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Xie P, Wu J, Lu M, Tian T, Wang D, Luo Z, Yang D, Li L, Yang X, Liu D, Cheng H, Tan J, Yang H, Zhu D. Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant. BMC Genomics 2024; 25:773. [PMID: 39118028 PMCID: PMC11312713 DOI: 10.1186/s12864-024-10680-w] [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: 04/01/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported. RESULTS The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense. CONCLUSIONS In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.
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Affiliation(s)
- Ping Xie
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Jingru Wu
- Affiliated Stomatological Hospital, Jiamusi University, Jiamusi, 154002, Heilongjiang, China
| | - Mengyue Lu
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Tongxin Tian
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Dongmei Wang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Zhiwen Luo
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Donghong Yang
- Affiliated Stomatological Hospital, Jiamusi University, Jiamusi, 154002, Heilongjiang, China
| | - Lili Li
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Xuewen Yang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Decai Liu
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Haitao Cheng
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Jiaxin Tan
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Hongsheng Yang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China.
| | - Dequan Zhu
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang, 550025, Guizhou, China.
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Cantu D, Massonnet M, Cochetel N. The wild side of grape genomics. Trends Genet 2024; 40:601-612. [PMID: 38777691 DOI: 10.1016/j.tig.2024.04.014] [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: 03/04/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.
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Affiliation(s)
- Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
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Gong Y, Xie X, Zhou G, Chen M, Chen Z, Li P, Huang H. Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria. BMC Genomics 2024; 25:546. [PMID: 38824587 PMCID: PMC11143693 DOI: 10.1186/s12864-024-10457-1] [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: 02/02/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed. RESULTS The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution. CONCLUSIONS The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.
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Affiliation(s)
- Yihui Gong
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
| | - Xin Xie
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Guihua Zhou
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Meiyu Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Zhiyin Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Peng Li
- Xiangtan Agricultural Science Research Institute, Xiangtan, 411100, China
| | - Hua Huang
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Zhang X, Li P, Wang J, Fu D, Zhao B, Dong W, Liu Y. Comparative genomic and phylogenetic analyses of mitochondrial genomes of hawthorn (Crataegus spp.) in Northeast China. Int J Biol Macromol 2024; 272:132795. [PMID: 38830497 DOI: 10.1016/j.ijbiomac.2024.132795] [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: 09/04/2023] [Revised: 01/18/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
Hawthorn (Crataegus spp.) plants are major sources of health food and medicines. Twenty species and seven variations of Crataegus are present in China. A variety of unique Crataegus species was found in their natural distribution in northeast China. In the present study, we assembled and annotated the mitochondrial genomes of five Crataegus species from northeastern China. The sizes of the newly sequenced mitochondrial genomes ranged from 245,907 bp to 410,837 bp. A total of 45-55 genes, including 12-19 transfer RNA genes, three ribosomal RNA genes, and 29-33 protein-coding genes (PCGs) were encoded by these mitochondrial genomes. Seven divergent hotspot regions were identified by comparative analyses: atp6, nad3, ccmFN, matR, nad1, nad5, and rps1. The most conserved genes among the Crataegus species, according to the whole-genome correlation analysis, were nad1, matR, nad5, ccmFN, cox1, nad4, trnQ-TTG, trnK-TTT, trnE-TTC, and trnM-CAT. Horizontal gene transfer between organellar genomes was common in Crataegus plants. Based on the phylogenetic trees of mitochondrial PCGs, C. maximowiczii, C. maximowiczii var. ninganensis, and C. bretschneideri shared similar maternal relationships. This study improves Crataegus mitochondrial genome resources and offers important insights into the taxonomy and species identification of this genus.
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Affiliation(s)
- Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; National Field Genebank for Hawthorn, Shenyang, Liaoning 110866, China
| | - Peihao Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Jian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Dongxu Fu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Baipeng Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; National Field Genebank for Hawthorn, Shenyang, Liaoning 110866, China
| | - Yuexue Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; National Field Genebank for Hawthorn, Shenyang, Liaoning 110866, China.
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Yu X, Ma Z, Liu S, Duan Z. Analysis of the Rhodomyrtus tomentosa mitochondrial genome: Insights into repeat-mediated recombination and intra-cellular DNA transfer. Gene 2024; 909:148288. [PMID: 38367854 DOI: 10.1016/j.gene.2024.148288] [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: 07/02/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
Plant mitochondrial genomes participate in encoding proteins crucial to the major producers of ATP in the cell and replication and heredity of their own DNA. The sequences and structure of the plant mitochondrial genomes profoundly impact these fundamental processes, and studies of plant mitochondrial genomes are needed. We reported the complete sequences of the Rhodomyrtus tomentosa mitochondrial genome here, totaling 400,482 bp. Nanopore ONT reads and PCR amplification provided evidence for recombination mediated by the eight repeat pairs for the R. tomentosa mitochondrial genome. Thirty-eight genes were identified in the R. tomentosa mitochondrial genome. Comparative analyses of the mitochondrial genome and plastome and PCR amplification suggest that five fragments of mitochondrial plastid DNA were unfunctional sequences resulting from intracellular gene transfer. Phylogenetic analysis based on each and all of the 27 mitochondrial protein-coding genes of nine Myrtales species revealed that R. tomentosa always clustered with other species of Myrtaceae. This study uncovered the enormous complexity of the R. tomentosa mitochondrial genome, the active repeat-mediated recombinations, the presence of mitochondrial plastid DNAs, and the topological incongruence of Myrtales among the single-gene trees.
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Affiliation(s)
- Xiaoli Yu
- School of Life Science, Huizhou University, Huizhou 516007, Guangdong, China.
| | - Zhengbing Ma
- Forestry Technology Extension Station of Huiyang, Huizhou 516211, Guangdong, China.
| | - Shu Liu
- School of Life Science, Huizhou University, Huizhou 516007, Guangdong, China.
| | - Zhonggang Duan
- School of Life Science, Huizhou University, Huizhou 516007, Guangdong, China.
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Yu Y, Wang X, Qu R, OuYang Z, Guo J, Zhao Y, Huang L. Extraction and analysis of high-quality chloroplast DNA with reduced nuclear DNA for medicinal plants. BMC Biotechnol 2024; 24:20. [PMID: 38637734 PMCID: PMC11025248 DOI: 10.1186/s12896-024-00843-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Obtaining high-quality chloroplast genome sequences requires chloroplast DNA (cpDNA) samples that meet the sequencing requirements. The quality of extracted cpDNA directly impacts the efficiency and accuracy of sequencing analysis. Currently, there are no reported methods for extracting cpDNA from Erigeron breviscapus. Therefore, we developed a suitable method for extracting cpDNA from E. breviscapus and further verified its applicability to other medicinal plants. RESULTS We conducted a comparative analysis of chloroplast isolation and cpDNA extraction using modified high-salt low-pH method, the high-salt method, and the NaOH low-salt method, respectively. Subsequently, the number of cpDNA copies relative to the nuclear DNA (nDNA ) was quantified via qPCR. As anticipated, chloroplasts isolated from E. breviscapus using the modified high-salt low-pH method exhibited intact structures with minimal cell debris. Moreover, the concentration, purity, and quality of E. breviscapus cpDNA extracted through this method surpassed those obtained from the other two methods. Furthermore, qPCR analysis confirmed that the modified high-salt low-pH method effectively minimized nDNA contamination in the extracted cpDNA. We then applied the developed modified high-salt low-pH method to other medicinal plant species, including Mentha haplocalyx, Taraxacum mongolicum, and Portulaca oleracea. The resultant effect on chloroplast isolation and cpDNA extraction further validated the generalizability and efficacy of this method across different plant species. CONCLUSIONS The modified high-salt low-pH method represents a reliable approach for obtaining high-quality cpDNA from E. breviscapus. Its universal applicability establishes a solid foundation for chloroplast genome sequencing and analysis of this species. Moreover, it serves as a benchmark for developing similar methods to extract chloroplast genomes from other medicinal plants.
