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Sebastin R, Kim J, Jo IH, Yu JK, Jang W, Han S, Park HS, AlGarawi AM, Hatamleh AA, So YS, Shim D, Chung JW. Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny. BMC PLANT BIOLOGY 2024; 24:797. [PMID: 39179978 PMCID: PMC11344449 DOI: 10.1186/s12870-024-05513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
The chloroplast (cp.) genome, also known as plastome, plays crucial roles in plant survival, adaptation, and evolution. The stable genetic structure of cp. genomes provides an ideal system for investigating species evolution. We sequenced three complete cp. genome sequences of Capsicum species and analyzed them using sequences of various Capsicum species retrieved from the NCBI database. The cp. genome of Capsicum species maintains a well-preserved quadripartite structure consisting of two inverted repeats (IRs) flanked by a large single copy (LSC) region and a small single copy (SSC) region. The sizes of cp. genome sequences ranged from 156,583 bp (C. lycianthoides) to 157,390 bp (C.pubescens). A total of 127-132 unique genes, including 83-87 protein-coding, 36-37 tRNA, and eight rRNA genes, were predicted. Comparison of cp. genomes of 10 Capsicum species revealed high sequence similarity in genome-wide organization and gene arrangements. Fragments of trnT-UGU/trnL-UAA, ccsA, ndhD, rps12, and ycf1 were identified as variable regions, and nucleotide variability of LSC and SSC was higher than that of IR. Phylogenetic speciation analysis showed that the major domesticated C. annuum species were the most extensively divergent species and closely related to C. tovarii and C. frutescens. Analysis of divergent times suggested that a substantial range of speciation events started occurring ~ 25.79 million years ago (Mya). Overall, comparative analysis of cp. genomes of Capsicum species not only offers new insights into their genetic variation and phylogenetic relationships, but also lays a foundation for evolutionary history, genetic diversity, conservation, and biological breeding of Capsicum species.
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Affiliation(s)
- Raveendar Sebastin
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jaewook Kim
- Department of Biology Education, Korea National University of Education, Cheongju, 28173, Republic of Korea
| | - Ick-Hyun Jo
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ju-Kyung Yu
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Woojong Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, 58245, Republic of Korea
| | - Seahee Han
- Honam National Institute of Biological Resources, Mokpo, 58762, Republic of Korea
| | - Hyun-Seung Park
- Department of Integrative Biological Sciences and Industry, Convergence Research Center for Natural Products, Sejong University, Seoul, 05006, Republic of Korea
| | - Amal Mohamed AlGarawi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Donghwan Shim
- Department of Biological Science, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Zhu J, Huang Y, Chai W, Xia P. Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights. Int J Mol Sci 2024; 25:8290. [PMID: 39125860 PMCID: PMC11312916 DOI: 10.3390/ijms25158290] [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: 05/25/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.
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Affiliation(s)
- Junqiao Zhu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Weiguo Chai
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China;
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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Wang J, Kan S, Liao X, Zhou J, Tembrock LR, Daniell H, Jin S, Wu Z. Plant organellar genomes: much done, much more to do. TRENDS IN PLANT SCIENCE 2024; 29:754-769. [PMID: 38220520 DOI: 10.1016/j.tplants.2023.12.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6000-6999, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Marine College, Shandong University, Weihai, 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiawei Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104-6030, USA.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Wang J, Kan J, Wang J, Yan X, Li Y, Soe T, Tembrock LR, Xing G, Li S, Wu Z, Jia M. The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history. FRONTIERS IN PLANT SCIENCE 2024; 15:1404071. [PMID: 38887455 PMCID: PMC11181306 DOI: 10.3389/fpls.2024.1404071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Backgrounds Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated. Methods We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes. Results The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved. Conclusion This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.
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Affiliation(s)
- Jie Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junhu Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xinlin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yi Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Thida Soe
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Zhiqiang Wu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Minlong Jia
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Jia M, Wang J, Cao D, Jiang C, Li W, Tembrock LR, Xing G, Li S, Wu Z. The pan-plastome of Hemerocallis citrina reveals new insights into the genetic diversity and cultivation history of an economically important food plant. BMC PLANT BIOLOGY 2024; 24:44. [PMID: 38200455 PMCID: PMC10782787 DOI: 10.1186/s12870-023-04668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Hemerocallis citrina Baroni (Huang hua cai in Chinese) is a perennial herbaceous plant grown for its flower buds that are eaten fresh or dried and is known as the vegetarian three treasures. The nuclear genome of H. citrina has been reported, but the intraspecific variation of the plastome (plastid genome) has not yet been studied. Therefore, the panplastome of this species collected from diverse locations is reported here for the first time. RESULTS In this study, 65 H. citrina samples were resequenced, de novo assembled, and aligned with the published plastome of H. citrina to resolve the H. citrina panplastome. The sizes of the 65 newly assembled complete plastomes of H. citrina ranged from 156,048 bp to 156,263 bp, and the total GC content ranged from 37.31 to 37.34%. The structure of the complete plastomes showed a typical tetrameric structure, including a large single copy (LSC), a small single copy (SSC), and a pair of inverted repeat regions (IRA and IRB). Many nucleotide variants were identified between plastomes, among which the variants in the intergenic spacer region were the most abundant, with the highest number of variants concentrated in the LSC region. Based on the phylogenetic tree constructed using the ML method, population structure analysis, and principal component analysis (PCA), the panplastome data were subdivided into five genetic clusters. The C5 genetic cluster was mostly represented by samples from Qidong, Hunan Province, while samples from Shanxi and Shaanxi Provinces were classified into the C4 genetic cluster. The greatest genetic diversity was found in the C1 genetic cluster, and the greatest genetic distance between any two clusters was found between the C4 and C5 clusters. CONCLUSION The resolution of the panplastome and the analysis of the population structure of H. citrina plastomes provide important data for future breeding projects and germplasm preservation.
