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Maryenti T, Koshimizu S, Onda N, Ishii T, Yano K, Okamoto T. Wheat Cybrid Plants, OryzaWheat, Regenerated from Wheat-Rice Hybrid Zygotes via in Vitro Fertilization System Possess Wheat-Rice Hybrid Mitochondria. PLANT & CELL PHYSIOLOGY 2024; 65:1344-1357. [PMID: 39107984 DOI: 10.1093/pcp/pcae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/20/2024] [Accepted: 07/06/2024] [Indexed: 09/04/2024]
Abstract
Hybridization generates biodiversity, and wide hybridization plays a pivotal role in enhancing and broadening the useful attributes of crops. The hybridization barrier between wheat and rice, the two most important cereals, was recently overcome by in vitro production of allopolyploid wheat-rice hybrid zygotes, which can develop and grow into mature plants. In the study, genomic sequences and compositions of the possible hybrid plants were investigated through short- and long-read sequencing analyses and fluorescence in situ hybridization (FISH)-based visualization. The possible hybrid possessed whole wheat nuclear and cytoplasmic DNAs and rice mitochondrial (mt) DNA, along with variable retention rates of rice mtDNA ranging from 11% to 47%. The rice mtDNA retained in the wheat cybrid, termed Oryzawheat, can be transmitted across generations. In addition to mitochondrial hybridization, translocation of rice chromosome 1 into wheat chromosome 6A was detected in a F1 hybrid individual. OryzaWheat can provide a new horizon for utilizing inter-subfamily genetic resources among wheat and rice belonging to different subfamilies, Pooideae and Ehrhartoideae, respectively.
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Affiliation(s)
- Tety Maryenti
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Shizuka Koshimizu
- Bioinformation and DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Nonoka Onda
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori 680-001, Japan
| | - Kentaro Yano
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
- WellGreen-i Co. Ltd., Kanagawa 215-0007, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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Sun N, Han F, Wang S, Shen F, Liu W, Fan W, Bi C. Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species. FRONTIERS IN PLANT SCIENCE 2024; 15:1446015. [PMID: 39228832 PMCID: PMC11368720 DOI: 10.3389/fpls.2024.1446015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/22/2024] [Indexed: 09/05/2024]
Abstract
Lycophytes and ferns represent one of the earliest-diverging lineages of vascular plants, with the Lycopodiaceae family constituting the basal clade among lycophytes. In this research, we successfully assembled and annotated the complete Lycopodium japonicum Thunb. (L. japonicum) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule with a size of 454,458 bp. 64 unique genes were annotated altogether, including 34 protein-coding genes, 27 tRNAs and 3 rRNAs. It also contains 32 group II introns, all of which undergo cis-splicing. We identified 195 simple sequence repeats, 1,948 dispersed repeats, and 92 tandem repeats in the L. japonicum mitogenome. Collinear analysis indicated that the mitogenomes of Lycopodiaceae are remarkably conserved compared to those of other vascular plants. We totally identified 326 RNA editing sites in 31 unique protein-coding genes with 299 sites converting cytosine to uracil and 27 sites the reverse. Notably, the L. japonicum mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% of the mitogenome. The maximum likelihood phylogenetic analysis based on 23 diverse land plant mitogenomes and plastid genomes supports the basal position of lycophytes within vascular plants and they form a sister clade to all other vascular lineages, which is consistent with the PPG I classification system. As the first reported mitogenome of Lycopodioideae subfamily, this study enriches our understanding of Lycopodium mitogenomes, and sets the stage for future research on mitochondrial diversity and evolution within the lycophytes and ferns.
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Affiliation(s)
- Ning Sun
- College of Information Science and Technology and Artificial Intelligence, Nanjing Forestry University, Nanjing, China
| | - Fuchuan Han
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Suyan Wang
- College of Information Science and Technology and Artificial Intelligence, Nanjing Forestry University, Nanjing, China
| | - Fei Shen
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wei Liu
- College of Optical, Mechanical and Electrical Engineering, Zhejiang A&F University, Hangzhou, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- New Cornerstone Science Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Changwei Bi
- College of Information Science and Technology and Artificial Intelligence, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, China
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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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Tao M, Chen J, Cui C, Xu Y, Xu J, Shi Z, Yun J, Zhang J, Ou GZ, Liu C, Chen Y, Zhu ZR, Pan R, Xu S, Chen XX, Rokas A, Zhao Y, Wang S, Huang J, Shen XX. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. NATURE AGING 2024; 4:1076-1088. [PMID: 38834883 DOI: 10.1038/s43587-024-00641-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Abstract
Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.
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Affiliation(s)
- Mei Tao
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Jiani Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunlai Cui
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yandong Xu
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Jingxiu Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zheyi Shi
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiaqi Yun
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junwei Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Zheng Ou
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeng-Rong Zhu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Suhong Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Xin Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yang Zhao
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Sibao Wang
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Jianhua Huang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China.
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China.
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Zhang X, Ding Z, Lou H, Han R, Ma C, Yang S. A Systematic Review and Developmental Perspective on Origin of CMS Genes in Crops. Int J Mol Sci 2024; 25:8372. [PMID: 39125940 PMCID: PMC11312923 DOI: 10.3390/ijms25158372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Cytoplasmic male sterility (CMS) arises from the incompatibility between the nucleus and cytoplasm as typical representatives of the chimeric structures in the mitochondrial genome (mitogenome), which has been extensively applied for hybrid seed production in various crops. The frequent occurrence of chimeric mitochondrial genes leading to CMS is consistent with the mitochondrial DNA (mtDNA) evolution. The sequence conservation resulting from faithfully maternal inheritance and the chimeric structure caused by frequent sequence recombination have been defined as two major features of the mitogenome. However, when and how these chimeric mitochondrial genes appear in the context of the highly conserved reproduction of mitochondria is an enigma. This review, therefore, presents the critical view of the research on CMS in plants to elucidate the mechanisms of this phenomenon. Generally, distant hybridization is the main mechanism to generate an original CMS source in natural populations and in breeding. Mitochondria and mitogenomes show pleomorphic and dynamic changes at key stages of the life cycle. The promitochondria in dry seeds develop into fully functioning mitochondria during seed imbibition, followed by massive mitochondria or mitogenome fusion and fission in the germination stage along with changes in the mtDNA structure and quantity. The mitogenome stability is controlled by nuclear loci, such as the nuclear gene Msh1. Its suppression leads to the rearrangement of mtDNA and the production of heritable CMS genes. An abundant recombination of mtDNA is also often found in distant hybrids and somatic/cybrid hybrids. Since mtDNA recombination is ubiquitous in distant hybridization, we put forward a hypothesis that the original CMS genes originated from mtDNA recombination during the germination of the hybrid seeds produced from distant hybridizations to solve the nucleo-cytoplasmic incompatibility resulting from the allogenic nuclear genome during seed germination.
