.
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Affiliation(s)
| | - Mariane B. Sobreiro
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Larissa R. Carvalho
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Renata O. Dias
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Ramilla S. Braga-Ferreira
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, Rondonópolis, Brazil
| | - Cintia P. Targueta
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | | | | | | | - José A. F. Diniz-filho
- Laboratório de Ecologia Teórica e Síntese, Universidade Federal de Goiás, Goiânia, Brazil
| | - Mariana P. C. Telles
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto Federal de Goiás, Goiás, Brazil
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Bandaranayake PCG, Naranpanawa N, Chandrasekara CHWMRB, Samarakoon H, Lokuge S, Jayasundara S, Bandaranayake AU, Pushpakumara DKNG, Wijesundara DSA. Chloroplast genome, nuclear ITS regions, mitogenome regions, and Skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka. PLoS One 2023; 18:e0291763. [PMID: 37729154 PMCID: PMC10511092 DOI: 10.1371/journal.pone.0291763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023] Open
Abstract
Cinnamomum species have gained worldwide attention because of their economic benefits. Among them, C. verum (synonymous with C. zeylanicum Blume), commonly known as Ceylon Cinnamon or True Cinnamon is mainly produced in Sri Lanka. In addition, Sri Lanka is home to seven endemic wild cinnamon species, C. capparu-coronde, C. citriodorum, C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum and C. sinharajaense. Proper identification and genetic characterization are fundamental for the conservation and commercialization of these species. While some species can be identified based on distinct morphological or chemical traits, others cannot be identified easily morphologically or chemically. The DNA barcoding using rbcL, matK, and trnH-psbA regions could not also resolve the identification of Cinnamomum species in Sri Lanka. Therefore, we generated Illumina Hiseq data of about 20x coverage for each identified species and a C. verum sample (India) and assembled the chloroplast genome, nuclear ITS regions, and several mitochondrial genes, and conducted Skmer analysis. Chloroplast genomes of all eight species were assembled using a seed-based method.According to the Bayesian phylogenomic tree constructed with the complete chloroplast genomes, the C. verum (Sri Lanka) is sister to previously sequenced C. verum (NC_035236.1, KY635878.1), C. dubium and C. rivulorum. The C. verum sample from India is sister to C. litseifolium and C. ovalifolium. According to the ITS regions studied, C. verum (Sri Lanka) is sister to C. verum (NC_035236.1), C. dubium and C. rivulorum. Cinnamomum verum (India) shares an identical ITS region with C. ovalifolium, C. litseifolium, C. citriodorum, and C. capparu-coronde. According to the Skmer analysis C. verum (Sri Lanka) is sister to C. dubium and C. rivulorum, whereas C. verum (India) is sister to C. ovalifolium, and C. litseifolium. The chloroplast gene ycf1 was identified as a chloroplast barcode for the identification of Cinnamomum species. We identified an 18 bp indel region in the ycf1 gene, that could differentiate C. verum (India) and C. verum (Sri Lanka) samples tested.
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Affiliation(s)
| | - Nathasha Naranpanawa
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - Hiruna Samarakoon
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. Lokuge
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. Jayasundara
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - Asitha U. Bandaranayake
- Faculty of Engineering, Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - D. K. N. G. Pushpakumara
- Faculty of Agriculture, Department of Crop Science, University of Peradeniya, Peradeniya, Sri Lanka
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9
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Xu Q, Li Z, Wu N, Yang J, Yuan L, Zhao T, Sima Y, Xu T. Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes (Basel) 2023; 14:1262. [PMID: 37372442 DOI: 10.3390/genes14061262] [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: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The genus Houpoea belongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species of Houpoea: Houpoea officinalis var officinalis (OO), Houpoea officinalis var. biloba (OB), and Houpoea rostrata (R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these three Houpoea plants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the three Houpoea plants, it is highly conservative, with only changes between H. rostrata and the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label for Houpoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates that Houpoea is a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties of H. officinalis var. officinalis, H. rostrata, H. officinalis var. biloba, Houpoea obovate, and Houpoea tripetala, which evolved and differentiated from the ancestors of Houpoea to the present Houpoea in the above order. This study provides valuable information on the genus Houpoea, enriches the CPG information on Houpoea genus, and provides genetic resources for the further classification of and phylogenetic research on Houpoea.
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Affiliation(s)
- Qinbin Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Zhuoran Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Nannan Wu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Jing Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Lang Yuan
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Tongxing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yongkang Sima
- Kunming Arboretum, Yunnan Academy of Forestry & Grassland Science, Kunming 650201, China
| | - Tao Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
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Wang X, Bai S, Zhang Z, Zheng F, Song L, Wen L, Guo M, Cheng G, Yao W, Gao Y, Li J. Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1179009. [PMID: 37229122 PMCID: PMC10203424 DOI: 10.3389/fpls.2023.1179009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K A/K S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
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Affiliation(s)
- Xiaomin Wang
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Shengyi Bai
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Fushun Zheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lina Song
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lu Wen
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Meng Guo
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Guoxin Cheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Wenkong Yao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Yanming Gao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jianshe Li
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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11
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Yang L, Deng S, Zhu Y, Da Q. Comparative chloroplast genomics of 34 species in subtribe Swertiinae (Gentianaceae) with implications for its phylogeny. BMC PLANT BIOLOGY 2023; 23:164. [PMID: 36977991 PMCID: PMC10044379 DOI: 10.1186/s12870-023-04183-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Subtribe Swertiinae, a medicinally significant and highly speciose Subtribe of family Gentianaceae. Despite previous extensive studies based on both morphology and molecular data, intergeneric and infrageneric relationships within subtribe Swertiinae remain controversial. METHODS Here, we employed four newly generated Swertia chloroplast genomes with thirty other published genomes to elucidate their genomic characteristics. RESULTS The 34 chloroplast genomes were small and ranged in size from 149,036 to 154,365 bp, each comprising two inverted repeat regions (size range 25,069-26,126 bp) that separated large single-copy (80,432-84,153 bp) and small single-copy (17,887-18,47 bp) regions, and all the chloroplast genomes showed similar gene orders, contents, and structures. These chloroplast genomes contained 129-134 genes each, including 84-89 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes of subtribe Swertiinae appeared to have lost some genes, such as rpl33, rpl2 and ycf15 genes. Comparative analyses revealed that two mutation hotspot regions (accD-psaI and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification in subtribe Swertiinae. Positive selection analyses showed that two genes (ccsA and psbB) had high Ka/Ks ratios, indicating that chloroplast genes may have undergone positive selection in their evolutionary history. Phylogenetic analysis showed that the 34 subtribe Swertiinae species formed a monophyletic clade, with Veratrilla, Gentianopsis and Pterygocalyx located at the base of the phylogenetic tree. Some genera of this subtribe, however, were not monophyletic, including Swertia, Gentianopsis, Lomatogonium, Halenia, Veratrilla and Gentianopsis. In addition, our molecular phylogeny was consistent with taxonomic classification of subtribe Swertiinae in the Roate group and Tubular group. The results of molecular dating showed that the divergence between subtrib Gentianinae and subtrib Swertiinae was estimated to occur in 33.68 Ma. Roate group and Tubular group in subtribe Swertiinae approximately diverged in 25.17 Ma. CONCLUSION Overall, our study highlighted the taxonomic utility of chloroplast genomes in subtribe Swertiinae, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of subtribe Swertiinae species.
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Affiliation(s)
- Lucun Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences, Xining, 81008, China.