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Affiliation(s)
- Minlong Jia
- College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6000-6999, Australia
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Dongmei Cao
- College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China.
| | - Congrong Jiang
- College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80525, USA
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China.
| | - Zhiqiang Wu
- College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
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Han B, Tong B, Zhang J, Bu Z, Zhao L, Xian Y, Li D, Xie X. Genomic divergence and demographic history of Quercus aliena populations. BMC PLANT BIOLOGY 2024; 24:39. [PMID: 38195447 PMCID: PMC10775429 DOI: 10.1186/s12870-023-04623-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND Quercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species' population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q. aliena individuals. RESULTS The whole chloroplast and nuclear genomes were used for this study. Phylogenetic analysis using the chloroplast genome dataset supported four clades of Q. aliena, while the nuclear dataset supported three major clades. Sex-biased dispersal had a critical role in causing discordance between the chloroplast and nuclear genomes. Population structure analysis showed two groups in Q. aliena. The effective population size sharply declined 1 Mya, coinciding with the Poyang Glaciation in Eastern China. Using genotype-climate association analyses, we found a positive correlation between allele frequency variation in SNPs and temperature, suggesting the species has the capacity to adapt to changing temperatures. CONCLUSION Overall, this study illustrates the genetic divergence, genomic variation, and evolutionary processes behind the demographic history of Q. aliena.
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Affiliation(s)
- Biao Han
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Boqiang Tong
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Jiliang Zhang
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Ziheng Bu
- School of Life Sciences, Shandong University, Qingdao, 266237, Shandong, China
| | - Lijun Zhao
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Yang Xian
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China
| | - Dezhu Li
- 3Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xiaoman Xie
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji'nan, 250102, Shandong, China.
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Alshegaihi RM. The complete chloroplast genome of the halophyte flowering plant Suaeda monoica from Jeddah, Saudi Arabia. Mol Biol Rep 2024; 51:60. [PMID: 38165474 DOI: 10.1007/s11033-023-09069-x] [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: 06/27/2023] [Accepted: 10/11/2023] [Indexed: 01/03/2024]
Abstract
The complete chloroplast genome (plastome) of the annual flowering halophyte herb Suaeda monoica Forssk. ex J. F. Gmel. family (Amaranthaceae) that grows in Jeddah, Saudi Arabia, was identified for the first time in this study. Suaeda monoica is a medicinal plant species whose taxonomic classification remains controversial. Further, studying the species is useful for current conservation and management efforts. In the current study, the full chloroplast genome S. monoica was reassembled using whole-genome next-generation sequencing and compared with the previously published chloroplast genomes of Suaeda species. The chloroplast genome size of Suaeda monoica was 151,789 bp, with a single large copy of 83,404 bp, a small single copy of 18,007 bp and two inverted repeats regions of 25,189 bp. GC content in the whole genome was 36.4%. The cp genome included 87 genes that coded for proteins, 37 genes coding for tRNA, 8 genes coding for rRNA and one non-coding pseudogene. Five chloroplast genome features were compared between S. monoica and S. japonica, S. glauca, S. salsa, S. malacosperma and S. physophora. Among Suaeda genus and equal to most angiosperms chloroplast genomes, the RSCU values were conservative. Two pseudogenes (accD and ycf1), rpl16 intron and ndhF-rpl32 intergenic spacer, were highlighted as suitable DNA barcodes for different Suaeda species. Phylogenetic analyses show Suaeda cluster into three main groups; one in which S. monoica was closer to S. salsa. The obtained result provided valuable information on the characteristics of the S. monoica chloroplast genome and the phylogenetic relationships.
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Affiliation(s)
- Rana M Alshegaihi
- Department of Biological Sciences, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
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Abd El Moneim D, Mansour H, Alshegaihi RM, Safhi FA, Alwutayd KM, Alshamrani R, Alamri A, Felembam W, Abuzaid AO, Magdy M. Evolutionary insights and expression dynamics of the CaNFYB transcription factor gene family in pepper ( Capsicum annuum) under salinity stress. Front Genet 2023; 14:1288453. [PMID: 38028611 PMCID: PMC10652888 DOI: 10.3389/fgene.2023.1288453] [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: 09/04/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: The Capsicum annuum nuclear factor Y subunit B (CaNFYB) gene family plays a significant role in diverse biological processes, including plant responses to abiotic stressors such as salinity. Methods: In this study, we provide a comprehensive analysis of the CaNFYB gene family in pepper, encompassing their identification, structural details, evolutionary relationships, regulatory elements in promoter regions, and expression profiles under salinity stress. Results and discussion: A total of 19 CaNFYB genes were identified and subsequently characterized based on their secondary protein structures, revealing conserved domains essential for their functionality. Chromosomal distribution showed a non-random localization of these genes, suggesting potential clusters or hotspots for NFYB genes on specific chromosomes. The evolutionary analysis focused on pepper and comparison with other plant species indicated a complex tapestry of relationships with distinct evolutionary events, including gene duplication. Moreover, promoter cis-element analysis highlighted potential regulatory intricacies, with notable occurrences of light-responsive and stress-responsive binding sites. In response to salinity stress, several CaNFYB genes demonstrated significant temporal expression variations, particularly in the roots, elucidating their role in stress adaptation. Particularly CaNFYB01, CaNFYB18, and CaNFYB19, play a pivotal role in early salinity stress response, potentially through specific regulatory mechanisms elucidated by their cis-elements. Their evolutionary clustering with other Solanaceae family members suggests conserved ancestral functions vital for the family's survival under stress. This study provides foundational knowledge on the CaNFYB gene family in C. annuum, paving the way for further research to understand their functional implications in pepper plants and relative species and their potential utilization in breeding programs to enhance salinity tolerance.