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Affiliation(s)
- Yifan Yu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
- School of Pharmacy, Jiangsu University, 212013, Zhenjiang, China
| | - Xinxin Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Renjun Qu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Zhen OuYang
- School of Pharmacy, Jiangsu University, 212013, Zhenjiang, China
| | - Juan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yujun Zhao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China.
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China.
- School of Pharmacy, Jiangsu University, 212013, Zhenjiang, China.
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Chen L, Dong X, Huang H, Xu H, Rono PC, Cai X, Hu G. Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant. BMC Genomics 2024; 25:322. [PMID: 38561677 PMCID: PMC10983754 DOI: 10.1186/s12864-024-10247-9] [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: 12/30/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported. RESULTS In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted. CONCLUSIONS This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.
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Affiliation(s)
- Lingling Chen
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Huang
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Haixia Xu
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiuzhen Cai
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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Zhao Z, Li Y, Zhai JW, Liu ZJ, Li MH. Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids. Int J Mol Sci 2024; 25:1578. [PMID: 38338856 PMCID: PMC10855806 DOI: 10.3390/ijms25031578] [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: 12/22/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants.
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Affiliation(s)
| | | | | | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (Y.L.); (J.-W.Z.)
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (Y.L.); (J.-W.Z.)
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9
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae). Ecol Evol 2024; 14:e10868. [PMID: 38274863 PMCID: PMC10809029 DOI: 10.1002/ece3.10868] [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: 06/10/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
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10
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Song Y, Du X, Li A, Fan A, He L, Sun Z, Niu Y, Qiao Y. Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl. BMC Genomics 2023; 24:708. [PMID: 37996801 PMCID: PMC10666317 DOI: 10.1186/s12864-023-09821-4] [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: 03/01/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated. RESULT The F. suspensa mitochondrial genome was obtained in the length of 535,692 bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea. CONCLUSION In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.
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Affiliation(s)
- Yun Song
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Xiaorong Du
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Aoxuan Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Amei Fan
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Longjiao He
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Zhe Sun
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yanbing Niu
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Yonggang Qiao
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
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11
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Li J, Cullis C. Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures. BIOLOGY 2023; 12:1244. [PMID: 37759643 PMCID: PMC10525999 DOI: 10.3390/biology12091244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes.
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Affiliation(s)
| | - Christopher Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA;
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12
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Cao Y, Yin D, Pang B, Li H, Liu Q, Zhai Y, Ma N, Shen H, Jia Q, Wang D. Assembly and phylogenetic analysis of the mitochondrial genome of endangered medicinal plant Huperzia crispata. Funct Integr Genomics 2023; 23:295. [PMID: 37691055 DOI: 10.1007/s10142-023-01223-9] [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: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Huperzia crispata is a traditional Chinese herb plant and has attracted special attention in recent years for its products Hup A can serve as an acetylcholinesterase inhibitor (AChEI). Although the chloroplast (cp) genome of H. crispata has been studied, there are no reports regarding the Huperzia mitochondrial (mt) genome since the previously reported H. squarrosa has been revised as Phlegmariurus squarrosus. The mt genome of H. crispata was sequenced using a combination of long-read nanopore and Illumina sequencing platforms. The entire H. crispata mt genome was assembled in a circular with a length of 412,594 bp and a total of 91 genes, including 45 tRNAs, 6 rRNAs, 37 protein-coding genes (PCGs), and 3 pseudogenes. Notably, the rps8 gene was present in P. squarrosus and a pseudogene rps8 was presented in H. crispata, which was lacking in most of Pteridophyta and Gymnospermae. Intron-encoded maturase (mat-atp9i85 and mat-cobi787) genes were present in H. crispata and P. squarrosus, but lost in other examined lycophytes, ferns, and Gymnospermae plants. Collinearity analysis showed that the mt genome of H. crispata and P. squarrossus is highly conservative compared to other ferns. Relative synonymous codon usage (RSCU) analysis showed that the amino acids most frequently found were phenylalanine (Phe) (4.77%), isoleucine (Ile) (4.71%), lysine (Lys) (4.26%), while arginine (Arg) (0.32%), and histidine (His) (0.42%) were rarely found. Simple sequence repeats (SSR) analysis revealed that a total of 114 SSRs were identified in the mt genome of H. crispata and account for 0.35% of the whole mt genome. Monomer repeats were the majority types of SSRs and represent 91.89% of the total SSRs. In addition, a total of 1948 interspersed repeats (158 forward, 147 palindromic, and 5 reverse repeats) with a length ranging from 30 bp to 14,945 bp were identified in the H. crispata mt genome and the 30-39-bp repeats were the most abundant type. Gene transfer analysis indicated that a total of 12 homologous fragments were discovered between the cp and mt genomes of H. crispata, accounting for 0.93% and 2.48% of the total cp and mt genomes, respectively. The phylogenetic trees revealed that H. crispata was the sister of P. squarrosus. The Ka/Ks analysis results suggested that most PCGs, except atp6 gene, were subject to purification selection during evolution. Our study provides extensive information on the features of the H. crispata mt genome and will help unravel evolutionary relationships, and molecular identification within lycophytes.
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Affiliation(s)
- Yu Cao
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China
| | - Dengpan Yin
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China
| | - Bo Pang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China
| | - Haibo Li
- Yuyao Seedling Management Station, Ningbo, Zhejiang, 315400, China
| | - Qiao Liu
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China
| | - Yufeng Zhai
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China
| | - Nan Ma
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China
| | - Hongjun Shen
- Ningbo Delai Medicinal Material Planting Co, Ltd, 315444, Ningbo, Zhejiang, 315444, China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China
| | - Dekai Wang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China.
