1
|
Jin X, Lin X, Wang S, Fang J. Complete Mitochondrial Genome of Chlorogomphus papilio (Odonata: Anisoptera: Chlorogomphidae) and Phylogenetic Analyses. BIOLOGY 2025; 14:493. [PMID: 40427682 DOI: 10.3390/biology14050493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 04/28/2025] [Accepted: 04/29/2025] [Indexed: 05/29/2025]
Abstract
This study aimed to elucidate the mitochondrial genome organization of Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, maximum likelihood, and maximum parsimony methods were employed to construct the mitochondrial phylogenetic tree of 25 species of Chlorogomphidae based on 16S rRNA and cox1 genes. We observed that the mitochondrial genome of C. papilio is 15,251 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region. All PCGs start with a typical ATN codon. While cox1, cox2, cox3, and nad5 end with an incomplete termination codon (T), the remaining PCGs terminate with TAG. The secondary structure of the 22 tRNAs showed that only the trnS1 gene lacked the dihydrouracil arm (DHU arm), whereas the rest formed a typical cloverleaf structure. Additionally, 32 G-U mismatches were observed in the secondary structure. Phylogenetic analyses indicated that C. papilio and C. magnificus are sister species. Divergence time analyses indicated that Chlorogomphidae originated around 111.04 Ma, with C. papilio diverging from the common ancestor shared with C. magnificus approximately 58.51 Ma. This divergence is likely linked to the Paleocene-Eocene Thermal Maximum (PETM) and the tectonic uplift of the Himalayas, which created warm, humid habitats and contributed to geographic isolation. This study contributes to a better understanding of the mitochondrial genome and phylogeny of C. papilio, providing valuable molecular markers for further genetic studies.
Collapse
Affiliation(s)
- Xiaoxiao Jin
- School of Life Sciences, Anhui University, Hefei 230601, China
| | - Xiaojia Lin
- Technology Center of Hangzhou Customs District, Hangzhou 310016, China
| | - Simeng Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Jie Fang
- School of Life Sciences, Anhui University, Hefei 230601, China
| |
Collapse
|
2
|
Chung KP. Cytoplasmic inheritance: The transmission of plastid and mitochondrial genomes across cells and generations. PLANT PHYSIOLOGY 2025; 198:kiaf168. [PMID: 40304456 PMCID: PMC12079397 DOI: 10.1093/plphys/kiaf168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/24/2025] [Accepted: 04/28/2025] [Indexed: 05/02/2025]
Abstract
In photosynthetic organisms, genetic material is stored in the nucleus and the two cytoplasmic organelles: plastids and mitochondria. While both the nuclear and cytoplasmic genomes are essential for survival, the inheritance of these genomes is subject to distinct laws. Cytoplasmic inheritance differs fundamentally from nuclear inheritance through two unique processes: vegetative segregation and uniparental inheritance. To illustrate the significance of these processes in shaping cytoplasmic inheritance, I will trace the journey of plastid and mitochondrial genomes, following their transmission from parents to progeny. The cellular and molecular mechanisms regulating their transmission along the path are explored. By providing a framework that encompasses the inheritance of both plastid and mitochondrial genomes across cells and generations, I aim to present a comprehensive overview of cytoplasmic inheritance and highlight the intricate interplay of cellular processes that determine inheritance patterns. I will conclude this review by summarizing recent breakthroughs in the field that have significantly advanced our understanding of cytoplasmic inheritance. This knowledge has paved the way for achieving the first instance of controlled cytoplasmic inheritance in plants, unlocking the potential to harness cytoplasmic genetics for crop improvement.
Collapse
Affiliation(s)
- Kin Pan Chung
- Laboratory of Plant Physiology, Wageningen University & Research, Wageningen 6708 PB, the Netherlands
| |
Collapse
|
3
|
Erić P, Veselinović MS, Patenković A, Tanasković M, Kenig B, Erić K, Inđić B, Stanovčić S, Jelić M. Mechanisms Maintaining Mitochondrial DNA Polymorphisms: The Role of Mito-Nuclear Interactions, Sex-Specific Selection, and Genotype-by-Environment Interactions in Drosophila subobscura. INSECTS 2025; 16:415. [PMID: 40332919 PMCID: PMC12027999 DOI: 10.3390/insects16040415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2025] [Revised: 04/01/2025] [Accepted: 04/11/2025] [Indexed: 05/08/2025]
Abstract
Experimental mito-nuclear introgression lines (MNILs) were established by backcrossing isofemale lines of D. subobscura originating from the same populations. MNILs were subjected to a series of life-history experiments designed to test the fitness of the bearers of different combinations of two main mtDNA haplotypes on their own nuclear background, as well as on the background of the opposite haplotype. By having 11 replicas of the four mito-nuclear combinations, we could test not only the adaptive significance of the differences between the two main haplotypes but also the influence of additional variation present within each of the 11 combinations on fitness. Testing the fitness of individuals of both sexes enabled us to examine if sex-specific selection has a role in maintaining the frequencies of the two mtDNA haplotypes in nature. Conducting the fitness assays on two different temperatures enabled us to test whether different temperatures favor specific mtDNA haplotypes or mito-nuclear genotypes and consequently promote stable sympatric mtDNA variation. The results show weak signature of genotype-by-environment interactions, and no sex-specific selection regarding differences between the two main haplotypes. However, individual models across different life-history components showed these two mechanisms at play in promoting mtDNA variability present in specific mito-nuclear crosses. Our models show that mito-nuclear interactions are, in fact, more important as units of selection.
Collapse
Affiliation(s)
- Pavle Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (M.T.); (K.E.)
| | - Marija Savić Veselinović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.J.)
| | - Aleksandra Patenković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (M.T.); (K.E.)
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (M.T.); (K.E.)
| | - Bojan Kenig
- The Center for Promotion of Science, Kralja Petra 46, 11000 Belgrade, Serbia;
| | - Katarina Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (M.T.); (K.E.)
| | - Boris Inđić
- Forest Microbial Genomics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Bajcsy-Zsilinszky str. 4, H-9400 Sopron, Hungary;
| | - Stefan Stanovčić
- Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444a, 11000 Belgrade, Serbia;
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.J.)
| |
Collapse
|
4
|
Wang H, Wang D, Shao B, Li J, Li Z, Chase MW, Li J, Feng Y, Wen Y, Qin S, Chen B, Wu Z, Jin X. Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera. Mol Biol Evol 2025; 42:msaf082. [PMID: 40189939 PMCID: PMC12022611 DOI: 10.1093/molbev/msaf082] [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: 10/12/2024] [Revised: 03/12/2025] [Accepted: 04/01/2025] [Indexed: 04/26/2025] Open
Abstract
The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.