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Affiliation(s)
- Xuemei Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China;
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Z.D.); (H.L.)
| | - Zhengpin Ding
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Z.D.); (H.L.)
| | - Hongbo Lou
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Z.D.); (H.L.)
| | - Rui Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Cunqiang Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Shengchao Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China;
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Qu K, Liu D, Sun L, Li M, Xia T, Sun W, Xia Y. De novo assembly and comprehensive analysis of the mitochondrial genome of Taxus wallichiana reveals different repeats mediate recombination to generate multiple conformations. Genomics 2024; 116:110900. [PMID: 39067796 DOI: 10.1016/j.ygeno.2024.110900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 07/09/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
Taxus plants are the exclusive source of paclitaxel, an anticancer drug with significant medicinal and economic value. Interspecies hybridization and gene introgression during evolution have obscured distinctions among Taxus species, complicating their phylogenetic classification. While the chloroplast genome of Taxus wallichiana, a widely distributed species in China, has been sequenced, its mitochondrial genome (mitogenome) remains uncharacterized.We sequenced and assembled the T. wallichiana mitogenome using BGI short reads and Nanopore long reads, facilitating comparisons with other gymnosperm mitogenomes. The T. wallichiana mitogenome spanning 469,949 bp, predominantly forms a circular configuration with a GC content of 50.51%, supplemented by 3 minor configurations mediated by one pair of LRs and two pairs of IntRs. It includes 32 protein-coding genes, 7 tRNA genes, and 3 rRNA genes, several of which exist in multiple copies.We detailed the mitogenome's structure, codon usage, RNA editing, and sequence migration between organelles, constructing a phylogenetic tree to elucidate evolutionary relationships. Unlike typical gymnosperm mitochondria, T. wallichiana shows no evidence of mitochondrial-plastid DNA transfer (MTPT), highlighting its unique genomic architecture. Synteny analysis indicated extensive genomic rearrangements in T. wallichiana, likely driven by recombination among abundant repetitive sequences. This study offers a high-quality T. wallichiana mitogenome, enhancing our understanding of gymnosperm mitochondrial evolution and supporting further cultivation and utilization of Taxus species.
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Affiliation(s)
- Kai Qu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China; National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China; National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Limin Sun
- Forestry College of Shandong Agricultural University, Taian 271018, China
| | - Meng Li
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Tiantian Xia
- Shandong Jianzhu University, Jinan 250101, China
| | - Weixia Sun
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Yufei Xia
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Wang H, Wu Z, Li T, Zhao J. Highly active repeat-mediated recombination in the mitogenome of the aquatic grass Hygroryza aristata. BMC PLANT BIOLOGY 2024; 24:644. [PMID: 38973002 PMCID: PMC11229283 DOI: 10.1186/s12870-024-05331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND Floating bamboo (Hygroryza aristata) is an endangered species with a narrow native distribution and is renowned for its unique aesthetic qualities, which holds significant ecological and ornamental value. However, the lack of genetic information research, with only one complete plastome available, significantly hampers conservation efforts and further research for this species. RESULTS In this research, we sequenced and assembled the organelle genomes of floating bamboo, including the mitogenome (587,847 bp) and plastome (135,675 bp). The mitogenome can recombine into various configurations, which are mediated by 25 repeat pairs (13 SRs, 6 MRs, 1 LR, and 5 CRs). LR1 and SR5 are particularly notable as they have the ability to combine with other contigs, forming complex repeat units that facilitate further homologous recombination. The rate of homologous recombination varies significantly among species, yet there is still a pronounced positive correlation observed between the length of these repeat pairs and the rate of recombination they mediate. The mitogenome integrates seven intact protein-coding genes from the chloroplast. The codon usage patterns in both organelles are similar, with a noticeable bias towards C and T on the third codon. The gene map of Poales shows the entire loss of rpl6, succinate dehydrogenase subunits (sdh3 and sdh4). Additionally, the BOP clade retained more variable genes compared to the PACMAD clade. CONCLUSIONS We provided a high-quality and well-annotated mitogenome for floating bamboo and demonstrated the presence of diverse configurations. Our study has revealed the correlation between repeat length and their corresponding recombination rate despite variations among species. Although the mitogenome can potentially exist in the form of a unicircular in vivo, this occurrence is rare and may not be stable.
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Affiliation(s)
- Huijun Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhigang Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Tao Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jindong Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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8
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Li S, Wang Z, Jing Y, Duan W, Yang X. Graph-based mitochondrial genomes of three foundation species in the Saccharum genus. PLANT CELL REPORTS 2024; 43:191. [PMID: 38977492 DOI: 10.1007/s00299-024-03277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/24/2024] [Indexed: 07/10/2024]
Abstract
KEY MESSAGE We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.
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Affiliation(s)
- Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Zhen Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yanfen Jing
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, 650221, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences /Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China.
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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9
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Wang J, Kan S, Liao X, Zhou J, Tembrock LR, Daniell H, Jin S, Wu Z. Plant organellar genomes: much done, much more to do. TRENDS IN PLANT SCIENCE 2024; 29:754-769. [PMID: 38220520 DOI: 10.1016/j.tplants.2023.12.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6000-6999, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Marine College, Shandong University, Weihai, 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiawei Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104-6030, USA.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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10
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Ortiz AJ, Sharbrough J. Genome-wide patterns of homoeologous gene flow in allotetraploid coffee. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11584. [PMID: 39184198 PMCID: PMC11342229 DOI: 10.1002/aps3.11584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/11/2024] [Accepted: 01/25/2024] [Indexed: 08/27/2024]
Abstract
Premise Allopolyploidy-a hybridization-induced whole-genome duplication event-has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages. Methods The ABBA-BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA-BABA test to characterize the extent and direction of HGF in allotetraploid Coffea arabica. Results We found that HGF is abundant in the C. arabica genome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid-targeted-but not mitochondrial-targeted-genes, as would be expected if plastid-nuclear incompatibilities exist between the two parent species. Discussion Together, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid-nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.
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Affiliation(s)
- Andre J. Ortiz
- Department of BiologyNew Mexico Institute of Mining and TechnologySocorroNew MexicoUSA
| | - Joel Sharbrough
- Department of BiologyNew Mexico Institute of Mining and TechnologySocorroNew MexicoUSA
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11
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Pozzi A. Ancestry affects the transcription of small mitochondrial RNAs in human lymphocytes. Mitochondrion 2024; 77:101907. [PMID: 38777221 DOI: 10.1016/j.mito.2024.101907] [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: 08/27/2023] [Revised: 04/29/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Mitochondrial mutations have been linked to changes in phenotypes such as fertility or longevity, however, these changes have been often inconsistent across populations for unknown reasons. A hypothesis that could explain this inconsistency is that some still uncharacterized mitochondrial products are mediating the phenotypic changes across populations. It has been hypothesized that one such product could be the small RNAs encoded in the mitochondrial genome, thus this work will provide new evidence for their existence and function. By using data from the 1000 genome project and knowledge from previously characterized nuclear small RNAs, this study found that 10 small RNAs encoded in tRNA fragments are consistently expressed in 450 individuals from five different populations. Furthermore, this study demonstrated that the expression of some small mitochondrial RNAs is different in individuals of African ancestry, similar to what was observed before in nuclear and mitochondria mRNAs. Lastly, we investigate the causes behind these differences in expression, showing that at least one of the mt-tRFs might be regulated by TRMT10B. The analyses presented in this work further support the small mitochondrial RNAs as functional molecules, and their population-specific expression supports the hypothesis that they act as a mediator between the nucleus and mitochondria differently across populations.