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13
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Cruz Plancarte D, Solórzano S. Structural and gene composition variation of the complete mitochondrial genome of Mammillaria huitzilopochtli (Cactaceae, Caryophyllales), revealed by de novo assembly. BMC Genomics 2023; 24:509. [PMID: 37653379 PMCID: PMC10468871 DOI: 10.1186/s12864-023-09607-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Structural descriptions of complete genomes have elucidated evolutionary processes in angiosperms. In Cactaceae (Caryophyllales), a high structural diversity of the chloroplast genome has been identified within and among genera. In this study, we assembled the first mitochondrial genome (mtDNA) for the short-globose cactus Mammillaria huitzilopochtli. For comparative purposes, we used the published genomes of 19 different angiosperms and the gymnosperm Cycas taitungensis as an external group for phylogenetic issues. RESULTS The mtDNA of M. huitzilopochtli was assembled into one linear chromosome of 2,052,004 bp, in which 65 genes were annotated. These genes account for 57,606 bp including 34 protein-coding genes (PCGs), 27 tRNAs, and three rRNAs. In the non-coding sequences, repeats were abundant, with a total of 4,550 (179,215 bp). In addition, five complete genes (psaC and four tRNAs) of chloroplast origin were documented. Negative selection was estimated for most (23) of the PCGs. The phylogenetic tree showed a topology consistent with previous analyses based on the chloroplast genome. CONCLUSIONS The number and type of genes contained in the mtDNA of M. huitzilopochtli were similar to those reported in 19 other angiosperm species, regardless of their phylogenetic relationships. Although other Caryophyllids exhibit strong differences in structural arrangement and total size of mtDNA, these differences do not result in an increase in the typical number and types of genes found in M. huitzilopochtli. We concluded that the total size of mtDNA in angiosperms increases by the lengthening of the non-coding sequences rather than a significant gain of coding genes.
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Affiliation(s)
- David Cruz Plancarte
- Laboratorio de Ecología Molecular y Evolución, Universidad Nacional Autónoma de México, FES Iztacala, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Mexico
- Posgrado en Ciencias Biológicas, UNAM, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Ciudad de México, 04510, Mexico
| | - Sofía Solórzano
- Laboratorio de Ecología Molecular y Evolución, Universidad Nacional Autónoma de México, FES Iztacala, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Mexico.
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14
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Zhou J, Niu J, Wang X, Yue J, Zhou S, Liu Z. Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses. BMC PLANT BIOLOGY 2023; 23:368. [PMID: 37488499 PMCID: PMC10367252 DOI: 10.1186/s12870-023-04376-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced. RESULTS The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029-155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61-67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported. CONCLUSIONS The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.
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Affiliation(s)
- Jing Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Junmei Niu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Xinyue Wang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Jiarui Yue
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Shilin Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Zhenwen Liu
- Yunnan Academy of Forestry and Grassland, Kunming, China.
- Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province, Kunming, China.
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming, China.
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15
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Zhou S, Zhi X, Yu R, Liu Y, Zhou R. Factors contributing to mitogenome size variation and a recurrent intracellular DNA transfer in Melastoma. BMC Genomics 2023; 24:370. [PMID: 37393222 DOI: 10.1186/s12864-023-09488-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Mitogenome sizes of seed plants vary substantially even among closely related species, which are often related to horizontal or intracellular DNA transfer (HDT or IDT) events. However, the mechanisms of this size variation have not been well characterized. RESULTS Here we assembled and characterized the mitogenomes of three species of Melastoma, a tropical shrub genus experiencing rapid speciation. The mitogenomes of M. candidum (Mc), M. sanguineum (Ms) and M. dodecandrum (Md) were assembled to a circular mapping chromosome of 391,595 bp, 395,542 bp and 412,026 bp, respectively. While the mitogenomes of Mc and Ms showed good collinearity except for a large inversion of ~ 150 kb, there were many rearrangements in the mitogenomes between Md and either Mc or Ms. Most non-alignable sequences (> 80%) between Mc and Ms are from gain or loss of mitochondrial sequences. Whereas, between Md and either Mc or Ms, non-alignable sequences in Md are mainly chloroplast derived sequences (> 30%) and from putative horizontal DNA transfers (> 30%), and those in both Mc and Ms are from gain or loss of mitochondrial sequences (> 80%). We also identified a recurrent IDT event in another congeneric species, M. penicillatum, which has not been fixed as it is only found in one of the three examined populations. CONCLUSIONS By characterizing mitochondrial genome sequences of Melastoma, our study not only helps understand mitogenome size evolution in closely related species, but also cautions different evolutionary histories of mitochondrial regions due to potential recurrent IDT events in some populations or species.
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Affiliation(s)
- Shuaixi Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xueke Zhi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Runxian Yu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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16
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Talavera A, Nie ZL, Ma ZY, Johnson G, Ickert-Bond SM, Zimmer EA, Wen J. Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis. Mol Phylogenet Evol 2023:107866. [PMID: 37354923 DOI: 10.1016/j.ympev.2023.107866] [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: 02/10/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.
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Affiliation(s)
- Alicia Talavera
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA; Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, 29071, Málaga, Spain.
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Zhi-Yao Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518000 China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Stefanie M Ickert-Bond
- UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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17
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Flack N, Drown M, Walls C, Pratte J, McLain A, Faulk C. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 2023; 5:lqad033. [PMID: 37025970 PMCID: PMC10071556 DOI: 10.1093/nargab/lqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Melissa Drown
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Carrie Walls
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jay Pratte
- Bloomington Parks and Recreation, Miller Park Zoo, Bloomington, IL 61701, USA
| | - Adam McLain
- Department of Biology and Chemistry, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
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Multichromosomal Mitochondrial Genome of Paphiopedilum micranthum: Compact and Fragmented Genome, and Rampant Intracellular Gene Transfer. Int J Mol Sci 2023; 24:ijms24043976. [PMID: 36835385 PMCID: PMC9966765 DOI: 10.3390/ijms24043976] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Orchidaceae is one of the largest families of angiosperms. Considering the large number of species in this family and its symbiotic relationship with fungi, Orchidaceae provide an ideal model to study the evolution of plant mitogenomes. However, to date, there is only one draft mitochondrial genome of this family available. Here, we present a fully assembled and annotated sequence of the mitochondrial genome (mitogenome) of Paphiopedilum micranthum, a species with high economic and ornamental value. The mitogenome of P. micranthum was 447,368 bp in length and comprised 26 circular subgenomes ranging in size from 5973 bp to 32,281 bp. The genome encoded for 39 mitochondrial-origin, protein-coding genes; 16 tRNAs (three of plastome origin); three rRNAs; and 16 ORFs, while rpl10 and sdh3 were lost from the mitogenome. Moreover, interorganellar DNA transfer was identified in 14 of the 26 chromosomes. These plastid-derived DNA fragments represented 28.32% (46,273 bp) of the P. micranthum plastome, including 12 intact plastome origin genes. Remarkably, the mitogenome of P. micranthum and Gastrodia elata shared 18% (about 81 kb) of their mitochondrial DNA sequences. Additionally, we found a positive correlation between repeat length and recombination frequency. The mitogenome of P. micranthum had more compact and fragmented chromosomes compared to other species with multichromosomal structures. We suggest that repeat-mediated homologous recombination enables the dynamic structure of mitochondrial genomes in Orchidaceae.