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Affiliation(s)
- Diaa Abd El Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Hassan Mansour
- Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Rahma Alshamrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amnah Alamri
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wessam Felembam
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amani Omar Abuzaid
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmoud Magdy
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
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Alshegaihi RM, Alshamrani SM. Genome-wide identification of CaARR-Bs transcription factor gene family in pepper and their expression patterns under salinity stress. PeerJ 2023; 11:e16332. [PMID: 37927789 PMCID: PMC10625354 DOI: 10.7717/peerj.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
In plants, ARRs-B transcription factors play a crucial role in regulating cytokinin signal transduction, abiotic stress resistance, and plant development. A number of adverse environmental conditions have caused severe losses for the pepper (Capsicum annuum L.)-a significant and economically important vegetable. Among the transcription factors of the type B-ARRs family, multiple members have different functions. In pepper, only a few members of the ARRs-B family have been reported and characterized. The current study aimed to characterize ARRs-B transcription factors in C. annuum, including phylogenetic relationships, gene structures, protein motif arrangement, and RT-qPCR expression analyses and their role in salinity stress. In total, ten genes encode CaARRs-B transcription factors (CaARR1 to CaARR10) from the largest subfamily of type-B ARRs were identified in C. annum. The genome-wide analyses of the CaARRs-B family in C. annuum were performed based on the reported ARRs-B genes in Arabidopsis. An analysis of homologous alignments of candidate genes, including their phylogenetic relationships, gene structures, conserved domains, and qPCR expression profiles, was conducted. In comparison with other plant ARRs-B proteins, CaARRs-B proteins showed gene conservation and potentially specialized functions. In addition, tissue-specific expression profiles showed that CaARRs-B genes were differentially expressed, suggesting functionally divergent. CaARRs-B proteins had a typical conserved domain, including AAR-like (pfam: PF00072) and Myb DNA binding (pfam: PF00249) domains. Ten of the CaARRs-B genes were asymmetrically mapped on seven chromosomes in Pepper. Additionally, the phylogenetic tree of CaARRs-B genes from C. annuum and other plant species revealed that CaARRs-B genes were classified into four clusters, which may have evolved conservatively. Further, using quantitative real-time qRT-PCR, the study assessed the expression patterns of CaARRs-B genes in Capsicum annuum seedlings subjected to salt stress. The study used quantitative real-time qRT-PCR to examine CaARRs-B gene expression in Capsicum annuum seedlings under salt stress. Roots exhibited elevated expression of CaARR2 and CaARR9, while leaves showed decreased expression for CaARR3, CaARR4, CaARR7, and CaARR8. Notably, no amplification was observed for CaARR10. This research sheds light on the roles of CaARRs-B genes in pepper's response to salinity stress. These findings enrich our comprehension of the functional implications of CaARRs-B genes in pepper, especially in responding to salinity stress, laying a solid groundwork for subsequent in-depth studies and applications in the growth and development of Capsicum annuum.
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Affiliation(s)
- Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
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Wang J, Liao X, Li Y, Ye Y, Xing G, Kan S, Nie L, Li S, Tembrock LR, Wu Z. Comparative Plastomes of Curcuma alismatifolia (Zingiberaceae) Reveal Diversified Patterns among 56 Different Cut-Flower Cultivars. Genes (Basel) 2023; 14:1743. [PMID: 37761883 PMCID: PMC10531169 DOI: 10.3390/genes14091743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Curcuma alismatifolia (Zingiberaceae) is an ornamental species with high economic value due to its recent rise in popularity among floriculturists. Cultivars within this species have mixed genetic backgrounds from multiple hybridization events and can be difficult to distinguish via morphological and histological methods alone. Given the need to improve identification resources, we carried out the first systematic study using plastomic data wherein genomic evolution and phylogenetic relationships from 56 accessions of C. alismatifolia were analyzed. The newly assembled plastomes were highly conserved and ranged from 162,139 bp to 164,111 bp, including 79 genes that code for proteins, 30 tRNA genes, and 4 rRNA genes. The A/T motif was the most common of SSRs in the assembled genomes. The Ka/Ks values of most genes were less than 1, and only two genes had Ka/Ks values above 1, which were rps15 (1.15), and ndhl (1.13) with petA equal to 1. The sequence divergence between different varieties of C. alismatifolia was large, and the percentage of variation in coding regions was lower than that in the non-coding regions. Such data will improve cultivar identification, marker assisted breeding, and preservation of germplasm resources.
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Affiliation(s)
- Jie Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (J.W.); (G.X.); (S.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Yongyao Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (J.W.); (G.X.); (S.L.)
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (J.W.); (G.X.); (S.L.)
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
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11
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Ibrahim AA, Alwutayd KM, Safhi FA, Alshegaihi RM, Alqurashi M, Alyamani A, Aloufi S, Alharthi B, Fayad E, Abd El-Moneim D. Characterization and comparative genomic analyses of complete chloroplast genome on Trema orientalis L. GENETIC RESOURCES AND CROP EVOLUTION 2023. [DOI: 10.1007/s10722-023-01678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/06/2023] [Indexed: 09/02/2023]
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Alshegaihi RM, Mansour H, Alrobaish SA, Al Shaye NA, Abd El-Moneim D. The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis. Genes (Basel) 2023; 14:genes14050976. [PMID: 37239336 DOI: 10.3390/genes14050976] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).