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Affiliation(s)
- Andrea Pozzi
- Faculty of Biology, Ludwig-Maximilians-Universität Munich, München, Germany; Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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12
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Qu K, Chen Y, Liu D, Guo H, Xu T, Jing Q, Ge L, Shu X, Xin X, Xie X, Tong B. Comprehensive analysis of the complete mitochondrial genome of Lilium tsingtauense reveals a novel multichromosome structure. PLANT CELL REPORTS 2024; 43:150. [PMID: 38789593 DOI: 10.1007/s00299-024-03232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
KEY MESSAGE Lilium tsingtauense mitogenome comprises 27 independent chromosome molecules, it undergoes frequent genomic recombination, and the rate of recombination and mutation between different repetitive sequences affects the formation of multichromosomal structures. Given the extremely large genome of Lily, which likely harbors additional genetic resources, it serves as an ideal material for studying the phylogenetic evolution of organisms. Although the Lilium chloroplast genome has been documented, the sequence of its mitochondrial genome (mitogenome) remains uncharted. Using BGI short reads and Nanopore long reads, we sequenced, assembled, and annotated the mitogenome of Lilium tsingtauense. This effort culminated in the characterization of Lilium's first complete mitogenome. Comparative analysis with other angiosperms revealed the unique multichromosomal structure of the L. tsingtauense mitogenome, spanning 1,125,108 bp and comprising 27 independent circular chromosomes. It contains 36 protein-coding genes, 12 tRNA genes, and 3 rRNA genes, with a GC content of 44.90%. Notably, three chromosomes in the L. tsingtauense mitogenome lack identifiable genes, hinting at the potential existence of novel genes and noncoding elements. The high degree of observed genome fragmentation implies frequent reorganization, with recombination and mutation rates among diverse repetitive sequences likely driving the formation of multichromosomal structures. Our comprehensive analysis, covering genome size, coding genes, structure, RNA editing, repetitive sequences, and sequence migration, sheds light on the evolutionary and molecular biology of multichromosomal mitochondria in Lilium. This high-quality mitogenome of L. tsingtauense not only enriches our understanding of multichromosomal mitogenomes but also establishes a solid foundation for future genome breeding and germplasm innovation in Lilium.
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Affiliation(s)
- Kai Qu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ying Chen
- Forestry Protection and Development Service Center of Shandong Province, Jinan, 250109, China
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China.
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China
| | - Ting Xu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China
| | - Qi Jing
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China
| | - Lei Ge
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China
| | - Xiuge Shu
- Shandong Academy of Forestry, Jinan, 250014, China
| | - Xiaowei Xin
- Shandong Drug and Food Vocational College, Weihai, 264210, China
| | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China.
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China.
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13
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Postel Z, Van Rossum F, Godé C, Schmitt E, Touzet P. Paternal leakage of plastids rescues inter-lineage hybrids in Silene nutans. ANNALS OF BOTANY 2024; 133:427-434. [PMID: 38141228 PMCID: PMC11006537 DOI: 10.1093/aob/mcad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/20/2023] [Indexed: 12/25/2023]
Abstract
BACKGROUND AND AIMS Organelle genomes are usually maternally inherited in angiosperms. However, biparental inheritance has been observed, especially in hybrids resulting from crosses between divergent genetic lineages. When it concerns the plastid genome, this exceptional mode of inheritance might rescue inter-lineage hybrids suffering from plastid-nuclear incompatibilities. Genetically differentiated lineages of Silene nutans exhibit strong postzygotic isolation owing to plastid-nuclear incompatibilities, highlighted by inter-lineage hybrid chlorosis and mortality. Surviving hybrids can exhibit variegated leaves, which might indicate paternal leakage of the plastid genome. We tested whether the surviving hybrids inherited the paternal plastid genome and survived thanks to paternal leakage. METHODS We characterized the leaf phenotype (fully green, variegated or white) of 504 surviving inter-lineage hybrids obtained from a reciprocal cross experiment among populations of four genetic lineages (W1, W2, W3 and E1) of S. nutans from Western Europe and genotyped 560 leaf samples (both green and white leaves for variegated hybrids) using six lineage-specific plastid single nucleotide polymorphisms. KEY RESULTS A high proportion of the surviving hybrids (≤98 %) inherited the paternal plastid genome, indicating paternal leakage. The level of paternal leakage depended on cross type and cross direction. The E1 and W2 lineages as maternal lineages led to the highest hybrid mortality and to the highest paternal leakage from W1 and W3 lineages in the few surviving hybrids. This was consistent with E1 and W2 lineages, which contained the most divergent plastid genomes. When W3 was the mother, more hybrids survived, and no paternal leakage was detected. CONCLUSIONS By providing a plastid genome potentially more compatible with the hybrid nuclear background, paternal leakage has the potential to rescue inter-lineage hybrids from plastid-nuclear incompatibilities. This phenomenon might slow down the speciation process, provided hybrid survival and reproduction can occur in the wild.
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Affiliation(s)
- Zoé Postel
- Univ Lille, CNRS, UMR 8198 – Evo-Eco-Paleo, F-59000 Lille, France
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Fabienne Van Rossum
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium
- Service général de l’Enseignement supérieur et de la Recherche scientifique, Fédération Wallonie Bruxelles, rue A. Lavallée 1, BE-1080 Brussels, Belgium
| | - Cécile Godé
- Univ Lille, CNRS, UMR 8198 – Evo-Eco-Paleo, F-59000 Lille, France
| | - Eric Schmitt
- Univ Lille, CNRS, UMR 8198 – Evo-Eco-Paleo, F-59000 Lille, France
| | - Pascal Touzet
- Univ Lille, CNRS, UMR 8198 – Evo-Eco-Paleo, F-59000 Lille, France
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14
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Sloan DB, Conover JL, Grover CE, Wendel JF, Sharbrough J. Polyploid plants take cytonuclear perturbations in stride. THE PLANT CELL 2024; 36:829-839. [PMID: 38267606 PMCID: PMC10980399 DOI: 10.1093/plcell/koae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/26/2024]
Abstract
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University,
Fort Collins, CO, USA
| | - Justin L Conover
- Department of Ecology and Evolutionary Biology, University of
Arizona, Tucson, AZ, USA
- Department of Molecular and Cellular Biology, University of
Arizona, Tucson, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and
Technology, Socorro, NM, USA
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15
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Feng G, Jiao Y, Ma H, Bian H, Nie G, Huang L, Xie Z, Ran Q, Fan W, He W, Zhang X. The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis. BMC Genomics 2024; 25:235. [PMID: 38438835 PMCID: PMC10910808 DOI: 10.1186/s12864-024-10145-0] [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: 09/16/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus. RESULTS In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22-23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52-53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis. CONCLUSIONS Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongjuan Jiao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huizhen Ma
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Haoyang Bian
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zheni Xie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qifan Ran
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Wenwen Fan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei He
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing, 402460, China.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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16
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Kan S, Liao X, Lan L, Kong J, Wang J, Nie L, Zou J, An H, Wu Z. Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U. Mol Biol Evol 2024; 41:msae043. [PMID: 38391484 PMCID: PMC10919925 DOI: 10.1093/molbev/msae043] [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: 10/24/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
The interaction and coevolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, 2 billion yr later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance versus cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features 3 diploid species that together have formed 3 separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in Brassica carinata (BBCC) and 2 varieties of Brassica juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these 2 separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the Brassica nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.
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Affiliation(s)
- Shenglong Kan
- Marine College, Shandong University, Weihai 264209, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150 Western Australia, Australia
| | - Jiali Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150 Western Australia, Australia
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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17
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Chen Y, Wang W, Yang Z, Peng H, Ni Z, Sun Q, Guo W. Innovative computational tools provide new insights into the polyploid wheat genome. ABIOTECH 2024; 5:52-70. [PMID: 38576428 PMCID: PMC10987449 DOI: 10.1007/s42994-023-00131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/14/2023] [Indexed: 04/06/2024]
Abstract
Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging. Recently, we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome. Here, we summarize the methodological innovations and applications of these tools and databases. A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits. Furthermore, we outline future perspectives on new advanced tools and databases, taking into consideration the unique features of bread wheat, to accelerate genomic-assisted wheat breeding.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
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18
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Lian Q, Li S, Kan S, Liao X, Huang S, Sloan DB, Wu Z. Association Analysis Provides Insights into Plant Mitonuclear Interactions. Mol Biol Evol 2024; 41:msae028. [PMID: 38324417 PMCID: PMC10875325 DOI: 10.1093/molbev/msae028] [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: 11/15/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Cytonuclear interaction refers to the complex and ongoing process of coevolution between nuclear and organelle genomes, which are responsible for cellular respiration, photosynthesis, lipid metabolism, etc. and play a significant role in adaptation and speciation. There have been a large number of studies to detect signatures of cytonuclear interactions. However, identification of the specific nuclear and organelle genetic polymorphisms that are involved in these interactions within a species remains relatively rare. The recent surge in whole genome sequencing has provided us an opportunity to explore cytonuclear interaction from a population perspective. In this study, we analyzed a total of 3,439 genomes from 7 species to identify signals of cytonuclear interactions by association (linkage disequilibrium) analysis of variants in both the mitochondrial and nuclear genomes across flowering plants. We also investigated examples of nuclear loci identified based on these association signals using subcellular localization assays, gene editing, and transcriptome sequencing. Our study provides a novel perspective on the investigation of cytonuclear coevolution, thereby enriching our understanding of plant fitness and offspring sterility.