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Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia. Sci Rep 2023; 13:770. [PMID: 36641495 PMCID: PMC9840629 DOI: 10.1038/s41598-022-24327-x] [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: 02/20/2022] [Accepted: 11/14/2022] [Indexed: 01/15/2023] Open
Abstract
Plant mitochondrial genomes (mitogenomes) are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitogenome of any species in the genus of Photinia has been reported. In this study, using NGS sequencing, we reported the mitogenome assembly and annotation of Photinia serratifolia, which is 473,579 bp in length, contains 38 protein-coding genes, 23 tRNAs, and 6 rRNAs, with 61 genes have no introns. The rps2 and rps11 genes are missing in the P. serratifolia mitogenome. Although there are more editing sites (488) in the P. serratifolia mitogenome than in most angiosperms, fewer editing types were found in the P. serratifolia mitogenome, showing a clear bias in RNA-editing. Phylogenetic analysis based on the mitogenomes of P. serratifolia and 8 other taxa of the Rosaceae family reflected the exact evolutionary and taxonomic status of P. serratifolia. However, Ka/Ks analysis revealed that 72.69% of the protein-coding genes in the P. serratifolia mitogenome had undergone negative selections, reflecting the importance of those genes in the P. serratifolia mitogenome. Collectively, these results will provide valuable information for the evolution of P. serratifolia and provide insight into the evolutionary relationships within Photinia and the Rosaceae family.
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Tang D, Huang S, Quan C, Huang Y, Miao J, Wei F. Mitochondrial genome characteristics and phylogenetic analysis of the medicinal and edible plant Mesona chinensis Benth. Front Genet 2023; 13:1056389. [PMID: 36712846 PMCID: PMC9878300 DOI: 10.3389/fgene.2022.1056389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
Mesona chinensis Benth (MCB) (or Platostoma palustre or Platostoma chinense) is an important edible and medicinal plant in China. However, the mitochondrial genome (mitogenome, or mtDNA) of MCB has not been characterized or reported yet. In this study, we first sequenced and characterized the complete mitogenome of MCB. The MCB mitogenome was 494,599 bp in length and encoded 59 genes containing 37 protein-coding genes (PCGs), 19 tRNAs, and 3 rRNAs. Gene transfer analysis revealed that a total of 12 transfer segments with more than 93% identity (total length of 25,427 bp) were detected in the MCB mitogenome. Simple sequence repeats (SSR) analysis showed that 212 simple sequence repeats (SSR) were identified. Repeat sequence analysis revealed 305 repeat sequences (158 forward and 147 palindromic repeats) ranging from 30 bp to 48,383 bp and the 30-39 bp repeats were the majority type. Relative synonymous codon usage (RSCU) analysis uncovered that in total, 9,947 codons were encoding the protein-coding genes (PCGs). Serine (909, 9.1%) and leucine (879, 8.8%) were the two most abundant amino acids, while terminator (32, .3%) was the least abundant amino acid. Ka/Ks analysis indicated that almost all genes were subject to purification selection, except ccmB. Analysis of Lamiaceae mitogenomes constitution revealed that atpB and atpE were unique to the Rotheca serrata and Salvia miltiorrhiza mitogenomes. mttB gene loss was unique to the Boea hygrometrica mitogenome. The core fragments of the Lamiaceae mitogenomes harbored a higher GC content than the specific and variable fragments. In addition, phylogenetic analysis revealed that MCB was closely related to Salvia miltiorrhiza based on the mitogenomes. The current study provided valuable genomic resources for understanding and utilizing this important medicinal plant in the future.
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Affiliation(s)
- Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Suhua Huang
- College of Pharmacy, Guangxi Medical University, Nanning, China
| | - Changqian Quan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yuan Huang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China,*Correspondence: Fan Wei, ; Jianhua Miao,
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China,*Correspondence: Fan Wei, ; Jianhua Miao,
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21
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Liu D, Qu K, Yuan Y, Zhao Z, Chen Y, Han B, Li W, El-Kassaby YA, Yin Y, Xie X, Tong B, Liu H. Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus. Front Genet 2023; 13:1050040. [PMID: 36761694 PMCID: PMC9907779 DOI: 10.3389/fgene.2022.1050040] [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: 09/21/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.
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Affiliation(s)
- Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China,State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai Qu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yangchen Yuan
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China,Hebei Hongya Mountain State-Owned Forest Farm, Baoding, China
| | - Zhiheng Zhao
- Guangxi Forestry Research Institute, Guangxi Key Laboratory of Special Non-wood Forest Cultivation &; Utilization, Nanning, China
| | - Ying Chen
- Forestry Protection and Development Service Center of Shandong Province, Jinan, China
| | - Biao Han
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada
| | | | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China,*Correspondence: Xiaoman Xie, ; Boqiang Tong, ; Hongshan Liu,
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China,*Correspondence: Xiaoman Xie, ; Boqiang Tong, ; Hongshan Liu,
| | - Hongshan Liu
- Hebei Hongya Mountain State-Owned Forest Farm, Baoding, China,*Correspondence: Xiaoman Xie, ; Boqiang Tong, ; Hongshan Liu,
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22
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Liu H, Qin L, Chen Y, Xu S, Zhou X, Zhu Y, Li B. The complete mitochondrial genome of Camellia nitidissima (Theaceae). Mitochondrial DNA B Resour 2023; 8:565-569. [PMID: 37200681 PMCID: PMC10187084 DOI: 10.1080/23802359.2023.2209211] [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: 11/22/2022] [Accepted: 04/26/2023] [Indexed: 05/20/2023] Open
Abstract
The mitochondrial genome of Camellia nitidissima was sequenced by Illumina and Pacbio sequencing. The results of sequences showed that a total length was 949,915 bp, and the GC content was 45.7% in assembled mitochondrial genome of C. nitidissima. 71 unigenes had been found, including 36 coding proteins and 35 non-coding proteins. Subsequently, the phylogenetic tree was built on 24 plants with the maximum-likelihood method, which had high bootstrap value and fited to the angiosperm phylogeny group classification (APG IV). The study's findings unravel the taxonomic status of C. nitidissima and benefit the evolution study.
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Affiliation(s)
- Hexia Liu
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Liu Qin
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources, Yulin Normal University, Yulin, China
| | - Yuling Chen
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Saiying Xu
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Xingwen Zhou
- College of Architecture and Planning, Fujian University of Technology, Fuzhou, China
| | - Yulin Zhu
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources, Yulin Normal University, Yulin, China
- Yulin Zhu College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Bo Li
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources, Yulin Normal University, Yulin, China
- CONTACT Bo Li
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23
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Wei L, Liu TJ, Hao G, Ge XJ, Yan HF. Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales. BMC Genomics 2022; 23:770. [PMID: 36424546 PMCID: PMC9686101 DOI: 10.1186/s12864-022-08983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales. RESULTS Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall. CONCLUSIONS The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.