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Affiliation(s)
- Rana M Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hassan Mansour
- Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Shouaa A Alrobaish
- Department of Biology, College of Science, Qassim University, Buraydah 52377, Saudi Arabia
| | - Najla A Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
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Zhou J, He W, Wang J, Liao X, Xiang K, Ma M, Liu Z, Li Y, Tembrock LR, Wu Z, Liu L. The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence. BMC PLANT BIOLOGY 2023; 23:212. [PMID: 37088810 PMCID: PMC10123988 DOI: 10.1186/s12870-023-04218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated. RESULTS In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya. CONCLUSIONS The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.
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Affiliation(s)
- Jiawei Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- College of Science, Health, Engineering and Education, Murdoch University, Western Australia, Perth, 6150, Australia
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Kunli Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingchuan Ma
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Yongyao Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhiqiang Wu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
- College of Horticulture, Shanxi Agricultural University, Shanxi, 030801, China.
| | - Longlong Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China.
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China.
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Hu Y, Sun Y, Zhu QH, Fan L, Li J. Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years. Curr Genomics 2023; 23:369-384. [PMID: 37920556 PMCID: PMC10173419 DOI: 10.2174/1389202924666221201140603] [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: 05/16/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 12/11/2022] Open
Abstract
The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.
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Affiliation(s)
- Yiyu Hu
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yanqing Sun
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jianhua Li
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Fiteha YG, Rashed MA, Ali RAM, Magdy M. Characterization and phylogenetic analysis of the complete mitochondrial genome of Mango tilapia (Sarotherodon galilaeus: Cichlidae). Mol Biol Rep 2023; 50:3945-3950. [PMID: 36781609 PMCID: PMC10042889 DOI: 10.1007/s11033-023-08288-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/17/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Sarotherodon galilaeus (Linné, 1758) is a member of the family Cichlidae, which is considered the most important aquaculture freshwater species endemic to Africa and the Middle East. The genetics and molecular biology of this species are rare. This requires more comprehensive mitochondrial genomes-based phylogenetics to enhance understanding of the relationship and delineate this species. METHODS AND RESULTS Here, we assembled the complete mitogenome of S. galilaeus using Illumina high-throughput sequencing technology. The mango tilapia mitogenome was 16,631 bp in length with an AT composition of 53.4% and 46.4% GC content. It encodes 37 genes comprising two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 13 protein-coding genes (PCGs) as well as the D-loop known as the control region. The phylogenetic tree was conducted to provide a relationship within the haplotilapiine lineage based on the maximum likelihood method, and the newly sequenced S. galilaeus was clustered with other Sarotherodon species. CONCLUSION Our results provide a new perception of the genetic basis of S. galilaeus species for further research on systematics, evolution, population genetics, and molecular ecology.
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Affiliation(s)
- Yosur G Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Zoology Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - M A Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - R A M Ali
- Zoology Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - M Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
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Lu RS, Hu K, Zhang FJ, Sun XQ, Chen M, Zhang YM. Pan-Plastome of Greater Yam ( Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses. Int J Mol Sci 2023; 24:ijms24043341. [PMID: 36834753 PMCID: PMC9968032 DOI: 10.3390/ijms24043341] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I-IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC-petN, trnL-rpl32, ndhD-ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.
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Affiliation(s)
- Rui-Sen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ke Hu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Feng-Jiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Xiao-Qin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Min Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Correspondence:
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Du S, Hu X, Guo Y, Wang S, Yang X, Wu Z, Huang Y. A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube. AOB PLANTS 2023; 15:plad006. [PMID: 37025103 PMCID: PMC10071050 DOI: 10.1093/aobpla/plad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/17/2023] [Indexed: 06/19/2023]
Abstract
Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.
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Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoyan Hu
- College of Food Science and Technology, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yuanting Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shengji Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | | | - Zhenzhen Wu
- Taian Dushihuaxiang Agricultural Technology Co., Ltd, Taian, Shandong, China
| | - Yuyin Huang
- Shandong Huinongtianxia Science and Technology Information Consulting Co., Ltd, Taian, Shandong, China
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops. Sci Rep 2022; 12:21600. [PMID: 36517490 PMCID: PMC9751094 DOI: 10.1038/s41598-022-25434-5] [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: 07/01/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Vaccinium is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to misidentification of species. The availability of more genomic information could help achieve higher phylogenetic resolution for the genus, provide molecular markers for berry crops identification, and a framework for efficient genetic engineering of chloroplasts. Therefore, in this study we assembled five Vaccinium chloroplast sequences representing the economically relevant berry types: northern highbush blueberry (V. corymbosum), southern highbush blueberry (V. corymbosum hybrids), rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium), and bilberry (V. myrtillus). Comparative analyses showed that the Vaccinium chloroplast genomes exhibited an overall highly conserved synteny and sequence identity among them. Polymorphic regions included the expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, indels, and single nucleotide polymorphisms. Based on their in silico discrimination power, we suggested variants that could be developed into molecular markers for berry crops identification. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events that occurred during northern and southern highbush blueberry domestication.
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Han B, Zhang MJ, Xian Y, Xu H, Cui CC, Liu D, Wang L, Li DZ, Li WQ, Xie XM. Variations in genetic diversity in cultivated Pistacia chinensis. FRONTIERS IN PLANT SCIENCE 2022; 13:1030647. [PMID: 36438104 PMCID: PMC9691265 DOI: 10.3389/fpls.2022.1030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.