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resource, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
| | - Shengxue Deng
- Qinghai Environmental Science Research and Design Institute Co. Ltd, Xining, 810007, China
| | - Yongqing Zhu
- Maqin County Forestry and Grassland Station, Maqin, 814000, China
| | - Qilin Da
- Bureau of Forestry in Hualong County, Hualong, 810900, China
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12
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Rakotonasolo RA, Dransfield S, Haevermans T, Ralimanana H, Vorontsova MS, Zhou MY, Li DZ. New insights into intergeneric relationships of Hickeliinae (Poaceae: Bambusoideae) revealed by complete plastid genomes. PLANT DIVERSITY 2023; 45:125-132. [PMID: 37069926 PMCID: PMC10105074 DOI: 10.1016/j.pld.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 06/19/2023]
Abstract
The Hickeliinae (Poaceae: Bambusoideae) is an ecologically and economically significant subtribe of tropical bamboos restricted to Madagascar, Comoros, Reunion Island, and a small part of continental Africa (Tanzania). Because these bamboos rarely flower, field identification is challenging, and inferring the evolutionary history of Hickeliinae from herbarium specimens is even more so. Molecular phylogenetic work is critical to understanding this group of bamboos. Here, comparative analysis of 22 newly sequenced plastid genomes showed that members of all genera of Hickeliinae share evolutionarily conserved plastome structures. We also determined that Hickeliinae plastome sequences are informative for phylogenetic reconstructions. Phylogenetic analysis showed that all genera of Hickeliinae are monophyletic, except for Nastus, which is paraphyletic and forms two distant clades. The type species of Nastus (Clade II) is endemic to Reunion Island and is not closely related to other sampled species of Nastus endemic to Madagascar (Clade VI). Clade VI (Malagasy Nastus) is sister to the Sokinochloa + Hitchcockella clade (Clade V), and both clades have a clumping habit with short-necked pachymorph rhizomes. The monotypic Decaryochloa is remarkable in having the longest floret in Bambuseae and forms a distinct Clade IV. Clade III, which has the highest generic diversity, consists of Cathariostachys, Perrierbambus, Sirochloa, and Valiha, which are also morphologically diverse. This work provides significant resources for further genetic and phylogenomic studies of Hickeliinae, an understudied subtribe of bamboo.
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Affiliation(s)
- Rivontsoa A. Rakotonasolo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Department Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, 101, Madagascar
- Kew Madagascar Conservation Center, Antananarivo, 101, Madagascar
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Soejatmi Dransfield
- Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Thomas Haevermans
- Institut de Systématique Évolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Centre National de La Recherche Scientifique, École Pratique des Hautes Études, Université des Antilles, Sorbonne Université, 45 Rue Buffon, CP 50, 75005, Paris, France
| | | | - Maria S. Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Yang C, Zhang N, Wu S, Jiang C, Xie L, Yang F, Yu Z. A Comparative Analysis of the Chloroplast Genomes of Three Lonicera Medicinal Plants. Genes (Basel) 2023; 14:genes14030548. [PMID: 36980821 PMCID: PMC10048777 DOI: 10.3390/genes14030548] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Both Lonicerae japonicae flos and Lonicerae similis flos are important components in traditional Chinese medicine (TCM) with precious medicinal value. However, the absence of studies on their chloroplast genomes and chromatography has considerably hindered the study of their evolutionary and phylogenetic relationships. In this study, the complete chloroplast (cp) genomes of Lonicera acuminata Wall. and Lonicera similis Hemsl. were sequenced using the Illumina sequencing platform and compared with that of Lonicera japonica Thunb., which has been previously reported. Furthermore, the chromatographic fingerprints of the three plants were constructed using HPLC and the content of quality marker (Q-Marker) was calculated. The annotation results showed that the two chloroplast genomes were typical quadripartite structures with lengths of 155,330 bp (L. acuminata) and 155,207 bp (L. similis). A total of 126 different genes were annotated, containing 82 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The expansion and contraction of the inverted repeat (IR) regions suggested that the boundary regions of IR/SC were comparatively conserved in the three species, and six regions (trnH-GUG-psbA, rps2-rpoC2, rbcL-psaI, trnN-GUU-ndhF, rps15-ycf1, and infA) with nucleotide diversity values (Pi) of variable sites higher than 1% were identified. Phylogenetic relation indicated that L. similis had a closer genetic relationship with L. japonica than L. acuminata. Additionally, the chromatographic fingerprints showed that the characteristic peaks of the three medicinal plants were similar, including Neochlorogenic acid, Chlorogenic acid, 4-Dicaffeoylquinic acid, Sweroside, Secoxyloganin, Luteoloside, Isochlorogenic acid A, Isochlorogenic acid B, and Isochlorogenic acid C. The content of chlorogenic acid and total phenolic acid in L. acuminata (7.4633 ± 0.4461%, 14.8953 ± 0.0728%) and L. similis (14.1055 ± 0.2566%, 21.9782 ± 0.1331%) was much higher than that of L. japonica (3.9729 ± 0.0928%, 6.0964 ± 0.1228%), respectively. This study provides appropriate information for species identification, phylogeny, quality assessment, and rational use of three medicinal plants of the genus Lonicera.
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Affiliation(s)
- Chenju Yang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Ni Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences/Guizhou Provincal Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Shaoxiong Wu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Chunyan Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Lian Xie
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Feng Yang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Zhengwen Yu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
- Correspondence:
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Bai X, Wang G, Ren Y, Su Y, Han J. Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1119041. [PMID: 36860895 PMCID: PMC9969298 DOI: 10.3389/fpls.2023.1119041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The Aristolochia, as an important genus comprised of over 400 species, has attracted much interest because of its unique chemical and pharmacological properties. However, the intrageneric taxonomy and species identification within Aristolochia have long been difficult because of the complexity of their morphological variations and lack of high-resolution molecular markers. METHODS In this study, we sampled 11 species of Aristolochia collected from distinct habitats in China, and sequenced their complete chloroplast (cp) genomes. RESULTS The 11 cp genomes of Aristolochia ranged in size from 159,375bp (A. tagala) to 160,626 bp (A. tubiflora), each containing a large single-copy (LSC) region (88,914-90,251 bp), a small single-copy (SSC) region (19,311-19,917 bp), and a pair of inverted repeats (IR) (25,175-25,698 bp). These cp genomes contained 130-131 genes each, including 85 protein-coding genes (CDS), 8 ribosomal RNA genes, and 37-38 transfer RNA genes. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in Aristolochia species. A. littoralis had the highest number of repeats (168), while A. tagala had the lowest number (42). The total number of simple sequence repeats (SSRs) is at least 99 in A. kwangsiensis, and, at most, 161 in A. gigantea. Interestingly, we detected eleven highly mutational hotspot regions, including six gene regions (clpP, matK, ndhF, psbT, rps16, trnK-UUU) and five intergenic spacer regions (ccsA-ndhD, psbZ-trnG-GCC, rpl33-rps18, rps16-trnQ-UUG, trnS-GCU-trnG-UCC). The phylogenetic analysis based on the 72 protein-coding genes showed that 11 Aristolochia species were divided into two clades which strongly supported the generic segregates of the subgenus Aristolochia and Siphisia. DISCUSSION This research will provide the basis for the classification, identification, and phylogeny of medicinal plants of Aristolochiaceae.
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15
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Zhang L, Huang YW, Huang JL, Ya JD, Zhe MQ, Zeng CX, Zhang ZR, Zhang SB, Li DZ, Li HT, Yang JB. DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes. Mol Ecol Resour 2023; 23:424-439. [PMID: 36219539 DOI: 10.1111/1755-0998.13719] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 01/04/2023]
Abstract
Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopted and the identification rate increased to 72%. It appears that nuclear genome data have a vital role in species identification and are expected to be used as next-generation nuclear barcodes.