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Affiliation(s)
- Lei Wei
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Tong-Jian Liu
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- grid.20561.300000 0000 9546 5767College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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24
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A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-Tea Tree Camellia gigantocarpa (Theaceae). DIVERSITY 2022. [DOI: 10.3390/d14100850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Camellia gigantocarpa is one of the oil-tea trees whose seeds can be used to extract high-quality vegetable oil. To date, there are no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus. In this paper, we present the first complete mitochondrial genomes of C. gigantocarpa obtained using PacBio Hi-Fi (high-fidelity) and Hi-C sequencing technologies to anchor the 970,410 bp genome assembly into a single sequence. A set of 44 protein-coding genes, 22 non-coding genes, 746 simple sequence repeats (SSRs), and more than 201 kb of repetitive sequences were annotated in the genome assembly. The high percentage of repetitive sequences in the mitochondrial genome of C. gigantocarpa (20.81%) and C.sinensis (22.15%, tea tree) compared to Arabidopsis thaliana (4.96%) significantly increased the mitogenome size in the genus Camellia. The comparison of the mitochondrial genomes between C. gigantocarpa and C. sinensis revealed genes exhibit high variance in gene order and low substitution rate within the genus Camellia. Information on the mitochondrial genome provides a better understanding of the structure and evolution of the genome in Camellia and may contribute to further study of the after-ripening process of oil-tea trees.
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Wang R, Ba Q, Zhang L, Wang W, Zhang P, Li G. Comparative analysis of mitochondrial genomes provides insights into the mechanisms underlying an S-type cytoplasmic male sterility (CMS) system in wheat (Triticum aestivum L.). Funct Integr Genomics 2022; 22:951-964. [PMID: 35678921 DOI: 10.1007/s10142-022-00871-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022]
Abstract
Cytoplasmic male sterility (CMS) has been widely used in crop cross breeding. There has been much research on wheat CMS. However, the correlation between S-type CMS and mitochondrial genome remains elusive. Herein, we sequenced the mitochondrial genome of wheat CMS line and compared it with the maintainer line. The results showed that the mitochondrial genome of CMS line encoded 26 tRNAs, 8 rRNAs, and 35 protein-coding genes, and the cob encoding complex III in which the protein coding gene is mutated. This protein is known to affect reactive oxygen (ROS) production. The analysis of ROS metabolism in developing anthers showed that the deficiency of antioxidants and antioxidant enzymes in the sterile system aggravated membrane lipid oxidation, resulting in ROS accumulation, and influencing the anther development. Herein, cob is considered as a candidate causative gene sequence for CMS.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Qingsong Ba
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China.
| | - Lanlan Zhang
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Weilun Wang
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Pengfei Zhang
- Xiangyang Academy of Agricultural Sciences, Hubei, 441057, People's Republic of China
| | - Guiping Li
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
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26
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Wee CC, Nor Muhammad NA, Subbiah VK, Arita M, Nakamura Y, Goh HH. Mitochondrial genome of Garcinia mangostana L. variety Mesta. Sci Rep 2022; 12:9480. [PMID: 35676406 PMCID: PMC9177603 DOI: 10.1038/s41598-022-13706-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/26/2022] [Indexed: 11/27/2022] Open
Abstract
Fruits of Garcinia mangostana L. (mangosteen) are rich in nutrients with xanthones found in the pericarp having great pharmaceutical potential. Mangosteen variety Mesta is only found in Malaysia, which tastes sweeter than the common Manggis variety in Southeast Asia. In this study, we report the complete mitogenome of G. mangostana L. variety Mesta with a total sequence length of 371,235 bp of which 1.7% could be of plastid origin. The overall GC content of the mitogenome is 43.8%, comprising 29 protein-coding genes, 3 rRNA genes, and 21 tRNA genes. Repeat and tandem repeat sequences accounted for 5.8% and 0.15% of the Mesta mitogenome, respectively. There are 333 predicted RNA-editing sites in Mesta mitogenome. These include the RNA-editing events that generated the start codon of nad1 gene and the stop codon of ccmFC gene. Phylogenomic analysis using both maximum likelihood and Bayesian analysis methods showed that the mitogenome of mangosteen variety Mesta was grouped under Malpighiales order. This is the first complete mitogenome from the Garcinia genus for future evolutionary studies.
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Affiliation(s)
- Ching-Ching Wee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | | | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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The complete mitochondrial genome of carnivorous Genlisea tuberosa (Lentibulariaceae): Structure and evolutionary aspects. Gene 2022; 824:146391. [PMID: 35259463 DOI: 10.1016/j.gene.2022.146391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022]
Abstract
Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced. The genome comprises 729,765 bp, encoding 80 identified genes of which 36 are protein-coding, 40 tRNA, four rRNA genes, and three pseudogenes. An intronic region from the cox1 gene was identified that encodes an endonuclease enzyme that is present in the other sequenced species of Lentibulariaceae. Chloroplast genes (pseudogene and complete) inserted in the MT genome were identified, showing possible horizontal transfer between organelles. In addition, 50 pairs of long repeats from 94 to 274 bp are present, possibly playing an important role in the maintenance of the MT genome. Phylogenetic analysis carried out with 34 coding mitochondrial genes corroborated the positioning of the species listed here within the family. The molecular dynamism in the mitogenome (e.g. the loss or pseudogenization of genes, insertion of foreign genes, the long repeats as well as accumulated mutations) may be reflections of the carnivorous lifestyle where a significant part of cellular energy was shifted for the adaptation of leaves into traps molding the mitochondrial DNA. The sequence and annotation of G. tuberosa's MT will be useful for further studies and serve as a model for evolutionary and taxonomic clarifications of the group as well as improving our comprehension of MT evolution.
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28
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Choi IS, Wojciechowski MF, Steele KP, Hunter SG, Ruhlman TA, Jansen RK. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:389-406. [PMID: 35061308 DOI: 10.1111/tpj.15676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Kelly P Steele
- Division of Science and Mathematics, Arizona State University, Mesa, AZ, 85212, USA
| | - Sarah G Hunter
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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29
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Maurin KJL, Smissen RD, Lusk CH. A dated phylogeny shows Plio-Pleistocene climates spurred evolution of antibrowsing defences in the New Zealand flora. THE NEW PHYTOLOGIST 2022; 233:546-554. [PMID: 34610149 PMCID: PMC9298021 DOI: 10.1111/nph.17766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Some plant traits may be legacies of coevolution with extinct megafauna. One example is the convergent evolution of 'divaricate' cage architectures in many New Zealand lineages, interpreted as a response to recently extinct flightless avian browsers whose ancestors arrived during the Paleogene period. Although experiments have confirmed that divaricate habit deters extant browsers, its abundance on frosty, droughty sites appears consistent with an earlier interpretation as a response to cold, dry Plio-Pleistocene climates. We used 45 protein-coding sequences from plastid genomes to reconstruct the evolutionary history of the divaricate habit in extant New Zealand lineages. Our dated phylogeny of 215 species included 91% of New Zealand eudicot divaricate species. We show that 86% of extant divaricate plants diverged from non-divaricate sisters within the last 5 Ma, implicating Plio-Pleistocene climates in the proliferation of cage architectures in New Zealand. Our results, combined with other recent findings, are consistent with the synthetic hypothesis that the browser-deterrent effect of cage architectures was strongly selected only when Plio-Pleistocene climatic constraints prevented woody plants from growing quickly out of reach of browsers. This is consistent with the abundance of cage architectures in other regions where plant growth is restricted by aridity or short frost-free periods.