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Affiliation(s)
- Biao Han
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Ming-Jia Zhang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yang Xian
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Hui Xu
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Cheng-Cheng Cui
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Dan Liu
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Lei Wang
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen-Qing Li
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Xiao-Man Xie
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
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21
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Carrizo García C, Barboza GE, Palombo N, Weiss-Schneeweiss H. Diversification of chiles ( Capsicum, Solanaceae) through time and space: New insights from genome-wide RAD-seq data. Front Genet 2022; 13:1030536. [PMID: 36330443 PMCID: PMC9622771 DOI: 10.3389/fgene.2022.1030536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Capsicum L. encompasses 43 American species, including the five domesticated worldwide consumed sweet and hot chiles. This study presents new, updated and age-calibrated phylogenetic hypothesis on the genus evolution incorporating nearly all currently accepted Capsicum species. A new model of spatial diversification of Capsicum is proposed based on analyses of several thousands of genome-wide RAD-seq derived SNPs. Maximum likelihood approaches were used to reconstruct phylogenies and to estimate dates of all major splits. Ancestral ranges were inferred and diversification events were modeled in a time frame using a Bayesian approach. Nine clades corresponding to genetically and (mostly) geographically well-defined lineages, which diversified starting around mid-upper Miocene, were recovered with strong support. The Northern and Central Andes were inferred to represent the most likely ancestral range of the genus Capsicum. A few early vicariant and dispersal events were estimated to have driven the geographic divergence of the main Capsicum clades. Each lineage was inferred to have diversified within a distinct region of South America and expanded geographically to different extent. Extant species diversification was inferred to have begun at the beginning of Pliocene and continued through the Pleistocene. The Central Andes, represented mainly by the territory of present-day Bolivia, were proposed to play a central role in the diversification of lineages comprising domesticated capsicums and their wild allies. The genome-wide approach allowed for high resolution and support of deep phylogenetic nodes providing novel insights into the affinities of major lineages and clades as well as on the geographic expansion of Capsicum. This study provides the first dated evolutionary history of the genus encompassing most of the chile species diversity.
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Affiliation(s)
- Carolina Carrizo García
- Multidisciplinary Institute of Plant Biology, Cordoba, Argentina
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Nahuel Palombo
- Multidisciplinary Institute of Plant Biology, Cordoba, Argentina
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22
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Sandoval-Padilla I, Zamora-Tavares MDP, Ruiz-Sánchez E, Pérez-Alquicira J, Vargas-Ponce O. Characterization of the plastome of Physaliscordata and comparative analysis of eight species of Physalis sensu stricto. PHYTOKEYS 2022; 210:109-134. [PMID: 36760406 PMCID: PMC9836641 DOI: 10.3897/phytokeys.210.85668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/07/2022] [Indexed: 06/18/2023]
Abstract
In this study, we sequenced, assembled, and annotated the plastome of Physaliscordata Mill. and compared it with seven species of the genus Physalis sensu stricto. Sequencing, annotating, and comparing plastomes allow us to understand the evolutionary mechanisms associated with physiological functions, select possible molecular markers, and identify the types of selection that have acted in different regions of the genome. The plastome of P.cordata is 157,000 bp long and presents the typical quadripartite structure with a large single-copy (LSC) region of 87,267 bp and a small single-copy (SSC) region of 18,501 bp, which are separated by two inverted repeat (IRs) regions of 25,616 bp each. These values are similar to those found in the other species, except for P.angulata L. and P.pruinosa L., which presented an expansion of the LSC region and a contraction of the IR regions. The plastome in all Physalis species studied shows variation in the boundary of the regions with three distinct types, the percentage of the sequence identity between coding and non-coding regions, and the number of repetitive regions and microsatellites. Four genes and 10 intergenic regions show promise as molecular markers and eight genes were under positive selection. The maximum likelihood analysis showed that the plastome is a good source of information for phylogenetic inference in the genus, given the high support values and absence of polytomies. In the Physalis plastomes analyzed here, the differences found, the positive selection of genes, and the phylogenetic relationships do not show trends that correspond to the biological or ecological characteristics of the species studied.
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Affiliation(s)
- Isaac Sandoval-Padilla
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - María del Pilar Zamora-Tavares
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Eduardo Ruiz-Sánchez
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Jessica Pérez-Alquicira
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
- Laboratorio Nacional de Identificación y Caracterización Vegetal A(LaniVeg), Consejo Nacional de Ciencia y Tecnología (CONACyT), Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoCONACYTMexico CityMexico
| | - Ofelia Vargas-Ponce
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
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23
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Pandey A, Chaudhary S, Bhat B. The Potential Role of Plastome Copy Number as a Quality Biomarker for Plant Products using Real-time Quantitative Polymerase Chain Reaction. Curr Genomics 2022; 23:289-298. [PMID: 36777877 PMCID: PMC9875542 DOI: 10.2174/1389202923666220513111643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/28/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Plastids are plant-specific semi-autonomous self-replicating organelles, containing circular DNA molecules called plastomes. Plastids perform crucial functions, including photosynthesis, stress perception and response, synthesis of metabolites, and storage. The plastome and plastid numbers have been shown to be modulated by developmental stage and environmental stimuli and have been used as a biomarker (identification of plant species) and biosensor (an indicator of abiotic and biotic stresses). However, the determination of plastome sequence and plastid number is a laborious process requiring sophisticated equipment. Methods: This study proposes using plastome copy number (PCN), which can be determined rapidly by real-time quantitative polymerase chain reaction (RT-qPCR) as a plant product quality biomarker. This study shows that the PCN log10 and range PCN log10 values calculated from RT-qPCR data, which was obtained for two years from leaves and lint samples of cotton and seed samples of cotton, rice, soybean, maize, and sesame can be used for assessing the quality of the samples. Results: Observation of lower range PCN log10 values for CS (0.31) and CR (0.58) indicated that the PCN showed little variance from the mean PCN log10 values for CS (3.81) and CR (3.85), suggesting that these samples might have encountered ambient environmental conditions during growth and/ or post-harvest storage and processing. This conclusion was further supported by observation of higher range PCN log10 values for RS (3.09) versus RP (0.05), where rice seeds in the RP group had protective hull covering compared to broken hull-less seeds in the RS group. To further support that PCN is affected by external factors, rice seeds treated with high temperatures and pathogens exhibited lower PCN values when compared to untreated seeds. Furthermore, the range PCN log10 values were found to be high for cotton leaf (CL) and lint (Clt) sample groups, 4.11 and 3.63, respectively, where leaf and lint samples were of different sizes, indicating that leaf samples might be of different developmental stage and lint samples might have been processed differently, supporting that the PCN is affected by both internal and external factors, respectively. Moreover, PCN log10 values were found to be plant specific, with oil containing seeds such as SeS (6.49) and MS (5.05) exhibiting high PCN log10 values compared to non-oil seeds such as SS (1.96). Conclusion: In conclusion, it was observed that PCN log10 values calculated from RT-qPCR assays were specific to plant species and the range of PCN log10 values can be directly correlated to the internal and external factors and, therefore might be used as a potential biomarker for assessing the quality of plant products.