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Affiliation(s)
- Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yi-Wei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meng-Qing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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16
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The Complete Chloroplast Genome Sequence of Machilus chuanchienensis (Lauraceae): Genome Structure and Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13122402. [PMID: 36553669 PMCID: PMC9778441 DOI: 10.3390/genes13122402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal model for the phylogenetic study of Lauraceae because of its simple structure and highly conserved features. There have been numerous reports of complete cp genome sequences in Lauraceae, but little is known about M. chuanchienensis. Here, the next-generation sequencing (NGS) was used to sequence the M. chuanchienensis cp genome. Then, a comprehensive comparative genome analysis was performed. The results revealed that the M. chuanchienensis's cp genome measured 152,748 base pairs (bp) with a GC content of 39.15% and coded 126 genes annotated, including comprising eight ribosomal RNA (rRNA), 36 transporter RNA (tRNA), and 82 protein-coding genes. In addition, the cp genome presented a typical quadripartite structure comprising a large single-copy (LSC; 93,811) region, a small single-copy (SSC; 18,803) region, and the inverted repeats (IRs; 20,067) region and contained 92 simple sequence repeat (SSR) locus in total. Phylogenetic relationships of 37 species indicated that M. chuanchienensis was a sister to M. balansae, M. melanophylla, and M. minutiflora. Further research on this crucial species may benefit significantly from these findings.
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Cai J, Qin HH, Lei JQ, Liu CK, He XJ, Zhou SD. The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data. BMC PLANT BIOLOGY 2022; 22:534. [PMID: 36380268 PMCID: PMC9667662 DOI: 10.1186/s12870-022-03919-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The genus Seseli L., which consists of 125-140 species distributed in the Old World from western Europe and northwestern Africa to China and Japan, is one of the largest and most taxonomically difficult genera of Apiaceae Lindl. Although several previous studies have been conducted on Seseli based on limited morphological characteristics and molecular fragments, a robust and comprehensive phylogeny of Seseli remains elusive. Plastomes provide abundant genetic information and have been widely used in studying plant phylogeny and evolution. Consequently, we newly generated the complete plastomes of eleven Seseli taxa. We combined plastome data and morphological characteristics to investigate the phylogeny of Seseli. RESULTS In our study, we observed that the genome length, gene numbers, IR/SC borders, and repeat composition of the eleven Seseli plastomes were variable. Several appropriate mutation hotspot regions may be developed as candidate DNA barcodes for evolution, phylogeny, and species identification of Seseli. The phylogenetic results identified that Seseli was not a monophyletic group. Moreover, the eleven newly sequenced Seseli taxa did not cluster with S. tortuosum (the type species of Seseli, belonging to the tribe Selineae), where S. delavayi clustered with Eriocycla belonging to the tribe Echinophoreae and the other ten belonged to Selineae. The comparative plastome and morphological characteristics analyses confirmed the reliability of the phylogenetic analyses and implied the complex evolution of Seseli. CONCLUSION Combining molecular and morphological data is efficient and useful for studying the phylogeny of Seseli. We suggest that "a narrow sense" of Seseli will be meaningful for further study and the current taxonomic system of Seseli needs to be revised. In summary, our study can provide new insights into the phylogenetic relationships and taxonomic framework of Seseli.
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Affiliation(s)
- Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huan-Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jia-Qing Lei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Xu YL, Shen HH, Du XY, Lu L. Plastome characteristics and species identification of Chinese medicinal wintergreens ( Gaultheria, Ericaceae). PLANT DIVERSITY 2022; 44:519-529. [PMID: 36540705 PMCID: PMC9751084 DOI: 10.1016/j.pld.2022.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/01/2022] [Accepted: 06/13/2022] [Indexed: 06/17/2023]
Abstract
Wintergreen oil is a folk medicine widely used in foods, pesticides, cosmetics and drugs. In China, nine out of 47 species within Gaultheria (Ericaceae) are traditionally used as Chinese medicinal wintergreens; however, phylogenetic approaches currently used to discriminating these species remain unsatisfactory. In this study, we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria. Each Gaultheria plastome contained 110 unique genes (76 protein-coding, 30 tRNA, and four rRNA genes). Duplication of trnfM, rps14, and rpl23 genes were detected, while all plastomes lacked ycf1 and ycf2 genes. Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene. Moreover, plastomes of Gaultheria leucocarpa var. yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene. Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales. Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species. Additionally, seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens. Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria. In addition, our findings provide important resources for identification of Chinese medicinal wintergreens.
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Affiliation(s)
- Yan-Ling Xu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, China
| | - Hao-Hua Shen
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, China
| | - Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lu Lu
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, China
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19
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Yang L, Li J, Zhou G. Comparative chloroplast genome analyses of 23 species in Swertia L. (Gentianaceae) with implications for its phylogeny. Front Genet 2022; 13:895146. [PMID: 36118878 PMCID: PMC9470856 DOI: 10.3389/fgene.2022.895146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022] Open
Abstract
Swertia L. is a large genus in the family Gentianaceae. Different chloroplast gene segments have been used to study systematic evolutionary relationships between species of Swertia L. However, as gene fragment–based phylogenies lack sufficient resolution, the systematic evolutionary relationships between Swertia L. species have remained unclear. We sequenced and annotated the complete chloroplast genomes of four Swertia species, namely, S. bifolia, S. tetraptera, S. franchetian, and S. przewalskii, using next generation sequencing and the plastid genome annotator tool. The chloroplast genome sequences of 19 additional species of Swertia L. were downloaded from the NCBI database and also assessed. We found that all 23 Swertia L. species had a similar genetic structure, that is, a ring tetrad structure, but with some clear differences. The chloroplast genomes of the 23 Swertia L. species were 149036–153691 bp long, averaging 152385 bp; the genomes contained 134 functional genes: 38 tRNA, eight rRNA, and 88 protein-encoding genes. A comparative analysis showed that chloroplasts genome of Swertia was conserved in terms of genome structure, codon preference, and repeat sequences, but it differed in terms of genome sizes, gene contents, and SC/IR boundary. Using Swertia wolfangiana as a reference, we found clear divergences in most of the non-coding and intergenic regions of the complete chloroplast genomes of these species; we also found that rpoC1, ccsA, ndhI, ndhA, and rps15 protein-coding genes had large variations. These highly variable hotspots will be useful for future phylogenetic and population genetic studies. Phylogenetic analysis with high bootstrap support showed that Swertia L. was not monophyletic. The classification of subgen. Swertia and subgen. Ophelia was supported by molecular data, which also partly supported the division of sect. Ophelia, sect. Platynema, sect. Poephila, sect. Swertia, and sect. Macranthos. However, the systematic positions of other groups and species require further exploration. The Swertia L formed at 29.60 Ma. Speciation of 10 species occurred in succession after 12 Ma and 13 species occurred in succession after 2.5 Ma. Our analysis provides insight into the unresolved evolutionary relationships of Swertia L. species.