Collapse
Affiliation(s)
- Hanchen Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Deyi Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Bingyi Shao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingrui Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhanghai Li
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming, China
| | - Mark W Chase
- Department of Environment and Agriculture, Curtin University, Bentley, Australia
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Jianwu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla County, Yunnan, China
| | - Yanlei Feng
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yingying Wen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shiyu Qin
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Binghua Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhiqiang Wu
- 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, China
| | - Xiaohua Jin
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
5
|
Chacko LA, Nakaoka H, Morris R, Marshall W, Ananthanarayanan V. Mitochondrial function regulates cell growth kinetics to actively maintain mitochondrial homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.31.646474. [PMID: 40236014 PMCID: PMC11996537 DOI: 10.1101/2025.03.31.646474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Mitochondria are not produced de novo in newly divided daughter cells, but are inherited from the mother cell during mitosis. While mitochondrial homeostasis is crucial for living cells, the feedback responses that maintain mitochondrial volume across generations of dividing cells remain elusive. Here, using a microfluidic yeast 'mother machine', we tracked several generations of fission yeast cells and observed that cell size and mitochondrial volume grew exponentially during the cell cycle. We discovered that while mitochondrial homeostasis relied on the 'sizer' mechanism of cell size maintenance, mitochondrial function was a critical determinant of the timing of cell division: cells born with lower than average amounts of mitochondria grew slower and thus added more mitochondria before they divided. Thus, mitochondrial addition during the cell cycle was tailored to the volume of mitochondria at birth, such that all cells ultimately contained the same mitochondrial volume at cell division. Quantitative modelling and experiments with mitochondrial DNA-deficient rho0 cells additionally revealed that mitochondrial function was essential for driving the exponential growth of cells. Taken together, we demonstrate a central role for mitochondrial activity in dictating cellular growth rates and ensuring mitochondrial volume homeostasis.
Collapse
|
6
|
Gao C, Wang S, Huang Y, Deng Y. Assembly and comparative analysis of the complete mitochondrial genome of Echinacanthus longipes (Acanthaceae), endemic to the Sino-Vietnamese karst flora. BMC Genomics 2025; 26:251. [PMID: 40087565 PMCID: PMC11908007 DOI: 10.1186/s12864-025-11448-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 03/05/2025] [Indexed: 03/17/2025] Open
Abstract
BACKGROUND Echinacanthus longipes is an endemic species in the Sino-Vietnamese karst flora in the family Acanthaceae. It displays distinctive environmental adaptation characteristics in karst regions. Although it provides an important model for understanding the role of limestone karst in speciation and endemism, the mitochondrial genome (mtDNA) of E. longipes has not been fully characterized. RESULTS Here, the mtDNA of E. longipes was successfully assembled as a complex structure in the form of two small circular and three linear molecules with a total length of 810,200 bp. The annotated results revealed 36 protein-coding genes (PCGs), 22 tRNA genes, and three rRNA genes in this mtDNA. Notably, substantial sequence repeats and more tRNAs translocations from the chloroplast to the mtDNA were identified. Among the PCGs of E. longipes, the majority of 401 RNA editing sites were involved in amino acid transitions to hydrophobic sites. The current phylogenetic analysis based on PCGs revealed the evolution of Lamiales and a close relationship between E. longipes and Avicennia marina. However, comparative analyses, including size, structure, GC contents, and genes, reflected the variation in the mitogenomes within Acanthaceae, and the collinearity analysis confirmed the low level of conservation in the genomes of related species in Lamiales. Moreover, the Ka/Ks analysis revealed that negative selection occurred on most PCGs, with the notable exception of ccmB, which underwent positive selection. Interestingly, the ccmB gene had the most protein editing sites. CONCLUSIONS This study will be invaluable for the mitochondrial study of Acanthaceae. It also provides extensive information for functional genetic and adaptive studies of Echinacanthus in karst regions in the future.
Collapse
Affiliation(s)
- Chunming Gao
- College of Biological and Environmental Engineering, Shandong University of Aeronautics, Binzhou, 256600, China
| | - Shu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yusong Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Guangxi Key Laboratory of Functional Phytochemicals Research and Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, Guangxi, 541006, China
| | - Yunfei Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou, 510650, China.
- Southeast Asia Bioaffiliationersity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar.
| |
Collapse
|
7
|
Yuan F, Zhou L, Wei X, Shang C, Zhang Z. Comparative Chloroplast Genomics Reveals Intrageneric Divergence in Salix. Int J Mol Sci 2025; 26:2248. [PMID: 40076872 PMCID: PMC11900436 DOI: 10.3390/ijms26052248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 02/22/2025] [Accepted: 02/27/2025] [Indexed: 03/14/2025] Open
Abstract
As the most diverse genus of Salicaceae, Salix is primarily distributed in the temperate zone of the Northern Hemisphere, encompassing 350-500 species worldwide. The genus's evolutionary history is complex due to significant genetic differentiation. Chloroplast genes, being highly conserved, serve as effective tools for studying uniparental inheritance and evolution. In this study, we sequenced and assembled the chloroplast genomes of five representative Salix species. Phylogenetic relationships were constructed using chloroplast genome data, and structural differences among lineages were compared. These Salix chloroplast genomes exhibited a typical quadripartite structure, with lengths ranging from 154,444 to 155,725 bp. We successfully annotated 131 genes, including 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Clade I showed higher variability in the SSC region, identifying five highly variable regions: petA-psbJ, rps16-rps3, ndhD, ccsA-ndhD, and ndhG-ndhI. Two rapidly evolving genes, ndhI and ycf4, were also identified. The total length of insertions and deletions (InDels) in Clade I was 1046 bp. Clade II exhibited greater variability in the LSC region, with four highly variable regions being identified: trnK-trnQ, ndhC-trnV, trnV, and psdE-petL. Four rapidly evolving genes-infA, rpoC1, rps18, and ycf1-were identified. The total length of InDels in Clade II was 1282 bp. Therefore, this study elucidated the chloroplast genome evolution across different Salix lineages, thereby providing deeper insights into intrageneric phylogenetic relationships.