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Affiliation(s)
- Amita Pandey
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
| | - Shifa Chaudhary
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
| | - Binu Bhat
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
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24
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Sun J, Wang S, Wang Y, Wang R, Liu K, Li E, Qiao P, Shi L, Dong W, Huang L, Guo L. Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies ( Arnebia, Boraginaceae) in China. FRONTIERS IN PLANT SCIENCE 2022; 13:920826. [PMID: 35755641 PMCID: PMC9218939 DOI: 10.3389/fpls.2022.920826] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/11/2022] [Indexed: 05/03/2023]
Abstract
Arnebiae Radix is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of Arnebia in China, and the two species Arnebia euchroma and Arnebia guttata are the source plants of Arnebiae Radix according to the Chinese Pharmacopoeia. Molecular markers that permit species identification and facilitate studies of the genetic diversity and divergence of the wild populations of these two source plants have not yet been developed. Here, we sequenced the chloroplast genomes of 56 samples of five Arnebia species using genome skimming methods. The Arnebia chloroplast genomes exhibited quadripartite structures with lengths from 149,539 and 152,040 bp. Three variable markers (rps16-trnQ, ndhF-rpl32, and ycf1b) were identified, and these markers exhibited more variable sites than universal chloroplast markers. The phylogenetic relationships among the five Arnebia species were completely resolved using the whole chloroplast genome sequences. Arnebia arose during the Oligocene and diversified in the middle Miocene; this coincided with two geological events during the late Oligocene and early Miocene: warming and the progressive uplift of Tianshan and the Himalayas. Our analyses revealed that A. euchroma and A. guttata have high levels of genetic diversity and comprise two and three subclades, respectively. The two clades of A. euchroma exhibited significant genetic differences and diverged at 10.18 Ma in the middle Miocene. Three clades of A. guttata diverged in the Pleistocene. The results provided new insight into evolutionary history of Arnebia species and promoted the conservation and exploitation of A. euchroma and A. guttata.
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Affiliation(s)
- Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ruishan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ping Qiao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linyuan Shi
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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25
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Magdy M, El-Sherbeny EA, Ramirez Sanchez A. The complete chloroplast genome of the Egyptian henbane ( Hyoscyamus muticus L., Solanaceae). Mitochondrial DNA B Resour 2022; 7:1109-1111. [PMID: 35801135 PMCID: PMC9255021 DOI: 10.1080/23802359.2022.2086493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Egyptian henbane (Hyoscyamus muticus L. Mant. Pl. 1767) is an important medicinal plant of the family Solanaceae. Its complete chloroplast (cp) genome was assembled using Illumina high-throughput sequencing technology to contribute to its conservation genetics studies. Here, we report the complete sequence of the chloroplast genome of H. muticus. The cp genome was 156,271 bp in length with an asymmetric base composition (30.9% A, 18.9% C, 18.6% G and 31.6% T). It encodes 132 genes comprising 87 protein-coding genes, 29 tRNA genes, and 8 rRNA genes. The overall GC content of the H. muticus chloroplast genome was 37.5%, and the corresponding values in the large single-copy (LSC), the small single-copy (SSC), and the inverted repeat (IR) regions were 35.5%, 31.5%, and 43.0%, respectively. The complete chloroplast genome sequence was deposited to the GenBank (NCBI, Accession number: MZ450974). The maximum likelihood phylogenetic analysis showed that the H. muticus and H. niger were clustered into one clade with strong support values, indicating their closer relationship.
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Affiliation(s)
- Mahmoud Magdy
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Esraa Attia El-Sherbeny
- Department of Genetics Resources, Desert Research Center, Ministry of Agriculture, Cairo, Egypt
| | - Agripina Ramirez Sanchez
- Faculty of Education Science, Santo Domino Autonomous University, Santo Domingo, Dominican Republic
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26
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Ashraf MF, Hou D, Hussain Q, Imran M, Pei J, Ali M, Shehzad A, Anwar M, Noman A, Waseem M, Lin X. Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance. Int J Mol Sci 2022; 23:651. [PMID: 35054836 PMCID: PMC8775971 DOI: 10.3390/ijms23020651] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.