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Affiliation(s)
| | - Rob D. Smissen
- Allan HerbariumManaaki Whenua – Landcare ResearchLincoln7640New Zealand
| | - Christopher H. Lusk
- Environmental Research InstituteThe University of WaikatoHamilton3240New Zealand
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30
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Yu R, Sun C, Liu Y, Zhou R. Shifts from cis-to trans-splicing of five mitochondrial introns in Tolypanthus maclurei. PeerJ 2021; 9:e12260. [PMID: 34703675 PMCID: PMC8489412 DOI: 10.7717/peerj.12260] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/15/2021] [Indexed: 01/20/2023] Open
Abstract
Shifts from cis-to trans-splicing of mitochondrial introns tend to correlate with relative genome rearrangement rates during vascular plant evolution, as is particularly apparent in some lineages of gymnosperms. However, although many angiosperms have also relatively high mitogenomic rearrangement rates, very few cis-to trans-splicing shifts except for five trans-spliced introns shared in seed plants have been reported. In this study, we sequenced and characterized the mitogenome of Tolypanthus maclurei, a hemiparasitic plant from the family Loranthaceae (Santalales). The mitogenome was assembled into a circular chromosome of 256,961 bp long, relatively small compared with its relatives from Santalales. It possessed a gene content of typical angiosperm mitogenomes, including 33 protein-coding genes, three rRNA genes and ten tRNA genes. Plastid-derived DNA fragments took up 9.1% of the mitogenome. The mitogenome contained one group I intron (cox1i729) and 23 group II introns. We found shifts from cis-to trans-splicing of five additional introns in its mitogenome, of which two are specific in T. maclurei. Moreover, atp1 is a chimeric gene and phylogenetic analysis indicated that a 356 bp region near the 3′ end of atp1 of T. maclurei was acquired from Lamiales via horizontal gene transfer. Our results suggest that shifts to trans-splicing of mitochondrial introns may not be uncommon among angiosperms.
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Affiliation(s)
- Runxian Yu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Chenyu Sun
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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31
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Li X, Li Y, Sylvester SP, Zang M, El‐Kassaby YA, Fang Y. Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. Ecol Evol 2021; 11:13401-13414. [PMID: 34646478 PMCID: PMC8495791 DOI: 10.1002/ece3.8063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein-coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein-coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH-psbA, trnK_UUU-rps16, trnfM_CAU-rps14, trnS_GCU-trnG_GCC, and atpF-atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.
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Affiliation(s)
- Xuan Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yongfu Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Steven Paul Sylvester
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Mingyue Zang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yanming Fang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
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Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, Jansen RK, Ruhlman TA. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:861-875. [PMID: 34021942 DOI: 10.1111/tpj.15351] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal de Bahia (UFBA), Rua Barão de Jeremoabo, s.n., Ondina, Salvador, Bahia, 40170-115, Brazil
| | - Haroldo C de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, Rio de Janeiro, 915 22460-030, Brazil
| | - Luciano P de Queiroz
- Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana, Bahia, 44036-900, Brazil
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Achakkagari SR, Tai HH, Davidson C, De Jong H, Strömvik MV. The complete mitogenome assemblies of ten diploid potato clones reveal recombination and overlapping variants. DNA Res 2021; 28:6319723. [PMID: 34254134 PMCID: PMC8386665 DOI: 10.1093/dnares/dsab009] [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: 04/30/2021] [Accepted: 07/07/2021] [Indexed: 01/30/2023] Open
Abstract
The potato mitogenome is complex and to understand various biological functions and nuclear-cytoplasmic interactions, it is important to characterize its gene content and structure. In this study, the complete mitogenome sequences of nine diploid potato clones along with a diploid Solanum okadae clone were characterized. Each mitogenome was assembled and annotated from Pacific Biosciences (PacBio) long-reads and 10X genomics short reads. The results show that each mitogenome consists of multiple circular molecules with similar structure and gene organization, though two groups (clones 07506-01, DW84-1457, 08675-21, and H412-1 in one group, and clones W5281-2, 12625-02, 12120-03, and 11379-03 in another group) could be distinguished, and two mitogenomes (clone 10908-06 and OKA15) were not consistent with those or with each other. Significant differences in the repeat structure of the ten mitogenomes were found, as was recombination events leading to multiple sub-genomic circles. Comparison between individual molecules revealed a translocation of ∼774 bp region located between a short repeat of 40 bp in molecule 3 of each mitogenome, and an insertion of the same in the molecule 2 of the 10908-06 mitogenome. Finally, phylogenetic analyses revealed a close relationship between the mitogenomes of these clones and previously published potato mitogenomes.
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Affiliation(s)
| | - Helen H Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
| | - Charlotte Davidson
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
| | - Hielke De Jong
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
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Filip E, Skuza L. Horizontal Gene Transfer Involving Chloroplasts. Int J Mol Sci 2021; 22:ijms22094484. [PMID: 33923118 PMCID: PMC8123421 DOI: 10.3390/ijms22094484] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/04/2023] Open
Abstract
Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.
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Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
- Correspondence:
| | - Lidia Skuza
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
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A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist. PLoS Biol 2021; 19:e3001126. [PMID: 33891594 PMCID: PMC8099122 DOI: 10.1371/journal.pbio.3001126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/05/2021] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin-antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.
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Qi X, Wang K, Yang L, Deng Z, Sun Z. The complete mitogenome sequence of the coral lily ( Lilium pumilum) and the Lanzhou lily ( Lilium davidii) in China. Open Life Sci 2021; 15:1060-1067. [PMID: 33817292 PMCID: PMC7874665 DOI: 10.1515/biol-2020-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 07/18/2020] [Accepted: 09/14/2020] [Indexed: 11/24/2022] Open
Abstract
Background The mitogenomes of higher plants are conserved. This study was performed to complete the mitogenome of two China Lilium species (Lilium pumilum Redouté and Lilium davidii var. unicolor (Hoog) cotton). Methods Genomic DNA was separately extracted from the leaves of L. pumilum and L. davidii in triplicate and used for sequencing. The mitogenome of Allium cepa was used as a reference. Genome assembly, annotation and phylogenetic tree were analyzed. Results The mitogenome of L. pumilum and L. davidii was 988,986 bp and 924,401 bp in length, respectively. There were 22 core protein-coding genes (including atp1, atp4, atp6, atp9, ccmB, ccmC, ccmFc, ccmFN1, ccmFN2, cob, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7 and nad9), one open reading frame and one ribosomal protein-coding gene (rps12) in the mitogenomes. Compared with the A. cepa mitogenome, the coding sequence of the 24 genes and intergenic spacers in L. pumilum and L. davidii mitogenome contained 1,621 and 1,617 variable sites, respectively. In the phylogenetic tree, L. pumilum and L. davidii were distinct from A. cepa (NC_030100). Conclusions L. pumilum and L. davidii mitogenomes have far distances from other plants. This study provided additional information on the species resources of China Lilium.
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Affiliation(s)
- Xiangying Qi
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Kaiqi Wang
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Liping Yang
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Zhenshan Deng
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Zhihong Sun
- China Lily Laboratory, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, Shaanxi, China
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Kim H, Kim J. Structural Mutations in the Organellar Genomes of Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara Show Dynamic Gene Transfer. Int J Mol Sci 2021; 22:ijms22073770. [PMID: 33916499 PMCID: PMC8038606 DOI: 10.3390/ijms22073770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/04/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022] Open
Abstract
Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria.