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Affiliation(s)
- Lucun Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences, Xining, China
| | - Jingjing Li
- College of Life Science, Qinghai Normal University, Xining, China
| | - Guoying Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences, Xining, China
- *Correspondence: Guoying Zhou,
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20
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Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species. Genes (Basel) 2022; 13:genes13091519. [PMID: 36140690 PMCID: PMC9498922 DOI: 10.3390/genes13091519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrocalamus farinosus is one of the essential bamboo species mainly used for food and timber in the southwestern region of China. In this study, the complete chloroplast (cp) genome of D. farinosus is sequenced, assembled, and the phylogenetic relationship analyzed. The cp genome has a circular and quadripartite structure, has a total length of 139,499 bp and contains 132 genes: 89 protein-coding genes, eight rRNAs and 35 tRNAs. The repeat analyses showed that three types of repeats (palindromic, forward and reverse) are present in the genome. A total of 51 simple sequence repeats are identified in the cp genome. The comparative analysis between different species belonging to Dendrocalamus revealed that although the cp genomes are conserved, many differences exist between the genomes. The analysis shows that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions are more conserved than the single-copy regions. Moreover, these results also indicate that rpoC2 may be used to distinguish between different bamboo species. Phylogenetic analysis results supported that D. farinosus was closely related to D. latiflorus. Furthermore, these bamboo species’ geographical distribution and rhizome types indicate two evolutionary pathways: one is from the tropics to the alpine zone, and the other is from the tropics to the warm temperate zone. Our study will be helpful in the determination of the cp genome sequences of D. farinosus, and provides new molecular data to understand the Bambusoideae evolution.
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21
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Wang Z, Cai Q, Wang Y, Li M, Wang C, Wang Z, Jiao C, Xu C, Wang H, Zhang Z. Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species. Front Genet 2022; 13:824610. [PMID: 35360853 PMCID: PMC8961065 DOI: 10.3389/fgene.2022.824610] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Theaceae species are dicotyledonous angiosperms with extremely high ornamental and economic value. The chloroplast genome is traditionally used to study species evolution, expression of chloroplast genes and chloroplast transformation. Codon usage bias (CUB) analysis is beneficial for investigations of evolutionary relationships and can be used to improve gene expression efficiency in genetic transformation research. However, there are relatively few systematic studies of the CUB in the chloroplast genomes of Theaceae species. In this study, CUB and nucleotide compositions parameters were determined by the scripts written in the Perl language, CodonW 1.4.2, CU.Win2000, RStudio and SPSS 23.0. The chloroplast genome data of 40 Theaceae species were obtained to analyse the codon usage (CU) characteristics of the coding regions and the influence of the source of variation on CUB. To explore the relationship between the CUB and gene expression levels in these 40 Theaceae plastomes, the synonymous codon usage order (SCUO) and measure independent of length and composition (MILC) values were determined. Finally, phylogenetic analysis revealed the genetic evolutionary relationships among these Theaceae species. Our results showed that based on the chloroplast genomes of these 40 Theaceae species, the CUB was for codons containing A/T bases and those that ended with A/T bases. Moreover, there was great commonality in the CUB of the Theaceae species according to comparative analysis of relative synonymous codon usage (RSCU) and relative frequency of synonymous codon (RFSC): these species had 29 identical codons with bias (RSCU > 1), and there were 19 identical high-frequency codons. The CUB of Theaceae species is mainly affected by natural selection. The SCUO value of the 40 Theaceae species was 0.23 or 0.24, and the chloroplast gene expression level was moderate, according to MILC values. Additionally, we observed a positive correlation between the SCUO and MILC values, which indicated that CUB might affect gene expression. Furthermore, the phylogenetic analysis showed that the evolutionary relationships in these 40 Theaceae species were relatively conserved. A systematic study on the CUB and expression of Theaceae species provides further evidence for their evolution and phylogeny.
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Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Yue Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Li
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Chenchen Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhaoxia Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Congcong Xu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Hongyan Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Zhaoliang Zhang,
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22
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Zeb U, Wang X, Fiaz S, Azizullah A, Shah AA, Ali S, Rahim F, Ullah H, Leghari UA, Wang W, Nawaz T. Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis. PLoS One 2022; 17:e0262040. [PMID: 35045089 PMCID: PMC8769304 DOI: 10.1371/journal.pone.0262040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/15/2021] [Indexed: 11/18/2022] Open
Abstract
Pinus is one of the most economical and ecological important conifers, model specie for studying sequence divergence and molecular phylogeney of gymnosperms. The less availability of information for genome resources enable researchers to conduct evolutionary studies of Pinus species. To improve understanding, we firstly reported, previously released chloroplast genome of 72 Pinus species, the sequence variations, phylogenetic relationships and genome divergence among Pinus species. The results displayed 7 divergent hotspot regions (trnD-GUC, trnY-GUA, trnH-GUG, ycf1, trnL-CAA, trnK-UUU and trnV-GAC) in studied Pinus species, which holds potential to utilized as molecular genetic markers for future phylogenetic studies in Pinnus species. In addition, 3 types of repeats (tandem, palindromic and dispersed) were also studied in Pinus species under investigation. The outcome showed P. nelsonii had the highest, 76 numbers of repeats, while P. sabiniana had the lowest, 13 13 numbers of repeats. It was also observed, constructed phylogenetic tree displayed division into two significant diverged clades: single needle (soft pine) and double-needle (hard pine). Theoutcome of present investigation, based on the whole chloroplast genomes provided novel insights into the molecular based phylogeny of the genus Pinus which holds potential for its utilization in future studies focusing genetic diversity in Pinnus species.
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Affiliation(s)
- Umar Zeb
- Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, Shaanxi, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Azizullah Azizullah
- Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Asad Ali Shah
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sajjad Ali
- Department of Botany, Bacha Khan University Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - Fazli Rahim
- Department of Botany, Bacha Khan University Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - Hafiz Ullah
- Departement of Botany, University of Chitral, Khyber Pakhtunkhwa, Pakistan
| | - Umed Ali Leghari
- Department of Agriculture, Mir Chakar Khan Rind University, Sibi, Balochistan, Pakistan
| | - Weiqiang Wang
- College of Life Sciences, Yan’an University, Yan’an, Shaanxi, China
| | - Taufiq Nawaz
- Department of Food Science and Technology, The University of Agriculture Peshawar, Khyber Pakhtunkhwa, Pakistan
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23
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Guo XX, Qu XJ, Zhang XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). BIOLOGY 2022; 11:biology11010063. [PMID: 35053061 PMCID: PMC8773369 DOI: 10.3390/biology11010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.
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Affiliation(s)
| | | | - Xue-Jie Zhang
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
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24
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Shidhi PR, Nadiya F, Biju VC, Vijayan S, Sasi A, Vipin CL, Janardhanan A, Aswathy S, Rajan VS, Nair AS. Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis, identification of mutational hotspots and evolutionary dynamics with species of Solanales. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1867-1884. [PMID: 34539121 PMCID: PMC8405790 DOI: 10.1007/s12298-021-01051-w] [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: 01/19/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa 'Evolvulus' could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01051-w.