Collapse
Affiliation(s)
| | | | | | - Ce Shang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (F.Y.); (L.Z.); (X.W.)
| | - Zhixiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (F.Y.); (L.Z.); (X.W.)
| |
Collapse
|
8
|
Yong Y, Wang Y, Wang D, Yuan X, Zhang Q. The organelle genomes of the endangered seagrass Zostera caespitosa reveal sequence divergences, massive gene transfer, and uncommon RNA editing types. FRONTIERS IN PLANT SCIENCE 2025; 16:1550467. [PMID: 40034153 PMCID: PMC11873085 DOI: 10.3389/fpls.2025.1550467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Accepted: 01/20/2025] [Indexed: 03/05/2025]
Abstract
Introduction Zostera caespitosa, a rare submerged angiosperm, is considered endemic to the northwestern Pacific. Methods This study assembled and compared the mitochondrial (mt) and chloroplast (cp) genomes of Z. caespitosa to understand the organelle evolutionary patterns. Results and discussion The cp genome (143,972 bp) was the second smallest within the seagrasses, whereas the mt genomes (192,246 bp) of Z. caespitosa and other seagrasses were smaller compared to those of other monocotyledons. The protein-coding genes (PCGs) in the organelle genome exhibit a strong A/U bias at codon endings, a selection-driven codon bias. The rates of nonsynonymous (Ka) and synonymous (Ks) substitutions in the mt genes of Zostera were two times higher than those in the cp genes. Additionally, 50 mitochondrial plastid DNA (MTPT) segments, totaling 44,662 bp, were identified, constituting 23.23% of the mt genome, which is significantly higher than those in most land plants. Phylogenetic analysis of 13 seagrass core cp-PCGs supported previous studies showing two genera in family Zosteraceae: Phyllospadix and Zostera, the latter comprising Zostera and Zosterella as subgenera. RNA editing was remarkably abundant in the 167 mt-PCGs and 172 in cp-PCGs, particularly in the cp genome. There are 11 different RNA editing types in the cp and 3 in the mt, most of which are C to U. Unexpectedly rare editing events, such as A to C, A to U, U to A, G to C, and U to G, have also been found in the cp.
Collapse
Affiliation(s)
- Yushun Yong
- Ocean School, Yantai University, Yantai, China
| | - Yulian Wang
- No. 6 Geological Team, Shandong Provincial Bureau of Geology and Mineral Resources, Weihai, China
| | - Dawei Wang
- No. 6 Geological Team, Shandong Provincial Bureau of Geology and Mineral Resources, Weihai, China
| | - Xingfang Yuan
- No. 6 Geological Team, Shandong Provincial Bureau of Geology and Mineral Resources, Weihai, China
| | | |
Collapse
|
9
|
Li ZZ, Wang Y, He XY, Li WG. The Taihangia mitogenome provides new insights into its adaptation and organelle genome evolution in Rosaceae. PLANTA 2025; 261:59. [PMID: 39939538 DOI: 10.1007/s00425-025-04629-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: 11/29/2024] [Accepted: 01/19/2025] [Indexed: 02/14/2025]
Abstract
MAIN CONCLUSION We present the first Taihangia mitogenome, uncovering frequent rearrangements and significant length variation in Rosaceae, likely driven by hybridization and repeat content, alongside widespread mito-chloroplast phylogenetic conflicts. Taihangia, an ancient and endangered monotypic genus within the subfamily Rosoideae of the family Rosaceae, is endemic to cliffs and serves as an ideal material for studying the adaptations of cliff-dwelling plants and the evolutionary processes of the Rosaceae family. In this study, the mitogenome and plastome of T. rupestris var. ciliata were assembled, with lengths of 265,633 bp and 155,467 bp, both exhibiting typical circular structures. Positive selection was detected in the nad4L and sdh4 genes, likely playing a role in adaptation to harsh environments. Comparative genomic analysis indicated that repetitive sequences are likely the main contributors to genome size variation in Rosaceae and also influence horizontal gene transfer between organelle genomes. In T. rupestris var. ciliata, 20 mitochondrial plastid DNA sequences were identified, including 16 complete plastid genes. Moreover, frequent rearrangements were observed in the non-coding regions of mitogenome within the subfamily Rosoideae, potentially linked to the complex evolutionary history and the presence of repetitive sequences. In contrast, coding regions remained highly conserved (over 83% similarity) to maintain essential mitochondrial functions. Phylogenomic analysis of the two organelle genomes revealed conflicts in the phylogenetic relationships within Rosaceae, potentially due to the inconsistent mutation rates and frequent hybridization events in the evolutionary history of the family. In conclusion, the organelle genome analysis of Taihangia provides crucial genomic resources for understanding the evolution and adaptation of Rosaceae species.
Collapse
Affiliation(s)
- Zhi-Zhong Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in WanjiangBasin Co-Funded By Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Ying Wang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in WanjiangBasin Co-Funded By Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Xiang-Yan He
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei-Guo Li
- School of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000, Henan, China.
| |
Collapse
|
10
|
Toups BS, Thomson RC, Brown JM. Complex Models of Sequence Evolution Improve Fit, But Not Gene Tree Discordance, for Tetrapod Mitogenomes. Syst Biol 2025; 74:86-100. [PMID: 39392926 DOI: 10.1093/sysbio/syae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 08/22/2024] [Accepted: 10/09/2024] [Indexed: 10/13/2024] Open
Abstract
Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial data sets as the previous study using 2 additional, more complex models of sequence evolution that each include a different biologically realistic aspect of the evolutionary process: A covarion model to incorporate site-specific rate variation across lineages (heterotachy), and a partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could, in fact, be biological in nature after all.
Collapse
Affiliation(s)
- Benjamin S Toups
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai'i, 3190 Maile Way, St. John 101, Honolulu, HI 96822, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
| |
Collapse
|
11
|
Fedotova EI, Berezhnov AV, Popov DY, Shitikova EY, Vinokurov AY. The Role of mtDNA Mutations in Atherosclerosis: The Influence of Mitochondrial Dysfunction on Macrophage Polarization. Int J Mol Sci 2025; 26:1019. [PMID: 39940788 PMCID: PMC11817597 DOI: 10.3390/ijms26031019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 01/06/2025] [Accepted: 01/15/2025] [Indexed: 02/16/2025] Open
Abstract
Atherosclerosis is a complex inflammatory process associated with high-mortality cardiovascular diseases. Today, there is a growing body of evidence linking atherosclerosis to mutations of mitochondrial DNA (mtDNA). But the mechanism of this link is insufficiently studied. Atherosclerosis progression involves different cell types and macrophages are one of the most important. Due to their high plasticity, macrophages can demonstrate pro-inflammatory and pro-atherogenic (macrophage type M1) or anti-inflammatory and anti-atherogenic (macrophage type M2) effects. These two cell types, formed as a result of external stimuli, differ significantly in their metabolic profile, which suggests the central role of mitochondria in the implementation of the macrophage polarization route. According to this, we assume that mtDNA mutations causing mitochondrial disturbances can play the role of an internal trigger, leading to the formation of macrophage M1 or M2. This review provides a comparative analysis of the characteristics of mitochondrial function in different types of macrophages and their possible associations with mtDNA mutations linked with inflammation-based pathologies including atherosclerosis.