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Affiliation(s)
- Hyoungtae Kim
- Institute of Agriculture Science and Technology, Chungbuk National University, Cheongju, Chungbuk 28644, Korea;
| | - Jungsung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
- Correspondence: ; Tel.: +82-43-261-2535
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Abstract
The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Robert K Jansen
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 2020; 21:241. [PMID: 32912315 PMCID: PMC7488116 DOI: 10.1186/s13059-020-02154-5] [Citation(s) in RCA: 1409] [Impact Index Per Article: 352.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified "baiting and iterative mapping" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).
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Affiliation(s)
- Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, 16801, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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Qiao J, Zhang X, Chen B, Huang F, Xu K, Huang Q, Huang Y, Hu Q, Wu X. Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica. BMC Genomics 2020; 21:480. [PMID: 32660507 PMCID: PMC7359470 DOI: 10.1186/s12864-020-06889-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
Background The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and certain detailed interspecific relationships within Brassica genus remains undetermined and somewhere confused. In the current high-throughput sequencing era, a systemic comparative genomic study based on a large population is necessary and would be crucial to resolve these questions. Results The chloroplast DNA and mitochondrial DNA were synchronously resequenced in a selected set of Brassica materials, which contain 72 accessions and maximally integrated the known Brassica species. The Brassica genomewide cpDNA and mtDNA variations have been identified. Detailed phylogenetic relationships inside and around Brassica genus have been delineated by the cpDNA- and mtDNA- variation derived phylogenies. Different from B. juncea and B. carinata, the natural B. napus contains three major cytoplasmic haplotypes: the cam-type which directly inherited from B. rapa, polima-type which is close to cam-type as a sister, and the mysterious but predominant nap-type. Certain sparse C-genome wild species might have primarily contributed the nap-type cytoplasm and the corresponding C subgenome to B. napus, implied by their con-clustering in both phylogenies. The strictly concurrent inheritance of mtDNA and cpDNA were dramatically disturbed in the B. napus cytoplasmic male sterile lines (e.g., mori and nsa). The genera Raphanus, Sinapis, Eruca, Moricandia show a strong parallel evolutional relationships with Brassica. Conclusions The overall variation data and elaborated phylogenetic relationships provide further insights into genetic understanding of Brassica, which can substantially facilitate the development of novel Brassica germplasms.
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Affiliation(s)
- Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Xiaojun Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | | | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Bi C, Lu N, Xu Y, He C, Lu Z. Characterization and Analysis of the Mitochondrial Genome of Common Bean ( Phaseolus vulgaris) by Comparative Genomic Approaches. Int J Mol Sci 2020; 21:E3778. [PMID: 32471098 PMCID: PMC7312688 DOI: 10.3390/ijms21113778] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.
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Affiliation(s)
- Changwei Bi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
| | - Yiqing Xu
- School of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, Jiangsu, China;
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, Jiangsu, China; (C.B.); (N.L.)
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Park HS, Jayakodi M, Lee SH, Jeon JH, Lee HO, Park JY, Moon BC, Kim CK, Wing RA, Newmaster SG, Kim JY, Yang TJ. Mitochondrial plastid DNA can cause DNA barcoding paradox in plants. Sci Rep 2020; 10:6112. [PMID: 32273595 PMCID: PMC7145815 DOI: 10.1038/s41598-020-63233-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 03/24/2020] [Indexed: 01/18/2023] Open
Abstract
The transfer of ancestral plastid genomes into mitochondrial genomes to generate mitochondrial plastid DNA (MTPT) is known to occur in plants, but its impacts on mitochondrial genome complexity and the potential for causing a false-positive DNA barcoding paradox have been underestimated. Here, we assembled the organelle genomes of Cynanchum wilfordii and C. auriculatum, which are indigenous medicinal herbs in Korea and China, respectively. In both species, it is estimated that 35% of the ancestral plastid genomes were transferred to mitochondrial genomes over the past 10 million years and remain conserved in these genomes. Some plastid barcoding markers co-amplified the conserved MTPTs and caused a barcoding paradox, resulting in mis-authentication of botanical ingredients and/or taxonomic mis-positioning. We identified dynamic and lineage-specific MTPTs that have contributed to mitochondrial genome complexity and might cause a putative barcoding paradox across 81 plant species. We suggest that a DNA barcoding guidelines should be developed involving the use of multiple markers to help regulate economically motivated adulteration.
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Affiliation(s)
- Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sae Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Hyeon Jeon
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Oh Lee
- Phyzen Genomics Institute, Seongnam, 13558, Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byeong Cheol Moon
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Ji Yeon Kim
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul, 01811, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Genome Sequences of Both Organelles of the Grapevine Rootstock Cultivar 'Börner'. Microbiol Resour Announc 2020; 9:9/15/e01471-19. [PMID: 32273371 PMCID: PMC7380517 DOI: 10.1128/mra.01471-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Genomic long reads of the interspecific grapevine rootstock cultivar ‘Börner’ (Vitis riparia GM183 × Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes, including the RNA editing sites. The organelle genomes in ‘Börner’ were maternally inherited from Vitis riparia. Genomic long reads of the interspecific grapevine rootstock cultivar ‘Börner’ (Vitis riparia GM183 × Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes, including the RNA editing sites. The organelle genomes in ‘Börner’ were maternally inherited from Vitis riparia.
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Li H, Gao Z, Chen Q, Li Q, Luo M, Wang J, Hu L, Zahid MS, Wang L, Zhao L, Song S, Xu W, Zhang C, Ma C, Wang S. Grapevine ABA receptor VvPYL1 regulates root hair development in Transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:190-200. [PMID: 32078897 DOI: 10.1016/j.plaphy.2020.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 06/10/2023]
Abstract
Root architecture is very important for plant growth. In this study, we characterized the process of root formation in grapevine (Vitis vinifera L.). Continuous observation of root morphology during development revealed that the establishment of root system could be divided into five stages: initial cultivation (stage I), preliminary development (stage II), even change (stage III), root system formation (stage IV), and root architecture stability (stage V). The level of abscisic acid (ABA) increased from stages II to IV and was stable at stage V. Quantitative expression analysis of 11 genes encoding ABA-related rate-limiting enzymes in different tissues showed that the expression of VvPYL1 was the highest in roots. Spatiotemporal expression analysis showed that VvPYL1 was highly expressed during stages II and III. Furthermore, VvPYL1 was highly expressed in lateral roots of grapevine seedlings in tissue culture. Overexpression of VvPYL1 in Arabidopsis thaliana resulted in longer root hairs compared with wild-type plants. Moreover, the root hair length of transgenic lines was hypersensitive to exogenously applied ABA. Additionally, VvPYL1 overexpressing plants showed greater drought tolerance and longer root hairs than wild-type plants under osmotic stress. These results suggest that VvPYL1 may play a key role in root development and drought resistance.
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Affiliation(s)
- Hui Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Qiuju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Luo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Hu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Salman Zahid
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Institute of Agro-food Science and Technology, Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan, China.