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Affiliation(s)
- Qun Lian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuai Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Zhang Z, Zhao J, Li J, Yao J, Wang B, Ma Y, Li N, Wang H, Wang T, Liu B, Gong L. Evolutionary trajectory of organelle-derived nuclear DNAs in the Triticum/Aegilops complex species. PLANT PHYSIOLOGY 2024; 194:918-935. [PMID: 37847157 PMCID: PMC10828211 DOI: 10.1093/plphys/kiad552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023]
Abstract
Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinyang Yao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yiqiao Ma
- Jilin Academy of Vegetable and Flower Science, Changchun 130033, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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20
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Iverson ENK, Criswell A, Havird JC. Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576402. [PMID: 38328137 PMCID: PMC10849488 DOI: 10.1101/2024.01.20.576402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.
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Affiliation(s)
- Erik N K Iverson
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Abby Criswell
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
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21
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Xu MRX, Liao ZY, Brock JR, Du K, Li GY, Chen ZQ, Wang YH, Gao ZN, Agarwal G, Wei KHC, Shao F, Pang S, Platts AE, van de Velde J, Lin HM, Teresi SJ, Bird K, Niederhuth CE, Xu JG, Yu GH, Yang JY, Dai SF, Nelson A, Braasch I, Zhang XG, Schartl M, Edger PP, Han MJ, Zhang HH. Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nat Commun 2023; 14:8357. [PMID: 38102128 PMCID: PMC10724154 DOI: 10.1038/s41467-023-43740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.
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Affiliation(s)
- Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhen-Yang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Guo-Yin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | | | - Ying-Hao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhong-Nan Gao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University, School of Life Sciences, Chongqing, China
| | | | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Jozefien van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hong-Min Lin
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jin-Gen Xu
- Jiujiang Academy of Agricultural Sciences, Jiujiang, China
| | - Guo-Hua Yu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Jian-Yuan Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Si-Fa Dai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, Germany.
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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22
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Liu Q, Wu Z, Tian C, Yang Y, Liu L, Feng Y, Li Z. Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1266797. [PMID: 38155854 PMCID: PMC10753190 DOI: 10.3389/fpls.2023.1266797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Introduction Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome. Methods In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated. Results and discussion The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.
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Affiliation(s)
- Qian Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yanting Yang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lemeng Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yumei Feng
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
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23
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Weaver RJ, McDonald AE. Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:149003. [PMID: 37557975 DOI: 10.1016/j.bbabio.2023.149003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.
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Affiliation(s)
- Ryan J Weaver
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Allison E McDonald
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada.
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24
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Baleva MV, Piunova UE, Chicherin IV, Levitskii SA, Kamenski PA. Diversity and Evolution of Mitochondrial Translation Apparatus. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1832-1843. [PMID: 38105202 DOI: 10.1134/s0006297923110135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 12/19/2023]
Abstract
The evolution of mitochondria has proceeded independently in different eukaryotic lines, which is reflected in the diversity of mitochondrial genomes and mechanisms of their expression in eukaryotic species. Mitochondria have lost most of bacterial ancestor genes by transferring them to the nucleus or eliminating them. However, mitochondria of almost all eukaryotic cells still retain relatively small genomes, as well as their replication, transcription, and translation apparatuses. The dependence on the nuclear genome, specific features of mitochondrial transcripts, and synthesis of highly hydrophobic membrane proteins in the mitochondria have led to significant changes in the translation apparatus inherited from the bacterial ancestor, which retained the basic structure necessary for protein synthesis but became more specialized and labile. In this review, we discuss specific properties of translation initiation in the mitochondria and how the evolution of mitochondria affected the functions of main factors initiating protein biosynthesis in these organelles.
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Affiliation(s)
- Mariya V Baleva
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ulyana E Piunova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ivan V Chicherin
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergey A Levitskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Piotr A Kamenski
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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25
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Yisilam G, Liu Z, Turdi R, Chu Z, Luo W, Tian X. Assembly and comparative analysis of the complete mitochondrial genome of Isopyrum anemonoides (Ranunculaceae). PLoS One 2023; 18:e0286628. [PMID: 37796878 PMCID: PMC10553351 DOI: 10.1371/journal.pone.0286628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/19/2023] [Indexed: 10/07/2023] Open
Abstract
Ranunculaceae is a large family of angiosperms comprising 2500 known species-a few with medicinal and ornamental values. Despite this, only two mitochondrial genomes (mitogenomes) of the family have been released in GenBank. Isopyrum anemonoides is a medicinal plant belonging to the family Ranunculaceae, and its chloroplast genome has recently been reported; however, its mitogenome remains unexplored. In this study, we assembled and analyzed the complete mitochondrial genome of I. anemonoides and performed a comparative analysis against different Ranunculaceae species, reconstructing the phylogenetic framework of Isopyrum. The circular mitogenome of I. anemonoides has a length of 206,722 bp, with a nucleotide composition of A (26.4%), T (26.4%), C (23.6%), and G (23.6%), and contains 62 genes, comprising 37 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Abundantly interspersed repetitive and simple sequence repeat (SSR) loci were detected in the I. anemonoides mitogenome, with tetranucleotide repeats accounting for the highest proportion of SSRs. By detecting gene migration, we observed gene exchange between the chloroplast and mitogenome in I. anemonoides, including six intact tRNA genes, six PCG fragments, and fragments from two rRNA genes. Comparative mitogenome analysis of three Ranunculaceae species indicated that the PCG contents were conserved and the GC contents were similar. Selective pressure analysis revealed that only two genes (nad1 and rpl5) were under positive selection during their evolution in Ranunculales, and two specific RNA editing sites (atp6 and mttB) were detected in the I. anemonoides mitogenome. Moreover, a phylogenetic analysis based on the mitogenomes of I. anemonoides and the other 15 taxa accurately reflected the evolutionary and taxonomic status of I. anemonoides. Overall, this study provides new insights into the genetics, systematics, and evolution of mitochondrial evolution in Ranunculaceae, particularly I. anemonoides.