Collapse
Affiliation(s)
- Evgeniya I. Fedotova
- Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino 142290, Russia; (E.I.F.); (A.V.B.)
- Cell Physiology and Pathology Laboratory, Orel State University, Orel 302026, Russia; (D.Y.P.); (E.Y.S.)
| | - Alexey V. Berezhnov
- Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino 142290, Russia; (E.I.F.); (A.V.B.)
- Cell Physiology and Pathology Laboratory, Orel State University, Orel 302026, Russia; (D.Y.P.); (E.Y.S.)
| | - Daniil Y. Popov
- Cell Physiology and Pathology Laboratory, Orel State University, Orel 302026, Russia; (D.Y.P.); (E.Y.S.)
| | - Elena Y. Shitikova
- Cell Physiology and Pathology Laboratory, Orel State University, Orel 302026, Russia; (D.Y.P.); (E.Y.S.)
| | - Andrey Y. Vinokurov
- Cell Physiology and Pathology Laboratory, Orel State University, Orel 302026, Russia; (D.Y.P.); (E.Y.S.)
| |
Collapse
|
12
|
Zhang H, Yan M, Li L, Jiang Z, Xiong Y, Wang Y, Akogwu CO, Tolulope OM, Zhou H, Sun Y, Wang H. Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer. BMC PLANT BIOLOGY 2025; 25:85. [PMID: 39838290 PMCID: PMC11752677 DOI: 10.1186/s12870-024-05969-7] [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: 09/11/2024] [Accepted: 12/13/2024] [Indexed: 01/23/2025]
Abstract
BACKGROUND Red raspberry (Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome. We sequenced and assembled the complete mitogenome of R. idaeus, and conducted a series of genetic investigations comparing it with the nuclear and chloroplast genomes, so as to better gain a comprehensive understanding of the species' genetic background. RESULTS The mitogenome is represented by one circular chromosome of 438,947 bp. Twenty-four core genes, nine variable genes, 26 tRNAs, and three rRNAs were annotated. A total of 52 SSRs and 38 tandem repeat sequences were identified. 533 pairs of dispersed repeats were detected, among which three pairs were found to have mediated the homologous recombination, resulting in one major conformation and seven minor conformations. Furthermore, 52 homologous sequences between the mitogenome and plastome were identified, including six complete protein-coding genes and 12 tRNA genes. We also detected 828 homologous fragments between the nuclear genome and mitogenome, including one trnM-CAU gene. CONCLUSIONS In this study, we presented the mitogenome of R. idaeus for the first time based on data obtained from Illumina and Oxford Nanopore sequencing platforms. Key characteristics of the mitogenome were examined, including its gene composition, repetitive elements, and homologous DNA fragments. Additionally, we identified multiple recombination events in the mitogenome mediated by repetitive sequences The high-quality and well-annotated mitogenome for the known fruit red raspberry will provide essential genetic information for species classification, evolution analysis, and even genetic improvement in Rubus in the future.
Collapse
Affiliation(s)
- Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghui Yan
- Dabie Mountain Laboratory, College of Tea and Food Science, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Xiong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yusheng Wang
- School of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Caleb Onoja Akogwu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Olutayo Mary Tolulope
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Zhou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
13
|
Li Y, Li S, Hua X, Xu Y, Chen S, Yu Z, Zhuang G, Lan Y, Yao W, Chen B, Zhang M, Zhang J. Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane. BMC Genomics 2025; 26:28. [PMID: 39794692 PMCID: PMC11724576 DOI: 10.1186/s12864-025-11210-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: 09/16/2024] [Accepted: 01/02/2025] [Indexed: 01/13/2025] Open
Abstract
BACKGROUND Sugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular "energy factories", provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS). RESULTS We performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species. CONCLUSION In this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane.
Collapse
Affiliation(s)
- Yihan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Shuangyu Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Yi Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Shuqi Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zehuai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Gui Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Yuhong Lan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China.
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
14
|
Collier SL, Farrell SN, Goodman CD, McFadden GI. Modes and mechanisms for the inheritance of mitochondria and plastids in pathogenic protists. PLoS Pathog 2025; 21:e1012835. [PMID: 39847585 PMCID: PMC11756805 DOI: 10.1371/journal.ppat.1012835] [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] [Indexed: 01/25/2025] Open
Abstract
Pathogenic protists are responsible for many diseases that significantly impact human and animal health across the globe. Almost all protists possess mitochondria or mitochondrion-related organelles, and many contain plastids. These endosymbiotic organelles are crucial to survival and provide well-validated and widely utilised drug targets in parasitic protists such as Plasmodium and Toxoplasma. However, mutations within the organellar genomes of mitochondria and plastids can lead to drug resistance. Such mutations ultimately challenge our ability to control and eradicate the diseases caused by these pathogenic protists. Therefore, it is important to understand how organellar genomes, and the resistance mutations encoded within them, are inherited during protist sexual reproduction and how this may impact the spread of drug resistance and future therapeutic approaches to target these organelles. In this review, we detail what is known about mitochondrial and plastid inheritance during sexual reproduction across different pathogenic protists, often turning to their better studied, nonpathogenic relatives for insight.
Collapse
Affiliation(s)
- Sophie L. Collier
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah N. Farrell
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Geoffrey I. McFadden
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
15
|
Carrari E, Bellandi A, Costafreda-Aumedes S, Dibari C, Ferrini F, Fineschi S, Giuntoli A, Manganelli Del Fa R, Moriondo M, Mozzo M, Padovan G, Riminesi C, Bindi M. A novel framework of smart monitoring to face the challenges of tree management in historic gardens. ENVIRONMENTAL RESEARCH 2024; 262:119790. [PMID: 39147189 DOI: 10.1016/j.envres.2024.119790] [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: 06/01/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
Historic gardens are green spaces characterised by tree stands with several veteran specimens of high artistic and cultural value. Such valuable plant components have to cope with biotic and abiotic stress factors as well as ongoing senescence processes. Maintaining tree health is therefore crucial to preserve their ecosystem services, but also to protect the monument and visitor health. In this context, finding smart, fast and cost-effective management solutions to monitor health and detect critical conditions for both stands and individual veteran trees can promote garden conservation. For this reason, we developed a novel framework based on Sentinel2 imagery, LiDAR sources and automatic cameras to identify risk spots regarding trees in historic gardens. The pilot study area consists of two closed Italian gardens from the 16th century, which were analysed as a unique Historic Garden System (HGS). The tree health status at stand level was assessed using a criterion based on the Normalized Difference Vegetation Index weighed on tree volume (NDVIt) and validated by a visual crown defoliation assessment. At the tree level, the health status of four veteran trees defined by the NDVIt was also evaluated using green chromatic coordinates (GCC) obtained from digital images acquired by cameras at daily intervals during one growing season. The 33% of the tree population was classified as being in poor health, i.e. "at risk". Veteran trees classified as "at risk" showed an anticipation of phenological phases and a lower GCC compared to reference trees. Despite variability determined by Sentinel medium resolution, the proposed framework showed good accuracy (0.74) for monitoring historical gardens. The semi-automatic risk point mapping system tested here proved to be effective in facilitating the management of historic gardens, which in turn could be applied in the wider context of urban greening.