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Liu X, Fu W, Tang Y, Zhang W, Song Z, Li L, Yang J, Ma H, Yang J, Zhou C, Davis CC, Wang Y. Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:877-892. [PMID: 31639183 DOI: 10.1093/jxb/erz456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
The plastid genomes (plastomes) of non-photosynthetic plants generally undergo gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.
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Affiliation(s)
- Xiaoqing Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Weirui Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiwei Tang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Plant Biology, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jianhua Yang
- College of Pharmacy, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, China
| | - Chan Zhou
- Department of Population and Quantitative Health Sciences, Massachusetts General Hospital, 55 Lake Ave, North Worcester, MA, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, USA
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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Dong Q, Xing X, Han Y, Wei X, Zhang S. De Novo Organelle Biogenesis in the Cyanobacterium TDX16 Released from the Green Alga <i>Haematococcus pluvialis</i>. Cell 2020. [DOI: 10.4236/cellbio.2020.91003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Liu W, Cai Y, Zhang Q, Chen L, Shu F, Ma X, Bian Y. The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences. Int J Biol Macromol 2019; 143:373-381. [PMID: 31830457 DOI: 10.1016/j.ijbiomac.2019.12.056] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 12/11/2022]
Abstract
The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.
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Affiliation(s)
- Wei Liu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingli Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Qianqian Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Shu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolong Ma
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
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Cecchin M, Marcolungo L, Rossato M, Girolomoni L, Cosentino E, Cuine S, Li‐Beisson Y, Delledonne M, Ballottari M. Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1289-1305. [PMID: 31437318 PMCID: PMC6972661 DOI: 10.1111/tpj.14508] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 05/05/2023]
Abstract
Chlorella vulgaris is a fast-growing fresh-water microalga cultivated on the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed us to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seq data obtained at two different irradiances of growth (high light, HL versus low light, LL) enabled us to identify 10 724 nuclear genes, coding for 11 082 transcripts. Moreover, 121 and 48 genes, respectively, were found in the chloroplast and mitochondrial genome. Functional annotation and expression analysis of nuclear, chloroplast and mitochondrial genome sequences revealed particular features of Chlorella vulgaris. Evidence of horizontal gene transfers from chloroplast to mitochondrial genome was observed. Furthermore, comparative transcriptomic analyses of LL versus HL provided insights into the molecular basis for metabolic rearrangement under HL versus LL conditions leading to enhanced de novo fatty acid biosynthesis and triacylglycerol accumulation. The occurrence of a cytosolic fatty acid biosynthetic pathway could be predicted and its upregulation upon HL exposure was observed, consistent with the increased lipid amount under HL conditions. These data provide a rich genetic resource for future genome editing studies, and potential targets for biotechnological manipulation of Chlorella vulgaris or other microalgae species to improve biomass and lipid productivity.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Luca Marcolungo
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Marzia Rossato
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Laura Girolomoni
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Emanuela Cosentino
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Stephan Cuine
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Yonghua Li‐Beisson
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Massimo Delledonne
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Matteo Ballottari
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
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Zhao N, Grover CE, Chen Z, Wendel JF, Hua J. Intergenomic gene transfer in diploid and allopolyploid Gossypium. BMC PLANT BIOLOGY 2019; 19:492. [PMID: 31718541 PMCID: PMC6852956 DOI: 10.1186/s12870-019-2041-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/20/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Intergenomic gene transfer (IGT) between nuclear and organellar genomes is a common phenomenon during plant evolution. Gossypium is a useful model to evaluate the genomic consequences of IGT for both diploid and polyploid species. Here, we explore IGT among nuclear, mitochondrial, and plastid genomes of four cotton species, including two allopolyploids and their model diploid progenitors (genome donors, G. arboreum: A2 and G. raimondii: D5). RESULTS Extensive IGT events exist for both diploid and allotetraploid cotton (Gossypium) species, with the nuclear genome being the predominant recipient of transferred DNA followed by the mitochondrial genome. The nuclear genome has integrated 100 times more foreign sequences than the mitochondrial genome has in total length. In the nucleus, the integrated length of chloroplast DNA (cpDNA) was between 1.87 times (in diploids) to nearly four times (in allopolyploids) greater than that of mitochondrial DNA (mtDNA). In the mitochondrion, the length of nuclear DNA (nuDNA) was typically three times than that of cpDNA. Gossypium mitochondrial genomes integrated three nuclear retrotransposons and eight chloroplast tRNA genes, and incorporated chloroplast DNA prior to divergence between the diploids and allopolyploid formation. For mitochondrial chloroplast-tRNA genes, there were 2-6 bp conserved microhomologies flanking their insertion sites across distantly related genera, which increased to 10 bp microhomologies for the four cotton species studied. For organellar DNA sequences, there are source hotspots, e.g., the atp6-trnW intergenic region in the mitochondrion and the inverted repeat region in the chloroplast. Organellar DNAs in the nucleus were rarely expressed, and at low levels. Surprisingly, there was asymmetry in the survivorship of ancestral insertions following allopolyploidy, with most numts (nuclear mitochondrial insertions) decaying or being lost whereas most nupts (nuclear plastidial insertions) were retained. CONCLUSIONS This study characterized and compared intracellular transfer among nuclear and organellar genomes within two cultivated allopolyploids and their ancestral diploid cotton species. A striking asymmetry in the fate of IGTs in allopolyploid cotton was discovered, with numts being preferentially lost relative to nupts. Our results connect intergenomic gene transfer with allotetraploidy and provide new insight into intracellular genome evolution.
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Affiliation(s)
- Nan Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding /Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education / Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Zhiwen Chen
- Laboratory of Cotton Genetics, Genomics and Breeding /Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education / Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding /Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education / Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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50
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Aguirre-Dugua X, Castellanos-Morales G, Paredes-Torres LM, Hernández-Rosales HS, Barrera-Redondo J, Sánchez-de la Vega G, Tapia-Aguirre F, Ruiz-Mondragón KY, Scheinvar E, Hernández P, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita. J Mol Evol 2019; 87:327-342. [PMID: 31701178 DOI: 10.1007/s00239-019-09916-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022]
Abstract
Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20-rps12 and trnL-trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL-trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL-trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.
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Affiliation(s)
- Xitlali Aguirre-Dugua
- Unidad de Biotecnología Y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, 54090, Tlalnepantla, Estado de México, Mexico.
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de La Biodiversidad, El Colegio de La Frontera Sur, Unidad Villahermosa, Carretera Villahermosa-Reforma km. 15.5, Ranchería El Guineo 2a Sección, 86280, Villahermosa, Tabasco, Mexico
| | - Leslie M Paredes-Torres
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Helena S Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Josué Barrera-Redondo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Fernando Tapia-Aguirre
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Karen Y Ruiz-Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Paulina Hernández
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas Y Pecuarias (INIFAP), Km 6.5 Carretera Celaya-San Miguel de Allende, 38110, Celaya, Gto., Mexico
| | - Rafael Lira-Saade
- Unidad de Biotecnología Y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De Los Barrios 1, Col. Los Reyes Iztacala, 54090, Tlalnepantla, Estado de México, Mexico.
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N Anexo Al Jardín Botánico, 04510, Ciudad de México, Mexico.
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