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Affiliation(s)
- Gulbar Yisilam
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Zhiyou Liu
- City Management and Service Centre of Tiemenguan, Xinjiang, China
| | - Rayhangul Turdi
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Zhenzhou Chu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Wei Luo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Xinmin Tian
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life science and Technology, Xinjiang University, Urumqi, Xinjiang, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Science, Guangxi Normal University, Ministry of Education, Guilin, 541004, China
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26
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Chen Y, Guo Y, Xie X, Wang Z, Miao L, Yang Z, Jiao Y, Xie C, Liu J, Hu Z, Xin M, Yao Y, Ni Z, Sun Q, Peng H, Guo W. Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae. PLANT PHYSIOLOGY 2023; 193:578-594. [PMID: 37249052 PMCID: PMC10469385 DOI: 10.1093/plphys/kiad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoming Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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27
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Yang W, Zou J, Wang J, Li N, Luo X, Jiang X, Li S. Variation in Rice Plastid Genomes in Wide Crossing Reveals Dynamic Nucleo-Cytoplasmic Interaction. Genes (Basel) 2023; 14:1411. [PMID: 37510315 PMCID: PMC10379430 DOI: 10.3390/genes14071411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Plastid genomes (plastomes) of angiosperms are well known for their relative stability in size, structure, and gene content. However, little is known about their heredity and variations in wide crossing. To such an end, the plastomes of five representative rice backcross inbred lines (BILs) developed from crosses of O. glaberrima/O. sativa were analyzed. We found that the size of all plastomes was about 134,580 bp, with a quadripartite structure that included a pair of inverted repeat (IR) regions, a small single-copy (SSC) region and a large single-copy (LSC) region. They contained 76 protein genes, 4 rRNA genes, and 30 tRNA genes. Although their size, structure, and gene content were stable, repeat-mediated recombination, gene expression, and RNA editing were extensively changed between the maternal line and the BILs. These novel discoveries demonstrate that wide crossing causes not only nuclear genomic recombination, but also plastome variation in plants, and that the plastome plays a critical role in coordinating the nuclear-cytoplasmic interaction.
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Affiliation(s)
- Weilong Yang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518036, China
| | - Jianing Zou
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Jiajia Wang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Nengwu Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Xiaoyun Luo
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Xiaofen Jiang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
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28
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Lynch M. Mutation pressure, drift, and the pace of molecular coevolution. Proc Natl Acad Sci U S A 2023; 120:e2306741120. [PMID: 37364099 PMCID: PMC10319038 DOI: 10.1073/pnas.2306741120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Most aspects of the molecular biology of cells involve tightly coordinated intermolecular interactions requiring specific recognition at the nucleotide and/or amino acid levels. This has led to long-standing interest in the degree to which constraints on interacting molecules result in conserved vs. accelerated rates of sequence evolution, with arguments commonly being made that molecular coevolution can proceed at rates exceeding the neutral expectation. Here, a fairly general model is introduced to evaluate the degree to which the rate of evolution at functionally interacting sites is influenced by effective population sizes (Ne), mutation rates, strength of selection, and the magnitude of recombination between sites. This theory is of particular relevance to matters associated with interactions between organelle- and nuclear-encoded proteins, as the two genomic environments often exhibit dramatic differences in the power of mutation and drift. Although genes within low Ne environments can drive the rate of evolution of partner genes experiencing higher Ne, rates exceeding the neutral expectation require that the former also have an elevated mutation rate. Testable predictions, some counterintuitive, are presented on how patterns of coevolutionary rates should depend on the relative intensities of drift, selection, and mutation.
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Affiliation(s)
- Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ85287
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29
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Postel Z, Mauri T, Lensink MF, Touzet P. What is the potential impact of genetic divergence of plastid ribosomal genes between Silene nutans lineages in hybrids? An in silico approach using the 3D structure of the plastid ribosome. FRONTIERS IN PLANT SCIENCE 2023; 14:1167478. [PMID: 37223795 PMCID: PMC10201985 DOI: 10.3389/fpls.2023.1167478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/25/2023]
Abstract
Introduction Following the integration of cyanobacteria into the eukaryotic cells, many genes were transferred from the plastid to the nucleus. As a result, plastid complexes are encoded both by plastid and nuclear genes. Tight co-adaptation is required between these genes as plastid and nuclear genomes differ in several characteristics, such as mutation rate and inheritance patterns. Among these are complexes from the plastid ribosome, composed of two main subunits: a large and a small one, both composed of nuclear and plastid gene products. This complex has been identified as a potential candidate for sheltering plastid-nuclear incompatibilities in a Caryophyllaceae species, Silene nutans. This species is composed of four genetically differentiated lineages, which exhibit hybrid breakdown when interlineage crosses are conducted. As this complex is composed of numerous interacting plastid-nuclear gene pairs, in the present study, the goal was to reduce the number of gene pairs that could induce such incompatibilities. Method We used the previously published 3D structure of the spinach ribosome to further elucidate which of the potential gene pairs might disrupt plastid-nuclear interactions within this complex. After modeling the impact of the identified mutations on the 3D structure, we further focused on one strongly mutated plastid-nuclear gene pair: rps11-rps21. We used the centrality measure of the mutated residues to further understand if the modified interactions and associated modified centralities might be correlated with hybrid breakdown. Results and discussion This study highlights that lineage-specific mutations in essential plastid and nuclear genes might disrupt plastid-nuclear protein interactions of the plastid ribosome and that reproductive isolation correlates with changes in residue centrality values. Because of this, the plastid ribosome might be involved in hybrid breakdown in this system.
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Affiliation(s)
- Zoé Postel
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Théo Mauri
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marc F. Lensink
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
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30
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Rossato M, Marcolungo L, De Antoni L, Lopatriello G, Bellucci E, Cortinovis G, Frascarelli G, Nanni L, Bitocchi E, Di Vittori V, Vincenzi L, Lucchini F, Bett KE, Ramsay L, Konkin DJ, Delledonne M, Papa R. CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes. Genome Res 2023; 33:787-797. [PMID: 37127332 PMCID: PMC10317117 DOI: 10.1101/gr.277628.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
High-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genome-wide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches for genotyping are progressively replacing traditional genotyping methods because of the lower ascertainment bias. However, genome-wide genotyping based on sequencing becomes expensive in species with large genomes and a high proportion of repetitive DNA. Here we describe the use of CRISPR-Cas9 technology to deplete repetitive elements in the 3.76-Gb genome of lentil (Lens culinaris), 84% consisting of repeats, thus concentrating the sequencing data on coding and regulatory regions (single-copy regions). We designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats and excluding repetitive regions overlapping annotated genes and putative regulatory elements based on ATAC-seq data. The novel depletion method removed ∼40% of reads mapping to repeats, increasing those mapping to single-copy regions by ∼2.6-fold. When analyzing 25 million fragments, this repeat-to-single-copy shift in the sequencing data increased the number of genotyped bases of ∼10-fold compared to nondepleted libraries. In the same condition, we were also able to identify ∼12-fold more genetic variants in the single-copy regions and increased the genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed because of low coverage. The method performed similarly regardless of the multiplexing level, type of library or genotypes, including different cultivars and a closely related species (L. orientalis). Our results showed that CRISPR-Cas9-driven repeat depletion focuses sequencing data on single-copy regions, thus improving high-density and genome-wide genotyping in large and repetitive genomes.
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Affiliation(s)
- Marzia Rossato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
- Genartis s.r.l., 37126 Verona, Italy
| | - Luca Marcolungo
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Luca De Antoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Gaia Cortinovis
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Leonardo Vincenzi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Filippo Lucchini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | | | - Massimo Delledonne
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
- Genartis s.r.l., 37126 Verona, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy;
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31
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Dembech E, Malatesta M, De Rito C, Mori G, Cavazzini D, Secchi A, Morandin F, Percudani R. Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions. Proc Natl Acad Sci U S A 2023; 120:e2218329120. [PMID: 37043529 PMCID: PMC10120013 DOI: 10.1073/pnas.2218329120] [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: 10/28/2022] [Accepted: 03/10/2023] [Indexed: 04/13/2023] Open
Abstract
Coevolution at the gene level, as reflected by correlated events of gene loss or gain, can be revealed by phylogenetic profile analysis. The optimal method and metric for comparing phylogenetic profiles, especially in eukaryotic genomes, are not yet established. Here, we describe a procedure suitable for large-scale analysis, which can reveal coevolution based on the assessment of the statistical significance of correlated presence/absence transitions between gene pairs. This metric can identify coevolution in profiles with low overall similarities and is not affected by similarities lacking coevolutionary information. We applied the procedure to a large collection of 60,912 orthologous gene groups (orthogroups) in 1,264 eukaryotic genomes extracted from OrthoDB. We found significant cotransition scores for 7,825 orthogroups associated in 2,401 coevolving modules linking known and unknown genes in protein complexes and biological pathways. To demonstrate the ability of the method to predict hidden gene associations, we validated through experiments the involvement of vertebrate malate synthase-like genes in the conversion of (S)-ureidoglycolate into glyoxylate and urea, the last step of purine catabolism. This identification explains the presence of glyoxylate cycle genes in metazoa and suggests an anaplerotic role of purine degradation in early eukaryotes.