Collapse
Affiliation(s)
- Elisa Carrari
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P. le Cascine 18, 50144, Florence, Italy.
| | - Andrea Bellandi
- Giardino della Villa di Castello - Villa medicea della Petraia (Direzione Regionale Musei della Toscana, Piazza dei Mozzi 2), Florence, Italy
| | - Sergi Costafreda-Aumedes
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P. le Cascine 18, 50144, Florence, Italy
| | - Camilla Dibari
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P. le Cascine 18, 50144, Florence, Italy
| | - Francesco Ferrini
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P. le Cascine 18, 50144, Florence, Italy
| | - Silvia Fineschi
- Institute of Heritage Science - CNR (CNR-ISPC), Via Madonna del Piano 10, Sesto Fiorentino, 50019, Florence, Italy
| | - Alberto Giuntoli
- Studio Bellesi Giuntoli, Via Giuliano Ricci 11E, 50141, Florence, Italy
| | - Rachele Manganelli Del Fa
- Institute of Heritage Science - CNR (CNR-ISPC), Via Madonna del Piano 10, Sesto Fiorentino, 50019, Florence, Italy
| | - Marco Moriondo
- Institute of BioEconomy - CNR (CNR-IBE), Via Madonna del Piano 10, Sesto Fiorentino, 50019, Florence, Italy
| | - Marco Mozzo
- Institute of Heritage Science - CNR (CNR-ISPC), Via Madonna del Piano 10, Sesto Fiorentino, 50019, Florence, Italy
| | - Gloria Padovan
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P. le Cascine 18, 50144, Florence, Italy
| | - Cristiano Riminesi
- Institute of Heritage Science - CNR (CNR-ISPC), Via Madonna del Piano 10, Sesto Fiorentino, 50019, Florence, Italy
| | - Marco Bindi
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P. le Cascine 18, 50144, Florence, Italy
| |
Collapse
|
16
|
Kriezis A, Vitale M, Morselli G, Crisanti A, Bernardini F. Unravelling the role of mitochondrial DNA in hybrid incompatibility within species of the Anopheles gambiae complex. Sci Rep 2024; 14:29467. [PMID: 39604462 PMCID: PMC11603187 DOI: 10.1038/s41598-024-80887-0] [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: 06/10/2024] [Accepted: 11/22/2024] [Indexed: 11/29/2024] Open
Abstract
Isolation mechanisms between mosquito species of the Anopheles gambiae complex, which includes major malaria vectors, remain poorly understood. In some cases, pre-zygotic barriers have been shown to limit gene flow between species of the complex, leading to a low level of hybridisation in nature. Post-zygotic mechanisms manifest with F1 hybrid males fully sterile and F1 hybrid females with reduced fertility. Genetic approaches combined with DNA sequencing techniques have highlighted the involvement of genomic regions in hybrid incompatibility with a predominant role of the X chromosome. In addition, differences in the phenotype of F1 hybrid males have been identified depending on the directionality of the parental cross used to generate them. All these studies have focused on the interaction of nuclear DNA elements in hybrid individuals. Given the role that mitochondrial DNA plays in genetic incompatibilities within other organisms and its unique inheritance pattern, commonly maternal, we conducted a genetic study that relied on the introgression of mitochondrial DNA between Anopheles gambiae and Anopheles arabiensis. The findings indicate that the mitochondrial switch does not appear to restore the fertility of F1 hybrid males, suggesting that mitochondrial DNA may not play a role in hybrid incompatibilities in these Anopheles species.
Collapse
Affiliation(s)
- Antonios Kriezis
- Department of Life Sciences, Imperial College London, London, UK
| | - Matteo Vitale
- Department of Life Sciences, Imperial College London, London, UK
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
| | | |
Collapse
|
17
|
Roussou R, Metzler D, Padovani F, Thoma F, Schwarz R, Shraiman B, Schmoller KM, Osman C. Real-time assessment of mitochondrial DNA heteroplasmy dynamics at the single-cell level. EMBO J 2024; 43:5340-5359. [PMID: 39103491 PMCID: PMC11574196 DOI: 10.1038/s44318-024-00183-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/07/2024] [Accepted: 07/17/2024] [Indexed: 08/07/2024] Open
Abstract
Mitochondrial DNA (mtDNA) is present in multiple copies within cells and is required for mitochondrial ATP generation. Even within individual cells, mtDNA copies can differ in their sequence, a state known as heteroplasmy. The principles underlying dynamic changes in the degree of heteroplasmy remain incompletely understood, due to the inability to monitor this phenomenon in real time. Here, we employ mtDNA-based fluorescent markers, microfluidics, and automated cell tracking, to follow mtDNA variants in live heteroplasmic yeast populations at the single-cell level. This approach, in combination with direct mtDNA tracking and data-driven mathematical modeling reveals asymmetric partitioning of mtDNA copies during cell division, as well as limited mitochondrial fusion and fission frequencies, as critical driving forces for mtDNA variant segregation. Given that our approach also facilitates assessment of segregation between intact and mutant mtDNA, we anticipate that it will be instrumental in elucidating the mechanisms underlying the purifying selection of mtDNA.