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Affiliation(s)
- P. R. Shidhi
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - F. Nadiya
- Department of Biotechnology, Inter University Centre for Genomics and Gene Technology, University of Kerala, Thiruvananthapuram, Kerala India
| | - V. C. Biju
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - Sheethal Vijayan
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - Anu Sasi
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - C. L. Vipin
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - Akhil Janardhanan
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - S. Aswathy
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - Veena S. Rajan
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
| | - Achuthsankar S. Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala India
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25
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Singh NV, Patil PG, Sowjanya RP, Parashuram S, Natarajan P, Babu KD, Pal RK, Sharma J, Reddy UK. Chloroplast Genome Sequencing, Comparative Analysis, and Discovery of Unique Cytoplasmic Variants in Pomegranate ( Punica granatum L.). Front Genet 2021; 12:704075. [PMID: 34394192 PMCID: PMC8356083 DOI: 10.3389/fgene.2021.704075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022] Open
Abstract
Here we report on comprehensive chloroplast (cp) genome analysis of 16 pomegranate (Punica granatum L.) genotypes representing commercial cultivars, ornamental and wild types, through large-scale sequencing and assembling using next-generation sequencing (NGS) technology. Comparative genome analysis revealed that the size of cp genomes varied from 158,593 bp (in wild, “1201” and “1181”) to 158,662 bp (cultivar, “Gul-e-Shah Red”) among the genotypes, with characteristic quadripartite structures separated by a pair of inverted repeats (IRs). The higher conservation for the total number of coding and non-coding genes (rRNA and tRNA) and their sizes, and IRs (IR-A and IR-B) were observed across all the cp genomes. Interestingly, high variations were observed in sizes of large single copy (LSC, 88,976 to 89,044 bp) and small single copy (SSC, 18,682 to 18,684 bp) regions. Although, the structural organization of newly assembled cp genomes were comparable to that of previously reported cp genomes of pomegranate (“Helow,” “Tunisia,” and “Bhagawa”), the striking differences were observed with the Lagerstroemia lines, viz., Lagerstroemia intermedia (NC_0346620) and Lagerstroemia speciosa (NC_031414), which clearly confirmed previous findings. Furthermore, phylogenetic analysis also revealed that members outside the genus Punica were clubbed into a separate clade. The contraction and expansion analysis revealed that the structural variations in IRs, LSC, and SSC have significantly accounted for the evolution of cp genomes of Punica and L. intermedia over the periods. Microsatellite survey across cp genomes resulted in the identification of a total of 233 to 234 SSRs, with majority of them being mono- (A/T or C/G, 164–165 numbers), followed by di- (AT/AT or AG/CT, 54), tri- (6), tetra- (8), and pentanucleotides (1). Furthermore, the comparative structural variant analyses across cp genomes resulted in the identification of many varietal specific SNP/indel markers. In summary, our study has offered a successful development of large-scale cp genomics resources to leverage future genetic, taxonomical, and phylogenetic studies in pomegranate.
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Affiliation(s)
| | | | - Roopa P Sowjanya
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | | | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, West Virginia, WV, United States
| | | | - Ram Krishna Pal
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, West Virginia, WV, United States
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26
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Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae. Sci Rep 2021; 11:14643. [PMID: 34282194 PMCID: PMC8289817 DOI: 10.1038/s41598-021-94137-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia.
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27
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Lee C, Ruhlman TA, Jansen RK. Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes. Genome Biol Evol 2021; 12:641-655. [PMID: 32282915 PMCID: PMC7426004 DOI: 10.1093/gbe/evaa076] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) of land plants have a conserved quadripartite structure in a gene-dense unit genome consisting of a large inverted repeat that separates two single copy regions. Recently, alternative plastome structures were suggested in Geraniaceae and in some conifers and Medicago the coexistence of inversion isomers has been noted. In this study, plastome sequences of two Cyperaceae, Eleocharis dulcis (water chestnut) and Eleocharis cellulosa (gulf coast spikerush), were completed. Unlike the conserved plastomes in basal groups of Poales, these Eleocharis plastomes have remarkably divergent features, including large plastome sizes, high rates of sequence rearrangements, low GC content and gene density, gene duplications and losses, and increased repetitive DNA sequences. A novel finding among these features was the unprecedented level of heteroplasmy with the presence of multiple plastome structural types within a single individual. Illumina paired-end assemblies combined with PacBio single-molecule real-time sequencing, long-range polymerase chain reaction, and Sanger sequencing data identified at least four different plastome structural types in both Eleocharis species. PacBio long read data suggested that one of the four E. dulcis plastome types predominates.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin.,Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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28
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Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea). FORESTS 2021. [DOI: 10.3390/f12070861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.
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29
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Wu L, Cui Y, Wang Q, Xu Z, Wang Y, Lin Y, Song J, Yao H. Identification and phylogenetic analysis of five Crataegus species (Rosaceae) based on complete chloroplast genomes. PLANTA 2021; 254:14. [PMID: 34180013 DOI: 10.1007/s00425-021-03667-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
The chloroplast genomes of the five Crataegus species were shown to have a conserved genome structure. Complete chloroplast genome sequences were more suitable than highly variable regions for the identification and phylogenetic analysis of Crataegus species. Hawthorn, which is commonly used as a traditional Chinese medicine, is one of the most popular sour fruits and has high economic value. Crataegus pinnatifida var. pinnatifida and C. pinnatifida var. major are frequently adulterated with other Crataegus species on the herbal medicine market. However, most Crataegus plants are difficult to identify using traditional morphological methods. Here, we compared five Crataegus chloroplast (CP) genomes comprising two newly sequenced (i.e., C. pinnatifida var. pinnatifida and C. pinnatifida var. major) and three previously published CP genomes. The CP genomes of the five Crataegus species had a conserved genome structure, gene content and codon usage. The total length of the CP genomes was 159,654-159,865 bp. A total of 129-130 genes, including 84-85 protein-coding genes, 37 tRNA genes and 8 rRNA genes, were annotated. Bioinformatics analysis revealed 96-103 simple sequence repeats (SSRs) and 48-70 long repeats in the five CP genomes. Combining the results of mVISTA and nucleotide diversity, five highly variable regions were screened for species identification and relationship studies. Maximum likelihood trees were constructed on the basis of complete CP genome sequences and highly variable regions. The results showed that the former had higher discriminatory power for Crataegus species, indicating that the complete CP genome could be used as a super-barcode to accurately authenticate the five Crataegus species.
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Affiliation(s)
- Liwei Wu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yingxian Cui
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Qing Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Zhichao Xu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yu Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Yulin Lin
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Hui Yao
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China.
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30
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Traditional System Versus DNA Barcoding in Identification of Bamboo Species: A Systematic Review. Mol Biotechnol 2021; 63:651-675. [PMID: 34002354 DOI: 10.1007/s12033-021-00337-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe. It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology overcomes the challenges associated with traditional methods along with prospects for future research.
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31
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Wei X, Li X, Chen T, Chen Z, Jin Y, Malik K, Li C. Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae. FEBS Open Bio 2021; 11:1704-1718. [PMID: 33932143 PMCID: PMC8167873 DOI: 10.1002/2211-5463.13170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
This article reports the complete chloroplast genome of Achnatherum inebrians, a poisonous herb that is widely distributed in the rangelands of Northern China. The genome is 137 714 bp in total and consists of a large single‐copy (81 758 bp) region and small single‐copy (12 682 bp) region separated by a pair of inverted repeats (21 637 bp). The genome contains 130 genes, including 84 protein‐coding genes, 38 tRNA genes and 8 ribosomal RNA genes, and the guanine + cytosine content is 36.17%. We subsequently performed comparative analysis of complete genomes from A. inebrians and other Poaceae‐related species from GenBank. Thirty‐eight simple sequence repeats were identified, further demonstrating rapid evolution in Poaceae. Finally, the phylogenetic trees of 37 species of Poaceae and 2 species of Amaranthaceae were constructed by using maximum likelihood and Bayesian inference methods, based on the genes of the complete chloroplast genome. We identified hotspots that can be used as molecular markers and barcodes for phylogenetic analysis, as well as for species identification. Phylogenetic analysis indicated that A. inebrians is a member of the genus Stipa rather than Achnatherum.