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Affiliation(s)
- Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Muhammad Imran
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Mohsin Ali
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Aamar Shehzad
- Maize Research Station, AARI, Faisalabad 38000, Pakistan;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Waseem
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
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27
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Liston A, Weitemier KA, Letelier L, Podani J, Zong Y, Liu L, Dickinson TA. Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PeerJ 2021; 9:e12418. [PMID: 34754629 PMCID: PMC8555502 DOI: 10.7717/peerj.12418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.
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Affiliation(s)
- Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Kevin A Weitemier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.,Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Lucas Letelier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - János Podani
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Lorand University, Budapest, Hungary
| | - Yu Zong
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America.,College of Chemistry & Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Lang Liu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy A Dickinson
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Zeng S, Li J, Yang Q, Wu Y, Yu J, Pei X, Yu J. Comparative plastid genomics of Mazaceae: focusing on a new recognized genus, Puchiumazus. PLANTA 2021; 254:99. [PMID: 34665332 DOI: 10.1007/s00425-021-03753-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Six Mazaceae plastomes were assembled in this study, including the newly recognized genus, Puchiumazus. Comparative plastid genomic analysis provided new insights into Mazaceae. The phylogenetic categorization of Mazus lanceifolius (Mazaceae) has long been uncertain. In 2021, the scholars Bo Li, D. G. Zhang, and C. L. Xiang republished M. lanceifolius as a new species Puchiumazus lanceifolius, within a new genus Puchiumazus. However, there is little plastome information on Mazaceae. Following the publishing of the new genus Puchiumazus, it is now necessary to study the Mazaceae plastome features to comprehensively understand this young family. The Mazaceae plastomes all have a typical quartile structure. The plastomes have a size ranging from 152,388 to 154,252 bp, and each plastome contains 112 unique genes, including 78 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. A comparative analysis showed that these plastome sequences are highly conserved. Furthermore, we identified four relatively hypervariable regions (trnQ-UUC-psbK, trnS-GCU- trnS-CGA, trnT-UGU-trnL-UAA and ycf1) that can be used as potential DNA barcodes for the identification of this clade. Phylogenetic relationships based on the whole plastome sequences of 25 samples of 14 genera of Lamiales placed M. lanceifolius in the basal clade of the family Mazaceae, with 100% bootstrap support. In summary, the M. lanceifolius results indicate that a new monotype genus (Puchiumazus) should be established at the whole-plastome level. This study provides plastid genomic resources for exploring the phylogeny of Mazaceae.
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Affiliation(s)
- Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Qiyi Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - You Wu
- College of Information and Electrical Engineering, Chongqing Three Gorges University, Chongqing, 404199, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Xiaoying Pei
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716, China.
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29
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Su HJ, Liang SL, Nickrent DL. Plastome variation and phylogeny of Taxillus (Loranthaceae). PLoS One 2021; 16:e0256345. [PMID: 34407123 PMCID: PMC8372910 DOI: 10.1371/journal.pone.0256345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/05/2021] [Indexed: 12/02/2022] Open
Abstract
Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35–40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90–93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.
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Affiliation(s)
- Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
- * E-mail:
| | - Shu-ling Liang
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
| | - Daniel L. Nickrent
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
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30
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Genome Sequence of an Okra Leaf Curl Virus from Egypt. Microbiol Resour Announc 2021; 10:e0053321. [PMID: 34292069 PMCID: PMC8297448 DOI: 10.1128/mra.00533-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A complete Okra leaf curl virus DNA-A was sequenced from okra in Egypt. Here, we report the complete genome sequence of this monopartite virus, comprising 2,764 bp and encoding 6 open reading frames (ORFs) with a GC content of 44.6% and 88.3% similarity to a virus reported earlier from Cameroon.
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31
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Barchi L, Rabanus‐Wallace MT, Prohens J, Toppino L, Padmarasu S, Portis E, Rotino GL, Stein N, Lanteri S, Giuliano G. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:579-596. [PMID: 33964091 PMCID: PMC8453987 DOI: 10.1111/tpj.15313] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 05/20/2023]
Abstract
Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | | | - Jaime Prohens
- COMAVUniversitat Politècnica de ValènciaCamino de Vera 14Valencia46022Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
| | - Ezio Portis
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
- Department of Crop SciencesCenter for Integrated Breeding Research (CiBreed)Georg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Sergio Lanteri
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
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32
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Simmonds SE, Smith JF, Davidson C, Buerki S. Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae). Mol Phylogenet Evol 2021; 163:107229. [PMID: 34129936 DOI: 10.1016/j.ympev.2021.107229] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152-161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.
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Affiliation(s)
- Sara E Simmonds
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | - James F Smith
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA
| | | | - Sven Buerki
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID 83725-1515, USA.
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33
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Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Sci Rep 2021; 11:9471. [PMID: 33947883 PMCID: PMC8096831 DOI: 10.1038/s41598-021-88160-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 02/02/2023] Open
Abstract
The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
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Affiliation(s)
- Jiawei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Hongmei Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The Second Peoples's Hospital of Nantong, Nantong, 226000, Jiangsu, China
| | - Bin Ai
- Foshan Green Development Innovation Research Institute, Foshan, 528000, Guangdong, China
| | - Wei Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cuijun Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhiqiang Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Sen Li
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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Xiao S, Xu P, Deng Y, Dai X, Zhao L, Heider B, Zhang A, Zhou Z, Cao Q. Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam). BMC Genomics 2021; 22:262. [PMID: 33849443 PMCID: PMC8042981 DOI: 10.1186/s12864-021-07544-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023] Open
Abstract
Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07544-y.