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Affiliation(s)
- Elena Dembech
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Carlo De Rito
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Francesco Morandin
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma43124, Italy
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
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32
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Cayuela H, Gaillard JM, Vieira C, Ronget V, Gippet JMW, Garcia TC, Marais GAB, Lemaître JF. Sex differences in adult lifespan and aging rate across mammals: a test of the 'Mother Curse hypothesis'. Mech Ageing Dev 2023; 212:111799. [PMID: 36948470 DOI: 10.1016/j.mad.2023.111799] [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: 06/15/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/24/2023]
Abstract
In many animal species, including humans, males have shorter lifespan and show faster survival aging than females. This differential increase in mortality between sexes could result from the accumulation of deleterious mutations in the mitochondrial genome of males due to the maternal mode of mtDNA inheritance. To date, empirical evidence supporting the existence of this mechanism - called the Mother Curse hypothesis - remains largely limited to a few study cases in humans and Drosophila. In this study, we tested whether the Mother Curse hypothesis accounts for sex differences in lifespan and aging rate across 128 populations of mammals (60 and 68 populations studied in wild and captive conditions, respectively) encompassing 104 species. We found that adult lifespan decreases with increasing mtDNA neutral substitution rate in both sexes in a similar way in the wild - but not in captivity. Moreover, the aging rate marginally increased with neutral substitution rate in males and females in the wild. Overall, these results indicate that the Mother Curse hypothesis is not supported across mammals. We further discuss the implication of these findings for our understanding of the evolution of sex differences in mortality and aging.
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Affiliation(s)
- Hugo Cayuela
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France.
| | - Jean-Michel Gaillard
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France
| | - Cristina Vieira
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France
| | - Victor Ronget
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France
| | - Jérôme M W Gippet
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Thamar Conde Garcia
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France
| | - Gabriel A B Marais
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jean-François Lemaître
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-769622, Villeurbanne, France
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33
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García Pascual B, Nordbotten JM, Johnston IG. Cellular and environmental dynamics influence species-specific extents of organelle gene retention. Proc Biol Sci 2023; 290:20222140. [PMID: 36883279 PMCID: PMC9993063 DOI: 10.1098/rspb.2022.2140] [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] [Indexed: 03/09/2023] Open
Abstract
Mitochondria and plastids rely on many nuclear-encoded genes, but retain small subsets of the genes they need to function in their own organelle DNA (oDNA). Different species retain different numbers of oDNA genes, and the reasons for these differences are not completely understood. Here, we use a mathematical model to explore the hypothesis that the energetic demands imposed by an organism's changing environment influence how many oDNA genes it retains. The model couples the physical biology of cell processes of gene expression and transport to a supply-and-demand model for the environmental dynamics to which an organism is exposed. The trade-off between fulfilling metabolic and bioenergetic environmental demands, and retaining genetic integrity, is quantified for a generic gene encoded either in oDNA or in nuclear DNA. Species in environments with high-amplitude, intermediate-frequency oscillations are predicted to retain the most organelle genes, whereas those in less dynamic or noisy environments the fewest. We discuss support for, and insight from, these predictions with oDNA data across eukaryotic taxa, including high oDNA gene counts in sessile organisms exposed to day-night and intertidal oscillations (including plants and algae) and low counts in parasites and fungi.
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Affiliation(s)
| | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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34
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Zhang S, Wang J, He W, Kan S, Liao X, Jordan DR, Mace ES, Tao Y, Cruickshank AW, Klein R, Yuan D, Tembrock LR, Wu Z. Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution. BMC PLANT BIOLOGY 2023; 23:91. [PMID: 36782130 PMCID: PMC9926791 DOI: 10.1186/s12870-023-04104-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism. RESULTS Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa. CONCLUSIONS We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.
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Affiliation(s)
- Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hubei, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - David R Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, 4370, Australia
| | - Emma S Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, 4370, Australia
| | - Alan W Cruickshank
- Department of Agriculture and Fisheries (DAF), Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland, 4370, Australia
| | - Robert Klein
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, Texas, 77845, USA
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hubei, Wuhan, 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China.
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35
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Sharbrough J, Bankers L, Cook E, Fields PD, Jalinsky J, McElroy KE, Neiman M, Logsdon JM, Boore JL. Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination. Mol Biol Evol 2023; 40:6980790. [PMID: 36625177 PMCID: PMC9874032 DOI: 10.1093/molbev/msad007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of the mitochondrial genome architecture and recombination. We used PacBio sequencing to reassemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by an assembly of short reads and likely corresponding to a large noncoding region commonly present in the mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy (LSC) region and a small single-copy (SSC) region separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of a "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between single-nucleotide polymorphisms in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.
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Affiliation(s)
| | - Laura Bankers
- Department of Biology, University of Iowa, Iowa City, IA
| | - Emily Cook
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801
| | - Peter D Fields
- Zoologisches Institut, University of Basel, Basel, Switzerland
| | | | - Kyle E McElroy
- Department of Biology, University of Iowa, Iowa City, IA,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, IA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA
| | - Jeffrey L Boore
- Phenome Health and Institute for Systems Biology, Seattle, WA
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36
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Morales J, Ehret G, Poschmann G, Reinicke T, Maurya AK, Kröninger L, Zanini D, Wolters R, Kalyanaraman D, Krakovka M, Bäumers M, Stühler K, Nowack ECM. Host-symbiont interactions in Angomonas deanei include the evolution of a host-derived dynamin ring around the endosymbiont division site. Curr Biol 2023; 33:28-40.e7. [PMID: 36480982 DOI: 10.1016/j.cub.2022.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/09/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
The trypanosomatid Angomonas deanei is a model to study endosymbiosis. Each cell contains a single β-proteobacterial endosymbiont that divides at a defined point in the host cell cycle and contributes essential metabolites to the host metabolism. Additionally, one endosymbiont gene, encoding an ornithine cyclodeaminase (OCD), was transferred by endosymbiotic gene transfer (EGT) to the nucleus. However, the molecular mechanisms mediating the intricate host/symbiont interactions are largely unexplored. Here, we used protein mass spectrometry to identify nucleus-encoded proteins that co-purify with the endosymbiont. Expression of fluorescent fusion constructs of these proteins in A. deanei confirmed seven host proteins to be recruited to specific sites within the endosymbiont. These endosymbiont-targeted proteins (ETPs) include two proteins annotated as dynamin-like protein and peptidoglycan hydrolase that form a ring-shaped structure around the endosymbiont division site that remarkably resembles organellar division machineries. The EGT-derived OCD was not among the ETPs, but instead localizes to the glycosome, likely enabling proline production in the glycosome. We hypothesize that recalibration of the metabolic capacity of the glycosomes that are closely associated with the endosymbiont helps to supply the endosymbiont with metabolites it is auxotrophic for and thus supports the integration of host and endosymbiont metabolic networks. Hence, scrutiny of endosymbiosis-induced protein re-localization patterns in A. deanei yielded profound insights into how an endosymbiotic relationship can stabilize and deepen over time far beyond the level of metabolite exchange.