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Affiliation(s)
- Xuekai Wei
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Xiuzhang Li
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Taixiang Chen
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Zhenjiang Chen
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Yuanyuan Jin
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Kamran Malik
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Chunjie Li
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
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32
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Liu Y, Su T, Peng M, Li J, Zhu X, Gou G, Dai Z. The complete chloroplast genome of Chimonobambusa hejiangensis (Poaceae: Arundinarieae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1285-1286. [PMID: 33855178 PMCID: PMC8018436 DOI: 10.1080/23802359.2021.1886007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Chimonobambusa hejiangensis is a kind of bamboo that has excellent edible and economic value, which is endemic to southwest China. The study used next-generation sequencing to obtain the complete chloroplast (cp) genome sequence of C. hejiangensis. The cp genome of C. hejiangensis has a total length of 138,908 bp, and consisted of an 82,495-bp large single-copy region, an 12,743-bp small single-copy region, and two 21,835-bp IR regions. In total, 112 unique genes were found in the cp genome, including 77 protein coding, 31 tRNA, and 4 rRNA genes. Phylogenetic analysis indicated that C.hejiangensis and C. tumidissinoda are sister species within the Arundinarieae genus, where Chimonocalamus and Ampelocalamus are more closely related to them.
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Affiliation(s)
- Yanjiang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China.,Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Ting Su
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China
| | - MaiMai Peng
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China.,Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Jiaxue Li
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China.,Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Xiao Zhu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China.,Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Guangqian Gou
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, Guizhou Province, China.,Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Zhaoxia Dai
- Bamboo Research Institute, Guizhou University, Guiyang, China.,College of Forestry, Guizhou University, Guiyang, China
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33
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Wang R, Liu K, Zhang XJ, Chen WL, Qu XJ, Fan SJ. Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:638597. [PMID: 33841465 PMCID: PMC8030268 DOI: 10.3389/fpls.2021.638597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.
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Affiliation(s)
- Rong Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Kuan Liu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Xue-Jie Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Wen-Li Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Shou-Jin Fan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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34
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Ya-Ping H, Jie Z, Zhao-Yan Y, Jia-Jia L, Ming-Ye X, Qi-Rong G. The complete chloroplast genome of Phyllostachys heteroclada f. solida (Poaceae). Mitochondrial DNA B Resour 2021; 6:566-567. [PMID: 33628931 PMCID: PMC7889091 DOI: 10.1080/23802359.2021.1875904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Phyllostachys heteroclada f. solida is a precious wood-use bamboo resource, with almost solid stem. The complete chloroplast genome of the Phyllostachys heteroclada f. solida was the first time to assemble from Illumina pair-end sequencing data in this work. The total genome size of Phyllostachys heteroclada f. solida was 156,559 bp in length, containing a large single-copy (LSC) region of 89,200 bp, a small single-copy (SSC) region of 14,876 bp, and a pair of inverted repeat (IR) regions of 23,798 bp. The overall GC content of the genome was 36.12%, and the corresponding values of the LSC, SSC, and IR regions were 36.98, 33.15, and 44.22%, respectively. A total of 136 genes were annotated, including 88 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis results strongly supported that Phyllostachys heteroclada f. solida was closely related to Phyllostachys reticulate.
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Affiliation(s)
- Hu Ya-Ping
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhou Jie
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yu Zhao-Yan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Li Jia-Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xu Ming-Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Guo Qi-Rong
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,International Center of Bamboo and Rattan, Beijing, China
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35
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Li W, Shi C, Li K, Zhang QJ, Tong Y, Zhang Y, Wang J, Clark L, Gao LZ. Draft genome of the herbaceous bamboo Raddia distichophylla. G3-GENES GENOMES GENETICS 2021; 11:6066164. [PMID: 33585868 PMCID: PMC8022951 DOI: 10.1093/g3journal/jkaa049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/01/2020] [Indexed: 11/19/2022]
Abstract
Bamboos are important nontimber forest plants widely distributed in the tropical and subtropical regions of Asia, Africa, America, and Pacific islands. They comprise the Bambusoideae in the grass family (Poaceae), including approximately 1700 described species in 127 genera. In spite of the widespread uses of bamboo for food, construction, and bioenergy, the gene repertoire of bamboo still remains largely unexplored. Raddia distichophylla (Schrad. ex Nees) Chase, belonging to the tribe Olyreae (Bambusoideae, Poaceae), is a diploid herbaceous bamboo with only slightly lignified stems. In this study, we report a draft genome assembly of the ∼589 Mb whole-genome sequence of R. distichophylla with a contig N50 length of 86.36 Kb. Repeat sequences account for ∼49.08% of the genome assembly, of which LTR retrotransposons occupy ∼35.99% of the whole genome. A total of 30,763 protein-coding genes were annotated in the R. distichophylla genome with an average transcript size of 2887 bp. Access to this herbaceous bamboo genome sequence will provide novel insights into biochemistry, molecular marker-assisted breeding programs, and germplasm conservation for bamboo species worldwide.
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Affiliation(s)
- Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Cong Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Kui Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Qun-Jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Jun Wang
- Institution of Sustainable Development, Southwest China Forestry University, Kunming 650224, China
| | - Lynn Clark
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011-1020, USA
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
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36
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Yu Z, Linying Z, Tao W, Guofu C, Yifeng H, Jinjun Y. The complete chloroplast genome of Phyllostachys angusta McClure (Poaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:187-188. [PMID: 33537438 PMCID: PMC7832504 DOI: 10.1080/23802359.2020.1860703] [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: 11/21/2022]
Abstract
Phyllostachys angusta McClure is a precious wood-use bamboo resource, with almost straight stem. The complete chloroplast genome of the P. angusta McClure was assembled for the first time from Illumina pair-end sequencing data in this work. The total genome size of P. angusta McClure was 139,678 bp in length, containing a large single-copy (LSC) region of 83,212 bp, a small single-copy (SSC) region of 12,870 bp, and a pair of inverted repeat (IR) regions of 21,798 bp. The overall GC content of the genome was 38.89%, and the corresponding values of the LSC, SSC, and IR regions were 36.97, 33.17, and 44.22%, respectively. A total of 131 genes were annotated, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis results strongly supported that P. angusta McClure was closely related to P. reticulate.
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Affiliation(s)
- Zheng Yu
- East China Inventory and Planning Institute of National Forestry and Grassland Administration, Hangzhou, China
| | - Zhao Linying
- East China Inventory and Planning Institute of National Forestry and Grassland Administration, Hangzhou, China
| | - Wang Tao
- East China Inventory and Planning Institute of National Forestry and Grassland Administration, Hangzhou, China
| | - Chen Guofu
- East China Inventory and Planning Institute of National Forestry and Grassland Administration, Hangzhou, China
| | - Hong Yifeng
- East China Inventory and Planning Institute of National Forestry and Grassland Administration, Hangzhou, China
| | - Yue Jinjun
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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37
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Yang W, Zou J, Yu Y, Long W, Li S. Repeats in mitochondrial and chloroplast genomes characterize the ecotypes of the Oryza. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:7. [PMID: 37309528 PMCID: PMC10236085 DOI: 10.1007/s11032-020-01198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/28/2020] [Indexed: 06/14/2023]
Abstract
Mitochondria and chloroplast are very important organelles for organism, participating in basic life activity. Their genomes contain many repeats which can lead to a variation of genome structure. Oryza is an important genus for human beings' nutrition. Several mitochondrial and chloroplast genomes of Oryza have been sequenced, which help us to insight the distribution and evolution of the repeats in Oryza species. In this paper, we compared six mitochondrial and 13 chloroplast genomes of Oryza and found that the structures of mitochondrial genomes were more diverse than chloroplast genomes. Since repeats can change the structure of the genome, resulting in the structural diversity of the genome, we analyzed all repeats and found 31 repeats in mitochondrial and 13 repeats in chloroplast genomes. Further, we developed 21 pairs of MRS molecular markers and 12 pairs of CRS molecular markers based on mitochondrial repeats and chloroplast repeats, respectively. These molecular markers can be used to detect the repeat-mediated recombination in Oryza mitochondrial and chloroplast genomes by PCR or fluorescence quantification. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-020-01198-6.