Collapse
Affiliation(s)
- Rodaria Roussou
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
- Graduate School Life Science Munich, 82152, Planegg-Martinsried, Germany
| | - Dirk Metzler
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Francesco Padovani
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Felix Thoma
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
- Graduate School Life Science Munich, 82152, Planegg-Martinsried, Germany
| | - Rebecca Schwarz
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Boris Shraiman
- Kavli Institute for Theoretical Physics, University of California, 93106, Santa Barbara, CA, USA
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.
| |
Collapse
|
18
|
Kaczmarczyk-Ziemba A, Wagner GK, Staniec B, Zagaja M, Pietrykowska-Tudruj E, Iorgu EI, Iorgu IŞ. Intraspecific diversity of Myrmecophilus acervorum (Orthoptera: Myrmecophilidae) indicating an ongoing cryptic speciation. Sci Rep 2024; 14:23984. [PMID: 39402267 PMCID: PMC11473668 DOI: 10.1038/s41598-024-75335-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 10/04/2024] [Indexed: 10/19/2024] Open
Abstract
Myrmecophilus acervorum, previously considered a parthenogenetic species widely-distributed in Europe, has been observed to have both sexes in populations inhabiting the central part of the distribution range. Specimens from those heterosexual populations have been found being infected with Wolbachia. New mitochondrial data (COI and 16S markers) revealed the well-supported differentiation of M. acervorum populations inhabiting western Polesie (Poland) and southern Europe. In turn, analyses of EF1α marker support the hypothesis on the unfinished lineage sorting at the nuclear DNA level. Interestingly, we found that parthenogenetic populations inhabiting western Polesie are infected with Wolbachia belonging to supergroup A, while endosymbionts occurring in sexual populations of M. acervorum observed in Romania belong to supergroup B. Furthermore, new and potentially diagnostic characteristics in the external structures of the eyes of M. acervorum were identified. The surface of ommatidia in specimens occurring in southern Europe was smooth. In contrast, the ommatidia surface of individuals collected in Poland was visibly sculptured. To sum up, the significant genetic variability found in the present case, and the differentiating morphological character, are almost certainly effects of cryptic species being present within M. acervorum. This is indicative of ongoing speciation within the populations of this insect, and of simultaneous unfinished lineage sorting at the nuclear DNA level.
Collapse
Affiliation(s)
- Agnieszka Kaczmarczyk-Ziemba
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Grzegorz K Wagner
- Department of Zoology and Nature Conservation, Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland.
| | - Bernard Staniec
- Department of Zoology and Nature Conservation, Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Mirosław Zagaja
- Department of Experimental Pharmacology, Institute of Rural Health, Jaczewskiego 2, 20-090, Lublin, Poland
| | - Ewa Pietrykowska-Tudruj
- Department of Zoology and Nature Conservation, Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Elena I Iorgu
- Faculty of Medicine and Biological Sciences, Ştefan cel Mare University of Suceava, Str. Universităţii 13, Suceava, 720229, Romania
| | - Ionuţ Ş Iorgu
- Faculty of Medicine and Biological Sciences, Ştefan cel Mare University of Suceava, Str. Universităţii 13, Suceava, 720229, Romania
| |
Collapse
|
19
|
Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2024; 23:579-594. [PMID: 37952099 PMCID: PMC11812042 DOI: 10.1093/bfgp/elad050] [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: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
Collapse
Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| |
Collapse
|
20
|
He X, Chen J, Li Z. Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement. Ecol Evol 2024; 14:e70248. [PMID: 39219575 PMCID: PMC11364858 DOI: 10.1002/ece3.70248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.
Collapse
Affiliation(s)
- Xiang‐Yan He
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in WanjiangBasin Co‐Funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- Aquatic Plant Research Center, Wuhan Botanical GardenChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jin‐Ming Chen
- Aquatic Plant Research Center, Wuhan Botanical GardenChinese Academy of SciencesWuhanChina
| | - Zhi‐Zhong Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in WanjiangBasin Co‐Funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| |
Collapse
|
21
|
Veeraragavan S, Johansen M, Johnston IG. Evolution and maintenance of mtDNA gene content across eukaryotes. Biochem J 2024; 481:1015-1042. [PMID: 39101615 PMCID: PMC11346449 DOI: 10.1042/bcj20230415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024]
Abstract
Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.
Collapse
Affiliation(s)
| | - Maria Johansen
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| |
Collapse
|
22
|
Wang L, Huo Z, Xu W, Zhou P, Nan W, Guo H, Zhang Q, Yang P, Alolga RN, Yin X, Li P, Lu X. Comparative plastomes of eight subgenus Chamaesyce plants and system authentication of Euphorbiae Humifusae Herba. Food Chem 2024; 447:139039. [PMID: 38518619 DOI: 10.1016/j.foodchem.2024.139039] [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: 10/06/2023] [Revised: 02/22/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
Euphorbiae Humifusae Herba (EHH) was provided with medicinal and edible uses, but frequently was adulterated with its closely related species. Hence, this study sought to identify EHH via an integrated approach comprising data from its morphological evaluation, HPLC analysis, comparative plastomes analysis and allele-specific PCR identification. First, the morphological characteristics of 8 subgenus Chamaesyce plants were summarized. Then, HPLC analysis showed that 18 batches of EHH were adulterated or unqualified. Furthermore, the plastomes of the 8 subg. Chamaesyce species were analyzed. Phylogenetic analysis revealed a sister relationship among the 8 subg. Chamaesyce species. The allele-specific PCR authentication was developed by the nucleotide polymorphisms (SNPs) and insertions or deletions (InDels) analysis. The results of allele-specific PCR showed that 27 batches of EHH were adulterated, indicating that the superior sensitivity of molecular authentication over the other methods used. This study provided a reference for rational use and phylogenetic research of EHH.
Collapse
Affiliation(s)
- Long Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Ziting Huo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Wenbo Xu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Peina Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Wenxiang Nan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Huijun Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Qianwen Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Raphael N Alolga
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Xiaojian Yin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China.
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, PR China; Medical Botanical Garden, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
23
|
Xu Y, Wang W, Huang J, Xu M, Wang B, Wu Y, Xie Y, Jian J. Kinship analysis and pedigree reconstruction by RAD sequencing in cattle. GIGABYTE 2024; 2024:1-15. [PMID: 39071179 PMCID: PMC11273509 DOI: 10.46471/gigabyte.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/12/2024] [Indexed: 07/30/2024] Open
Abstract
Kinship and pedigree, used for estimating inbreeding, heritability, selection, and gene flow, are useful for breeding and animal conservation. However, as the size of crossbred populations increases, inaccurate generation and parentage assignment in livestock farms increase. Restriction-site-associated DNA sequencing is a cost-effective platform for single nucleotide polymorphism (SNP) discovery and genotyping. Here, we performed a kinship analysis and pedigree reconstruction for Angus and Xiangxi yellow cattle. A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping. The identified SNP panel included 7,305 SNPs capturing the maximum difference between paternal and maternal genome information, allowing us to distinguish F1 from F2 generations with 90% accuracy. In conclusion, we provided a low-cost and efficient SNP panel for kinship analyses and the improvement of local genetic resources, which are valuable for breed improvement, local resource utilization, and conservation.