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Affiliation(s)
- Shizhuo Xiao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Pan Xu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yitong Deng
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Xibin Dai
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Lukuan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Bettina Heider
- International Potato Center, Av.La Molina 1895, La Molina, Lima, Peru
| | - An Zhang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Zhilin Zhou
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China.
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35
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Zhang B, Hu F, Cai X, Cheng J, Zhang Y, Lin H, Hu K, Wu Z. Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin ( Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:783496. [PMID: 35069640 PMCID: PMC8767146 DOI: 10.3389/fpls.2021.783496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/13/2021] [Indexed: 05/14/2023]
Abstract
Pungency is a unique characteristic of chili peppers (Capsicum spp.) caused by capsaicinoids. The evolutionary emergence of pungency is thought to be a derived trait within the genus Capsicum. However, it is not well-known how pungency has varied during Capsicum domestication and specialization. In this study, we applied a comparative metabolomics along with transcriptomics analysis to assess various changes between two peppers (a mildly pungent cultivated pepper BB3 and its hot progenitor chiltepin) at four stages of fruit development, focusing on pungency variation. A total of 558 metabolites were detected in two peppers. In comparison with chiltepin, capsaicinoid accumulation in BB3 was almost negligible at the early stage. Next, 412 DEGs associated with the capsaicinoid accumulation pathway were identified through coexpression analysis, of which 18 genes (14 TFs, 3 CBGs, and 1 UGT) were deemed key regulators due to their high coefficients. Based on these data, we speculated that downregulation of these hub genes during the early fruit developmental stage leads to a loss in pungency during Capsicum domestication (from chiltepin to BB3). Of note, a putative UDP-glycosyltransferase, GT86A1, is thought to affect the stabilization of capsaicinoids. Our results lay the foundation for further research on the genetic diversity of pungency traits during Capsicum domestication and specialization.
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Affiliation(s)
- Bipei Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Fang Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xiaotao Cai
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ying Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hui Lin
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
- *Correspondence: Kailin Hu,
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Zhiming Wu,
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36
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Barrett CF. Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L. PeerJ 2020; 8:e9315. [PMID: 32587799 PMCID: PMC7304433 DOI: 10.7717/peerj.9315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/17/2020] [Indexed: 12/12/2022] Open
Abstract
Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
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37
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Li B, Lin F, Huang P, Guo W, Zheng Y. Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing. Biol Res 2020; 53:21. [PMID: 32410692 PMCID: PMC7227249 DOI: 10.1186/s40659-020-00289-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 04/29/2020] [Indexed: 01/25/2023] Open
Abstract
Background Liriodendron chinense ranges widely in subtropical China and northern Vietnam; however, it inhabits several small, isolated populations and is now an endangered species due to its limited seed production. The objective of this study was to develop a set of nuclear SSR (simple sequence repeats) and multiple chloroplast genome markers for genetic studies in L. chinense and their characterization in diverse germplasm. Results We performed low-coverage whole genome sequencing of the L. chinense from four genotypes, assembled the chloroplast genome and identified nuclear SSR loci by searching in contigs for SSR motifs. Comparative analysis of the four chloroplast genomes of L. chinense revealed 45 SNPs, 17 indels, 49 polymorphic SSR loci, and five small inversions. Most chloroplast intraspecific polymorphisms were located in the interspaces of single-copy regions. In total, 6147 SSR markers were isolated from low-coverage whole genome sequences. The most common SSR motifs were dinucleotide (70.09%), followed by trinucleotide motifs (23.10%). The motif AG/TC (33.51%) was the most abundant, followed by TC/AG (25.53%). A set of 13 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 109 L. chinense individuals, representing distinct varieties or germplasm. The number of alleles per locus ranged from 8 to 28 with an average of 21 alleles. The expected heterozygosity (He) varied from 0.19 to 0.93 and the observed heterozygosity (Ho) ranged from 0.11 to 0.79. Conclusions The genetic resources characterized and tested in this study provide a valuable tool to detect polymorphisms in L. chinense for future genetic studies and breeding programs.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Wenying Guo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China. .,Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China. .,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China.
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Sawicki J, Bączkiewicz A, Buczkowska K, Górski P, Krawczyk K, Mizia P, Myszczyński K, Ślipiko M, Szczecińska M. The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes. Genes (Basel) 2020; 11:E299. [PMID: 32178248 PMCID: PMC7140840 DOI: 10.3390/genes11030299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 01/16/2023] Open
Abstract
The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.
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Affiliation(s)
- Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Alina Bączkiewicz
- Department of Genetics, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland; (A.B.); (K.B.)
| | - Katarzyna Buczkowska
- Department of Genetics, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland; (A.B.); (K.B.)
| | - Piotr Górski
- Department of Botany, Poznań University of Life Sciences, 60-625 Poznań, Poland;
| | - Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Patryk Mizia
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
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Magdy M, Ouyang B. The complete mitochondrial genome of the chiltepin pepper ( Capsicum annuum var. glabriusculum), the wild progenitor of Capsicum annuum L. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:683-684. [PMID: 33366702 PMCID: PMC7748824 DOI: 10.1080/23802359.2020.1714496] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The complete mitochondrial genome of chiltepin pepper (Capsicum annuum var glabriusculum) was sequenced. The mitogenome of the American bird pepper was 505,190 bp, with 44.4% of GC content. A total of 218 genes were fully annotated, including 190 CDS (31 known genes and 158 open reading frames), three rRNA, and 25 tRNA genes. The gene synteny and number were equal to those of C. annuum var annuum, except for the partial annotation of ATP subunit 6 and the absence of ORF172 and ORF104b. The complete mt genome sequence was deposited to the GenBank (NCBI, Accession number: MN196478).
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Affiliation(s)
- Mahmoud Magdy
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.,Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
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