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Affiliation(s)
- Jorge Morales
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Georg Ehret
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Tobias Reinicke
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Anay K Maurya
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Lena Kröninger
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Davide Zanini
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Rebecca Wolters
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Dhevi Kalyanaraman
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Michael Krakovka
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Miriam Bäumers
- Center for Advanced Imaging, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany; Molecular Proteomics Laboratory, Biological and Medical Research Centre (BMFZ), Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Eva C M Nowack
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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37
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Sloan DB, Warren JM, Williams AM, Kuster SA, Forsythe ES. Incompatibility and Interchangeability in Molecular Evolution. Genome Biol Evol 2023; 15:evac184. [PMID: 36583227 PMCID: PMC9839398 DOI: 10.1093/gbe/evac184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Jessica M Warren
- Center for Mechanisms of Evolution, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Alissa M Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, Colorado
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38
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Marszalek J, Craig EA, Tomiczek B. J-Domain Proteins Orchestrate the Multifunctionality of Hsp70s in Mitochondria: Insights from Mechanistic and Evolutionary Analyses. Subcell Biochem 2023; 101:293-318. [PMID: 36520311 DOI: 10.1007/978-3-031-14740-1_10] [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] [Indexed: 06/17/2023]
Abstract
Mitochondrial J-domain protein (JDP) co-chaperones orchestrate the function of their Hsp70 chaperone partner(s) in critical organellar processes that are essential for cell function. These include folding, refolding, and import of mitochondrial proteins, maintenance of mitochondrial DNA, and biogenesis of iron-sulfur cluster(s) (FeS), prosthetic groups needed for function of mitochondrial and cytosolic proteins. Consistent with the organelle's endosymbiotic origin, mitochondrial Hsp70 and the JDPs' functioning in protein folding and FeS biogenesis clearly descended from bacteria, while the origin of the JDP involved in protein import is less evident. Regardless of their origin, all mitochondrial JDP/Hsp70 systems evolved unique features that allowed them to perform mitochondria-specific functions. Their modes of functional diversification and specialization illustrate the versatility of JDP/Hsp70 systems and inform our understanding of system functioning in other cellular compartments.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bartlomiej Tomiczek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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39
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Chrzanowska-Lightowlers ZM, Lightowlers RN. Translation in Mitochondrial Ribosomes. Methods Mol Biol 2023; 2661:53-72. [PMID: 37166631 DOI: 10.1007/978-1-0716-3171-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitochondrial protein synthesis is essential for the life of aerobic eukaryotes. Without it, oxidative phosphorylation cannot be coupled. Evolution has shaped a battery of factors and machinery that are key to production of just a handful of critical proteins. In this general concept chapter, we attempt to briefly summarize our current knowledge of the overall process in mitochondria from a variety of species, breaking this down to the four parts of translation: initiation, elongation, termination, and recycling. Where appropriate, we highlight differences between species and emphasize gaps in our understanding. Excitingly, with the current revolution in cryoelectron microscopy and mitochondrial genome editing, it is highly likely that many of these gaps will be resolved in the near future. However, the absence of a faithful in vitro reconstituted system to study mitochondrial translation is still problematic.
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Affiliation(s)
- Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK.
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
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40
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Rozov SM, Zagorskaya AA, Konstantinov YM, Deineko EV. Three Parts of the Plant Genome: On the Way to Success in the Production of Recombinant Proteins. PLANTS (BASEL, SWITZERLAND) 2022; 12:38. [PMID: 36616166 PMCID: PMC9824153 DOI: 10.3390/plants12010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are the most important product of current industrial biotechnology. They are indispensable in medicine (for diagnostics and treatment), food and chemical industries, and research. Plant cells combine advantages of the eukaryotic protein production system with simplicity and efficacy of the bacterial one. The use of plants for the production of recombinant proteins is an economically important and promising area that has emerged as an alternative to traditional approaches. This review discusses advantages of plant systems for the expression of recombinant proteins using nuclear, plastid, and mitochondrial genomes. Possibilities, problems, and prospects of modifications of the three parts of the genome in light of obtaining producer plants are examined. Examples of successful use of the nuclear expression platform for production of various biopharmaceuticals, veterinary drugs, and technologically important proteins are described, as are examples of a high yield of recombinant proteins upon modification of the chloroplast genome. Potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated. Although these opportunities have not yet been exploited, potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated.
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Affiliation(s)
- Sergey M. Rozov
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Alla A. Zagorskaya
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Yuri M. Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, Lermontova Str. 132, Irkutsk 664033, Russia
| | - Elena V. Deineko
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
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41
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Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention. Cell Syst 2022; 13:874-884.e5. [PMID: 36115336 DOI: 10.1016/j.cels.2022.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 01/26/2023]
Abstract
Mitochondria and plastids power complex life. Why some genes and not others are retained in their organelle DNA (oDNA) genomes remains a debated question. Here, we attempt to identify the properties of genes and associated underlying mechanisms that determine oDNA retention. We harness over 15k oDNA sequences and over 300 whole genome sequences across eukaryotes with tools from structural biology, bioinformatics, machine learning, and Bayesian model selection. Previously hypothesized features, including the hydrophobicity of a protein product, and less well-known features, including binding energy centrality within a protein complex, predict oDNA retention across eukaryotes, with additional influences of nucleic acid and amino acid biochemistry. Notably, the same features predict retention in both organelles, and retention models learned from one organelle type quantitatively predict retention in the other, supporting the universality of these features-which also distinguish gene profiles in more recent, independent endosymbiotic relationships. A record of this paper's transparent peer review process is included in the supplemental information.
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42
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Weaver RJ, Rabinowitz S, Thueson K, Havird JC. Genomic Signatures of Mitonuclear Coevolution in Mammals. Mol Biol Evol 2022; 39:6775223. [PMID: 36288802 PMCID: PMC9641969 DOI: 10.1093/molbev/msac233] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial (mt) and nuclear-encoded proteins are integrated in aerobic respiration, requiring co-functionality among gene products from fundamentally different genomes. Different evolutionary rates, inheritance mechanisms, and selection pressures set the stage for incompatibilities between interacting products of the two genomes. The mitonuclear coevolution hypothesis posits that incompatibilities may be avoided if evolution in one genome selects for complementary changes in interacting genes encoded by the other genome. Nuclear compensation, in which deleterious mtDNA changes are offset by compensatory nuclear changes, is often invoked as the primary mechanism for mitonuclear coevolution. Yet, direct evidence supporting nuclear compensation is rare. Here, we used data from 58 mammalian species representing eight orders to show strong correlations between evolutionary rates of mt and nuclear-encoded mt-targeted (N-mt) proteins, but not between mt and non-mt-targeted nuclear proteins, providing strong support for mitonuclear coevolution across mammals. N-mt genes with direct mt interactions also showed the strongest correlations. Although most N-mt genes had elevated dN/dS ratios compared to mt genes (as predicted under nuclear compensation), N-mt sites in close contact with mt proteins were not overrepresented for signs of positive selection compared to noncontact N-mt sites (contrary to predictions of nuclear compensation). Furthermore, temporal patterns of N-mt and mt amino acid substitutions did not support predictions of nuclear compensation, even in positively selected, functionally important residues with direct mitonuclear contacts. Overall, our results strongly support mitonuclear coevolution across ∼170 million years of mammalian evolution but fail to support nuclear compensation as the major mode of mitonuclear coevolution.