Collapse
Affiliation(s)
- Yiming Xu
- Animal Husbandry and Aquatic Affairs Center, Lianyuan City 417100, Hunan Province, China
| | - Wanqiu Wang
- BGI Genomics, BGI Center, 9 Yunhua Road, Yantian District, Shenzhen, 518081, China
| | - Jiefeng Huang
- Loudi Municipal Bureau of Agriculture and Rural Affairs, Loudi City 417000, Hunan Province, China
| | - Minjie Xu
- People’s Government of Shexian County 056400, Hebei Province, China
| | - Binhu Wang
- BGI Genomics, BGI Center, 9 Yunhua Road, Yantian District, Shenzhen, 518081, China
| | - Yingsong Wu
- People’s Government of Shexian County 056400, Hebei Province, China
| | - Yongzhong Xie
- Animal Husbandry and Aquatic Affairs Center, Lianyuan City 417100, Hunan Province, China
| | - Jianbo Jian
- BGI Genomics, BGI Center, 9 Yunhua Road, Yantian District, Shenzhen, 518081, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| |
Collapse
|
24
|
Ben-Hur S, Sernik S, Afar S, Kolpakova A, Politi Y, Gal L, Florentin A, Golani O, Sivan E, Dezorella N, Morgenstern D, Pietrokovski S, Schejter E, Yacobi-Sharon K, Arama E. Egg multivesicular bodies elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization. Nat Commun 2024; 15:5715. [PMID: 38977659 PMCID: PMC11231261 DOI: 10.1038/s41467-024-50041-5] [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: 09/20/2023] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
Mitochondria are maternally inherited, but the mechanisms underlying paternal mitochondrial elimination after fertilization are far less clear. Using Drosophila, we show that special egg-derived multivesicular body vesicles promote paternal mitochondrial elimination by activating an LC3-associated phagocytosis-like pathway, a cellular defense pathway commonly employed against invading microbes. Upon fertilization, these egg-derived vesicles form extended vesicular sheaths around the sperm flagellum, promoting degradation of the sperm mitochondrial derivative and plasma membrane. LC3-associated phagocytosis cascade of events, including recruitment of a Rubicon-based class III PI(3)K complex to the flagellum vesicular sheaths, its activation, and consequent recruitment of Atg8/LC3, are all required for paternal mitochondrial elimination. Finally, lysosomes fuse with strings of large vesicles derived from the flagellum vesicular sheaths and contain degrading fragments of the paternal mitochondrial derivative. Given reports showing that in some mammals, the paternal mitochondria are also decorated with Atg8/LC3 and surrounded by multivesicular bodies upon fertilization, our findings suggest that a similar pathway also mediates paternal mitochondrial elimination in other flagellated sperm-producing organisms.
Collapse
Affiliation(s)
- Sharon Ben-Hur
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shoshana Sernik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sara Afar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alina Kolpakova
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Politi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Liron Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Florentin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Sivan
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Nili Dezorella
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - David Morgenstern
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalised Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Schejter
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Yacobi-Sharon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eli Arama
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
25
|
Burzyński A, Śmietanka B, Fernández-Pérez J, Lubośny M. The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species. Sci Rep 2024; 14:14465. [PMID: 38914611 PMCID: PMC11196677 DOI: 10.1038/s41598-024-63764-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 05/31/2024] [Indexed: 06/26/2024] Open
Abstract
Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
Collapse
Affiliation(s)
- Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Jenyfer Fernández-Pérez
- Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| |
Collapse
|
26
|
Tang J, Zhang L, Su J, Ye Q, Li Y, Liu D, Cui H, Zhang Y, Ye Z. Insights into Fungal Mitochondrial Genomes and Inheritance Based on Current Findings from Yeast-like Fungi. J Fungi (Basel) 2024; 10:441. [PMID: 39057326 PMCID: PMC11277600 DOI: 10.3390/jof10070441] [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: 04/17/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
The primary functions of mitochondria are to produce energy and participate in the apoptosis of cells, with them being highly conserved among eukaryotes. However, the composition of mitochondrial genomes, mitochondrial DNA (mtDNA) replication, and mitochondrial inheritance varies significantly among animals, plants, and fungi. Especially in fungi, there exists a rich diversity of mitochondrial genomes, as well as various replication and inheritance mechanisms. Therefore, a comprehensive understanding of fungal mitochondria is crucial for unraveling the evolutionary history of mitochondria in eukaryotes. In this review, we have organized existing reports to systematically describe and summarize the composition of yeast-like fungal mitochondrial genomes from three perspectives: mitochondrial genome structure, encoded genes, and mobile elements. We have also provided a systematic overview of the mechanisms in mtDNA replication and mitochondrial inheritance during bisexual mating. Additionally, we have discussed and proposed open questions that require further investigation for clarification.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (J.T.)
| |
Collapse
|
27
|
Zhang J, Liu G, Wei J. Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica. PLANTA 2024; 260:23. [PMID: 38850310 DOI: 10.1007/s00425-024-04386-2] [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: 11/16/2023] [Accepted: 03/10/2024] [Indexed: 06/10/2024]
Abstract
MAIN CONCLUSION In this study, we assembled the first complete mitochondrial genome of Setaria italica and confirmed the multi-branched architecture. The foxtail millet (Setaria italica) holds significant agricultural importance, particularly in arid and semi-arid regions. It plays a pivotal role in diversifying dietary patterns and shaping planting strategies. Although the chloroplast genome of S. italica has been elucidated in recent studies, the complete mitochondrial genome remains largely unexplored. In this study, we employed PacBio HiFi sequencing platforms to sequence and assemble the complete mitochondrial genome. The mitochondrial genome spans a total length of 446,614 base pairs and harbors a comprehensive set of genetic elements, including 33 unique protein-coding genes (PCGs), encompassing 24 unique mitochondrial core genes and 9 variable genes, along with 20 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. Our analysis of mitochondrial PCGs revealed a pronounced codon usage preference. For instance, the termination codon exhibits a marked preference for UAA, while alanine (Ala) exhibits a preference for GCU, and glutamine (Gln) favors CAA. Notably, the maximum Relative Synonymous Codon Usage (RSCU) values for cysteine (Cys) and phenylalanine (Phe) are both below 1.2, indicating a lack of strong codon usage preference for these amino acids. Phylogenetic analyses consistently place S. italica in close evolutionary proximity to Chrysopogon zizanioides, relative to other Panicoideae plants. Collinearity analysis showed that a total of 39 fragments were identified to display homology with both the mitochondrial and chloroplast genomes. A total of 417 potential RNA-editing sites were discovered across the 33 mitochondrial PCGs. Notably, all these editing events involved the conversion of cytosine (C) to uracil (U). Through the employment of PCR validation coupled with Sanger sequencing for the anticipated editing sites of these codons, RNA-editing events were conclusively identified at two specific loci: nad4L-2 and atp6-1030. The results of this study provide a pivotal foundation for advanced genomic breeding research in foxtail millet. Furthermore, they impart essential insights that will be instrumental for forthcoming investigations into the evolutionary and molecular dynamics of Panicoideae species.