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Affiliation(s)
- Weilong Yang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Jianing Zou
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Yajie Yu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Weixiong Long
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072 China
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38
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Chloroplast-based DNA barcode analysis indicates high discriminatory potential of matK locus in Himalayan temperate bamboos. 3 Biotech 2020; 10:534. [PMID: 33214981 DOI: 10.1007/s13205-020-02508-7] [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: 07/07/2020] [Accepted: 10/24/2020] [Indexed: 10/23/2022] Open
Abstract
The study was conducted to evaluate the discriminatory potential of selected chloroplast-based DNA barcode regions for identifying and resolving phylogeny of the Indian bamboos. Among 11 chloroplast markers screened, only four, namely matK, rbcL, psbK-I and rps16-trnQ showed successful amplification in 88 genotypes of 30 Indian bamboo taxa under Bambuseae and Arundinarieae tribes. A total of 244 sequences were generated for the four chloroplast regions. Tree-based analysis demonstrated that none of the tested regions successfully discriminated the taxa under Bambuseae tribe. Importantly, our highly concerned Himalayan temperate bamboo species under Arundinarieae tribe, were successfully discriminated by matK locus with high bootstrap support (>60%). Sequence comparisons revealed that the discriminatory power demonstrated by matK region actually lies in the few unique fixed nucleotides (UFNs) despite the overall DNA polymorphism. Although, rps16-trnQ region was found to be the most polymorphic and revealed high genetic divergence among different taxonomic levels, it could not successfully discriminated the taxa with strong statistical support. In a taxonomically difficult plant group like bamboos, whose genome is relatively more complex and has a slow rate of molecular evolution, it is difficult to get a universal marker. Further, highly variable barcode regions utilized in other species may not be informative, and thus, the development of DNA barcodes for different taxonomic levels, such as lineages or tribes could be a viable approach.
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Ren T, Li ZX, Xie DF, Gui LJ, Peng C, Wen J, He XJ. Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships. BMC PLANT BIOLOGY 2020; 20:519. [PMID: 33187470 PMCID: PMC7663912 DOI: 10.1186/s12870-020-02696-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/12/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. RESULTS Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. CONCLUSION The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.
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Affiliation(s)
- Ting Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zi-Xuan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ling-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang Peng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jun Wen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Wu L, Nie L, Xu Z, Li P, Wang Y, He C, Song J, Yao H. Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Paeonia Section Moutan Species (Paeoniaceae). Front Genet 2020; 11:980. [PMID: 33193580 PMCID: PMC7533573 DOI: 10.3389/fgene.2020.00980] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/03/2020] [Indexed: 01/06/2023] Open
Abstract
Analysis of the relationships among wild species of section Moutan in the plant genus Paeonia has traditionally been problematic. Interspecies relationships cannot be effectively determined using phenotypic traits alone or through analysis of nuclear or chloroplast DNA fragments. Elucidation of complete chloroplast genome sequences will aid the identification and phylogeny of these species. In this study, the complete chloroplast genomes of three sect. Moutan plants were sequenced and analyzed. Comparative and phylogenetic analyses of the complete chloroplast genomes of all eight species of sect. Moutan were then conducted. The three complete chloroplast genomes gained in this study showed four-part annular structures, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. There was greater variation in the noncoding regions of the sequences than in the conserved protein-coding regions. Sequence variations in the small single copy (SSC) regions and large single copy (LSC) regions were considerably greater than those in the inverted repeat (IR) regions. Phylogenetic analysis revealed that the species of sect. Moutan clustered in one branch and then subdivided into smaller branches. As for the three complete chloroplast genome sequences obtained in this study, Paeonia jishanensis clustered with another P. jishanensis sequence from the GenBank database, Paeonia qiui clustered with Paeonia rockii, and Paeonia delavayi var. lutea clustered with Paeonia ludlowii. It was also found that the complete chloroplast genomes, LSC regions, and SSC regions all showed great abilities in identification and phylogenetic analysis of the species of sect. Moutan, while IRs regions and highly variable regions were not suitable for the species of sect. Moutan.
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Affiliation(s)
- Liwei Wu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Liping Nie
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Zhichao Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Pei Li
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Chunnian He
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Hui Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
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Sharpe RM, Williamson-Benavides B, Edwards GE, Dhingra A. Methods of analysis of chloroplast genomes of C 3, Kranz type C 4 and Single Cell C 4 photosynthetic members of Chenopodiaceae. PLANT METHODS 2020; 16:119. [PMID: 32874195 PMCID: PMC7457496 DOI: 10.1186/s13007-020-00662-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis, and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. RESULTS Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C3, Kranz type C4 and single cell C4 (SSC4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. CONCLUSIONS This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.
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Affiliation(s)
- Richard M. Sharpe
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Bruce Williamson-Benavides
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
| | - Gerald E. Edwards
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
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Hishamuddin MS, Lee SY, Ng WL, Ramlee SI, Lamasudin DU, Mohamed R. Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships. Sci Rep 2020; 10:13034. [PMID: 32747724 PMCID: PMC7400740 DOI: 10.1038/s41598-020-70030-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/17/2020] [Indexed: 11/28/2022] Open
Abstract
Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
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Affiliation(s)
- Muhammad Syahmi Hishamuddin
- Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Shiou Yih Lee
- Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900, Sepang, Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Dhilia Udie Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Rozi Mohamed
- Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
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Rossarolla MD, Tomazetti TC, Vieira LN, Guerra MP, Klabunde GHF, Scherer RF, Pescador R, Nodari RO. Identification and characterization of SSR markers of Guadua chacoensis (Rojas) Londoño & P.M. Peterson and transferability to other bamboo species. 3 Biotech 2020; 10:273. [PMID: 32523867 DOI: 10.1007/s13205-020-02268-4] [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: 01/30/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022] Open
Abstract
The aim of this study was to develop simple sequence repeat (SSR) markers for genetic studies on G. chacoensis, as well as to evaluate their transferability to other bamboo species. Genomic DNA was isolated from G. chacoensis and its partial sequencing was used to find SSR loci. The obtained sequencing data were de novo assembled using the software CLC Genomics Workbench® 8.0v. The SSR loci primers were identified and designed with the software SSRLocator. The selected markers were validated using 56 plants sampled in seven populations from southern Brazil. The markers with potential polymorphism were selected and fluorescently labeled for characterization by capillary electrophoresis. In total, 92 SSR loci were found in G. chacoensis contigs. Suitable primers were designed for 70 SSR loci, and the remaining 22 SSR loci did not have sequences for primer development. Out of 35 selected SSR markers, after PCR optimization, 10 with high polymorphism potential were characterized. These loci can be used in genetic analyses of G. chacoensis and all of them were successfully transferred to other bamboo species. Non-polymorphic loci require further tests with additional plants, from different populations, to identify possibilities of their use.