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Affiliation(s)
- Ryan J Weaver
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA.,Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA
| | | | - Kiley Thueson
- Department of Integrative Biology, University of Texas, Austin, TX
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX
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Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements. Nat Commun 2022; 13:6132. [PMID: 36253367 PMCID: PMC9576764 DOI: 10.1038/s41467-022-33582-5] [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: 01/30/2022] [Accepted: 09/22/2022] [Indexed: 12/24/2022] Open
Abstract
Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.
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44
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Marszalek J, Craig EA. Interaction of client—the scaffold on which FeS clusters are build—with J-domain protein Hsc20 and its evolving Hsp70 partners. Front Mol Biosci 2022; 9:1034453. [PMID: 36310602 PMCID: PMC9596805 DOI: 10.3389/fmolb.2022.1034453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
In cells molecular chaperone systems consisting of Hsp70 and its obligatory J-domain protein (JDP) co-chaperones transiently interact with a myriad of client proteins—with JDPs typically recruiting their partner Hsp70 to interact with particular clients. The fundamentals of this cyclical interactions between JDP/Hsp70 systems and clients are well established. Much less is known about other aspects of JDP/Hsp70 system function, including how such systems evolved over time. Here we discuss the JDP/Hsp70 system involved in the biogenesis of iron-sulfur (FeS) clusters. Interaction between the client protein, the scaffold on which clusters are built, and its specialized JDP Hsc20 has stayed constant. However, the system’s Hsp70 has changed at least twice. In some species Hsc20’s Hsp70 partner interacts only with the scaffold, in others it has many JDP partners in addition to Hsc20 and interacts with many client proteins. Analysis of this switching of Hsp70 partners has provided insight into the insulation of JDP/Hsp70 systems from one another that can occur when more than one Hsp70 is present in a cellular compartment, as well as how competition among JDPs is balanced when an Hsp70 partner is shared amongst a number of JDPs. Of particularly broad relevance, even though the scaffold’s interactions with Hsc20 and Hsp70 are functionally critical for the biogenesis of FeS cluster-containing proteins, it is the modulation of the Hsc20-Hsp70 interaction per se that allows Hsc20 to function with such different Hsp70 partners.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- *Correspondence: Jaroslaw Marszalek, ; Elizabeth A. Craig,
| | - Elizabeth A. Craig
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI, United States
- *Correspondence: Jaroslaw Marszalek, ; Elizabeth A. Craig,
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45
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Tilney CL, Hubbard KA. Expression of nuclear-encoded, haptophyte-derived ftsH genes support extremely rapid PSII repair and high-light photoacclimation in Karenia brevis (Dinophyceae). HARMFUL ALGAE 2022; 118:102295. [PMID: 36195421 DOI: 10.1016/j.hal.2022.102295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
Karenia brevis, a neurotoxic dinoflagellate that produces brevetoxins, is endemic to the Gulf of Mexico and can grow at high irradiances typical of surface waters found there. To build upon a growing number of studies addressing high-light tolerance in K. brevis, specific photobiology and molecular mechanisms underlying this capacity were evaluated in culture. Since photosystem II (PSII) repair cycle activity can be crucial to high light tolerance in plants and algae, the present study assessed this capacity in K. brevis and characterized the ftsH-like genes which are fundamental to this process. Compared with cultures grown in low-light, cultures grown in high-light showed a 65-fold increase in PSII photoinactivation, a ∼50-fold increase in PSII repair, enhanced nonphotochemical quenching (NPQ), and depressed Fv/Fm. Repair rates were among the fastest reported in phytoplankton. Publicly available K. brevis transcriptomes (MMETSP) were queried for ftsH-like sequences and refined with additional sequencing from two K. brevis strains. The genes were phylogenetically related to haptophyte orthologs, implicating acquisition during tertiary endosymbiosis. RT-qPCR of three of the four ftsH-like homologs revealed that poly-A tails predominated in all homologs, and that the most highly expressed homolog had a 5' splice leader and amino-acid motifs characteristic of chloroplast targeting, indicating nuclear encoding for this plastid-targeted gene. High-light cultures showed a ∼1.5-fold upregulation in mRNA expression of the thylakoid-associated genes. Overall, in conjunction with NPQ mechanisms, rapid PSII repair mediated by a haptophyte-derived ftsH prevents chronic photoinhibition in K. brevis. Our findings continue to build the case that high-light photobiology-supported by the acquisition and maintenance of tertiary endosymbiotic genes-is critical to the success of K. brevis in the Gulf of Mexico.
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Affiliation(s)
- Charles L Tilney
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA; Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, Québec, G5M 1L7, Canada.
| | - Katherine A Hubbard
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA
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46
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Kang Z, Chen F, Wu W, Liu R, Chen T, Xu F. UPRmt and coordinated UPRER in type 2 diabetes. Front Cell Dev Biol 2022; 10:974083. [PMID: 36187475 PMCID: PMC9523447 DOI: 10.3389/fcell.2022.974083] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial unfolded protein response (UPRmt) is a molecular mechanism that maintains mitochondrial proteostasis under stress and is closely related to various metabolic diseases, such as type 2 diabetes (T2D). Similarly, the unfolded protein response of the endoplasmic reticulum (UPRER) is responsible for maintaining proteomic stability in the endoplasmic reticulum (ER). Since the mitochondria and endoplasmic reticulum are the primary centers of energy metabolism and protein synthesis in cells, respectively, a synergistic mechanism must exist between UPRmt and UPRER to cooperatively resist stresses such as hyperglycemia in T2D. Increasing evidence suggests that the protein kinase RNA (PKR)-like endoplasmic reticulum kinase (PERK) signaling pathway is likely an important node for coordinating UPRmt and UPRER. The PERK pathway is activated in both UPRmt and UPRER, and its downstream molecules perform important functions. In this review, we discuss the mechanisms of UPRmt, UPRER and their crosstalk in T2D.
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Affiliation(s)
- Zhanfang Kang
- Department of Basic Medical Research, Qingyuan People’s Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Feng Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Wanhui Wu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Rui Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Tianda Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Fang Xu
- Department of Basic Medical Research, Qingyuan People’s Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Fang Xu,
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47
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The recipe for cytonuclear interaction begins with a superabundance of plastid and mitochondrial mRNAs. Proc Natl Acad Sci U S A 2022; 119:e2211133119. [PMID: 35943977 PMCID: PMC9407606 DOI: 10.1073/pnas.2211133119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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48
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Forsythe ES, Grover CE, Miller ER, Conover JL, Arick MA, Chavarro MCF, Leal-Bertioli SCM, Peterson DG, Sharbrough J, Wendel JF, Sloan DB. Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels. Proc Natl Acad Sci U S A 2022; 119:e2204187119. [PMID: 35858449 PMCID: PMC9335225 DOI: 10.1073/pnas.2204187119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/14/2022] [Indexed: 01/21/2023] Open
Abstract
Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.
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Affiliation(s)
- Evan S. Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Justin L. Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Mark A. Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762
| | - M. Carolina F. Chavarro
- Institute of Plant Breeding, Genetics and Genomics, Athens, GA 30602
- Bayer Crop Science, Chesterfield, MO 63017
| | | | - Daniel G. Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
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49
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Camus MF, Alexander-Lawrie B, Sharbrough J, Hurst GDD. Inheritance through the cytoplasm. Heredity (Edinb) 2022; 129:31-43. [PMID: 35525886 PMCID: PMC9273588 DOI: 10.1038/s41437-022-00540-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.
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Affiliation(s)
- M Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England
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50
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Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. Sci Rep 2022; 12:11040. [PMID: 35773462 PMCID: PMC9247169 DOI: 10.1038/s41598-022-15076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia.
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