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Affiliation(s)
- Márcia D Rossarolla
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
| | - Tiago C Tomazetti
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
| | - Leila N Vieira
- Programa de Pós-Graduação em Botânica, Universidade Federal do Paraná, Av. Cel. Francisco H. dos Santos, 100, Curitiba, Paraná 81531-980 Brazil
| | - Miguel P Guerra
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
- Programa de Pós-graduação em Ecossistemas Agrícolas e Naturais, Universidade Federal de Santa Catarina, Campus Curitibanos, Rodovia Ulysses Gaboardi 3000, Curitibanos, Santa Catarina 89520-000 Brazil
| | - Gustavo H F Klabunde
- Estação Experimental de Itajaí, Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Rodovia Antônio Heil, n°6800, Itajaí, Santa Catarina 88318-112 Brazil
| | - Ramon F Scherer
- Estação Experimental de Itajaí, Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Rodovia Antônio Heil, n°6800, Itajaí, Santa Catarina 88318-112 Brazil
| | - Rosete Pescador
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
| | - Rubens O Nodari
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
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Ślipiko M, Myszczyński K, Buczkowska K, Bączkiewicz A, Szczecińska M, Sawicki J. Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes. BMC PLANT BIOLOGY 2020; 20:243. [PMID: 32466772 PMCID: PMC7257191 DOI: 10.1186/s12870-020-02435-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 05/10/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification. RESULTS On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%. CONCLUSIONS This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data.
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Affiliation(s)
- Monika Ślipiko
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Buczkowska
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Alina Bączkiewicz
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae). Mol Phylogenet Evol 2020; 146:106758. [DOI: 10.1016/j.ympev.2020.106758] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 11/19/2022]
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Armijos Carrion AD, Hinsinger DD, Strijk JS. ECuADOR-Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines. PeerJ 2020; 8:e8699. [PMID: 32292644 PMCID: PMC7147433 DOI: 10.7717/peerj.8699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/06/2020] [Indexed: 11/25/2022] Open
Abstract
Background With the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardized metadata curation approaches have become increasingly critical for the post-processing stages of biological data. Especially in organelle-based studies using circular chloroplast genome datasets, the assembly of the main structural regions in random order and orientation represents a major limitation in our ability to easily generate “ready-to-align” datasets for phylogenetic reconstruction, at both small and large taxonomic scales. In addition, current practices discard the most variable regions of the genomes to facilitate the alignment of the remaining coding regions. Nevertheless, no software is currently available to perform curation to such a degree, through simple detection, organization and positioning of the main plastome regions, making it a time-consuming and error-prone process. Here we introduce a fast and user friendly software ECuADOR, a Perl script specifically designed to automate the detection and reorganization of newly assembled plastomes obtained from any source available (NGS, sanger sequencing or assembler output). Methods ECuADOR uses a sliding-window approach to detect long repeated sequences in draft sequences, which then identifies the inverted repeat regions (IRs), even in case of artifactual breaks or sequencing errors and automates the rearrangement of the sequence to the widely used LSC–Irb–SSC–IRa order. This facilitates rapid post-editing steps such as creation of genome alignments, detection of variable regions, SNP detection and phylogenomic analyses. Results ECuADOR was successfully tested on plant families throughout the angiosperm phylogeny by curating 161 chloroplast datasets. ECuADOR first identified and reordered the central regions (LSC–Irb–SSC–IRa) for each dataset and then produced a new annotation for the chloroplast sequences. The process took less than 20 min with a maximum memory requirement of 150 MB and an accuracy of over 99%. Conclusions ECuADOR is the sole de novo one-step recognition and re-ordination tool that provides facilitation in the post-processing analysis of the extra nuclear genomes from NGS data. The program is available at https://github.com/BiodivGenomic/ECuADOR/.
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Affiliation(s)
- Angelo D Armijos Carrion
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Damien D Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China.,Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | - Joeri S Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China.,Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, PR China
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Su Q, Liu L, Zhao M, Zhang C, Zhang D, Li Y, Li S. The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference. PeerJ 2020; 8:e8678. [PMID: 32181055 PMCID: PMC7060751 DOI: 10.7717/peerj.8678] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/03/2020] [Indexed: 11/20/2022] Open
Abstract
The D genome progenitor of bread wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14), which is naturally distributed in Central Eurasia, ranging from northern Syria and Turkey to western China, is considered a potential genetic resource for improving bread wheat. In this study, the chloroplast (cp) genomes of 17 Ae. tauschii accessions were reconstructed. The cp genome sizes ranged from 135,551 bp to 136,009 bp and contained a typical quadripartite structure of angiosperms. Within these genomes, we identified a total of 124 functional genes, including 82 protein-coding genes, 34 transfer RNA genes and eight ribosomal RNA genes, with 17 duplicated genes in the IRs. Although the comparative analysis revealed that the genomic structure (gene order, gene number and IR/SC boundary regions) is conserved, a few variant loci were detected, predominantly in the non-coding regions (intergenic spacer regions). The phylogenetic relationships determined based on the complete genome sequences were consistent with the hypothesis that Ae. tauschii populations in the Yellow River region of China originated in South Asia not Xinjiang province or Iran, which could contribute to more effective utilization of wild germplasm resources. Furthermore, we confirmed that Ae. tauschii was derived from monophyletic speciation rather than hybrid speciation at the cp genome level. We also identified four variable genomic regions, rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20, showing high levels of nucleotide polymorphisms, which may accordingly prove useful as cpDNA markers in studying the intraspecific genetic structure and diversity of Ae. tauschii.
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Affiliation(s)
- Qing Su
- Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, China
| | - Luxian Liu
- Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, China
| | - Mengyu Zhao
- Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, China
| | - Cancan Zhang
- Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, China
| | - Dale Zhang
- Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, China
| | - Youyong Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Suoping Li
- Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, China
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49
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Asaf S, Khan AL, Lubna, Khan A, Khan A, Khan G, Lee IJ, Al-Harrasi A. Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata. Sci Rep 2020; 10:3881. [PMID: 32127603 PMCID: PMC7054531 DOI: 10.1038/s41598-020-60803-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
Plantago ovata (Plantaginaceae) is an economically and medicinally important species, however, least is known about its genomics and evolution. Here, we report the first complete plastome genome of P. ovata and comparison with previously published genomes of related species from Plantaginaceae. The results revealed that P. ovata plastome size was 162,116 bp and that it had typical quadripartite structure containing a large single copy region of 82,084 bp and small single copy region of 5,272 bp. The genome has a markedly higher inverted repeat (IR) size of 37.4 kb, suggesting large-scale inversion of 13.8 kb within the expanded IR regions. In addition, the P. ovata plastome contains 149 different genes, including 43 tRNA, 8 rRNA, and 98 protein-coding genes. The analysis revealed 139 microsatellites, of which 71 were in the non-coding regions. Approximately 32 forward, 34 tandem, and 17 palindromic repeats were detected. The complete genome sequences, 72 shared genes, matK gene, and rbcL gene from related species generated the same phylogenetic signals, and phylogenetic analysis revealed that P. ovata formed a single clade with P. maritima and P. media. The divergence time estimation as employed in BEAST revealed that P. ovata diverged from P. maritima and P. media about 11.0 million years ago (Mya; 95% highest posterior density, 10.06-12.25 Mya). In conclusion, P. ovata had significant variation in the IR region, suggesting a more stable P. ovata plastome genome than that of other Plantaginaceae species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Adil Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Oldenburg, Germany
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
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50
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Wang W, Chen S, Guo W, Li Y, Zhang X. Tropical plants evolve faster than their temperate relatives: a case from the bamboos (Poaceae: Bambusoideae) based on chloroplast genome data. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1773312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Wencai Wang
- Molecular Genetics Group, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China
- Molecular Genetics Group, Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China
| | - Siyun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan Province, PR China
| | - Wei Guo
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, PR China
| | - Yongquan Li
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, PR China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, PR China
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