Collapse
Affiliation(s)
- Jiewei Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| |
Collapse
|
28
|
Sakamoto W, Takami T. Plastid Inheritance Revisited: Emerging Role of Organelle DNA Degradation in Angiosperms. PLANT & CELL PHYSIOLOGY 2024; 65:484-492. [PMID: 37702423 DOI: 10.1093/pcp/pcad104] [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: 07/06/2023] [Revised: 08/15/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
Plastids are essential organelles in angiosperms and show non-Mendelian inheritance due to their evolution as endosymbionts. In approximately 80% of angiosperms, plastids are thought to be inherited from the maternal parent, whereas other species transmit plastids biparentally. Maternal inheritance can be generally explained by the stochastic segregation of maternal plastids after fertilization because the zygote is overwhelmed by the maternal cytoplasm. In contrast, biparental inheritance shows the transmission of organelles from both parents. In some species, maternal inheritance is not absolute and paternal leakage occurs at a very low frequency (∼10-5). A key process controlling the inheritance mode lies in the behavior of plastids during male gametophyte (pollen) development, with accumulating evidence indicating that the plastids themselves or their DNAs are eliminated during pollen maturation or at fertilization. Cytological observations in numerous angiosperm species have revealed several critical steps that mutually influence the degree of plastid transmission quantitatively among different species. This review revisits plastid inheritance from a mechanistic viewpoint. Particularly, we focus on a recent finding demonstrating that both low temperature and plastid DNA degradation mediated by the organelle exonuclease DEFECTIVE IN POLLEN ORGANELLE DNA DEGRADATION1 (DPD1) influence the degree of paternal leakage significantly in tobacco. Given these findings, we also highlight the emerging role of DPD1 in organelle DNA degradation.
Collapse
Affiliation(s)
- Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-2 Chuo, Kurashiki, Okayama, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-2 Chuo, Kurashiki, Okayama, 710-0046 Japan
| |
Collapse
|
29
|
Kuo HC, Schoneman T, Gao LM, Gruezo WS, Amoroso VB, Yang Y, Yang KC, Chien CT, Möller M, Wang CN. A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines. Front Genet 2024; 15:1372309. [PMID: 38756448 PMCID: PMC11096487 DOI: 10.3389/fgene.2024.1372309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.
Collapse
Affiliation(s)
- Hao-Chih Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Travis Schoneman
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - William Sm. Gruezo
- Plant Biology Division, College of Arts and Sciences, Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Victor B. Amoroso
- Center for Biodiversity Research and Extension in Mindanao (CEBREM), Central Mindanao University, Mindanao, Philippines
| | - Yang Yang
- Tainan District Agricultural Research and Extension Station, Ministry of Agriculture, Tainan, Taiwan
| | - Kuo-Cheng Yang
- General Education Center, Providence University, Taichung, Taiwan
| | - Ching-Te Chien
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
30
|
Chen S, Safiul Azam FM, Akter ML, Ao L, Zou Y, Qian Y. The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification. FRONTIERS IN PLANT SCIENCE 2024; 15:1356912. [PMID: 38745930 PMCID: PMC11092384 DOI: 10.3389/fpls.2024.1356912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024]
Abstract
Introduction Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety. Methods The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum. Results and discussion The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium. Conclusion Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.
Collapse
Affiliation(s)
- Shixi Chen
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Fardous Mohammad Safiul Azam
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Mst. Lovely Akter
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Li Ao
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Yuanchao Zou
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Ye Qian
- Branch of The First Affiliated Hospital of Xinjiang Medical University, Changji, Xinjiang, China
| |
Collapse
|
31
|
Chen L, Dong X, Huang H, Xu H, Rono PC, Cai X, Hu G. Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant. BMC Genomics 2024; 25:322. [PMID: 38561677 PMCID: PMC10983754 DOI: 10.1186/s12864-024-10247-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported. RESULTS In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted. CONCLUSIONS This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.
Collapse
Affiliation(s)
- Lingling Chen
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Huang
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Haixia Xu
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiuzhen Cai
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hubei Jiangxia Laboratory, Wuhan, 430200, China.
| |
Collapse
|
32
|
Ortiz SC, Hull CM. Biogenesis, germination, and pathogenesis of Cryptococcus spores. Microbiol Mol Biol Rev 2024; 88:e0019623. [PMID: 38440970 PMCID: PMC10966950 DOI: 10.1128/mmbr.00196-23] [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: 03/06/2024] Open
Abstract
SUMMARYSpores are primary infectious propagules for the majority of human fungal pathogens; however, relatively little is known about their fundamental biology. One strategy to address this deficiency has been to develop the basidiospores of Cryptococcus into a model for pathogenic spore biology. Here, we provide an update on the state of the field with a comprehensive review of the data generated from the study of Cryptococcus basidiospores from their formation (sporulation) and differentiation (germination) to their roles in pathogenesis. Importantly, we provide support for the presence of basidiospores in nature, define the key characteristics that distinguish basidiospores from yeast cells, and clarify their likely roles as infectious particles. This review is intended to demonstrate the importance of basidiospores in the field of Cryptococcus research and provide a solid foundation from which researchers who wish to study sexual spores in any fungal system can launch their studies.
Collapse
Affiliation(s)
- Sébastien C. Ortiz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christina M. Hull
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
33
|
Hénault M, Marsit S, Charron G, Landry CR. The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate. eLife 2024; 12:RP89277. [PMID: 38411604 PMCID: PMC10911583 DOI: 10.7554/elife.89277] [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: 02/28/2024] Open
Abstract
Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, structural variants (SVs) can affect the genomic distribution of TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger TE mobilization and thus increase TE load in hybrids. We previously tested this hypothesis (Hénault et al., 2020) by performing a large-scale evolution experiment by mutation accumulation (MA) on multiple hybrid genotypes within and between wild populations of the yeasts Saccharomyces paradoxus and Saccharomyces cerevisiae. Using aggregate measures of TE load with short-read sequencing, we found no evidence for TE load increase in hybrid MA lines. Here, we resolve the genomes of the hybrid MA lines with long-read phasing and assembly to precisely characterize the role of SVs in shaping the TE landscape. Highly contiguous phased assemblies of 127 MA lines revealed that SV types like polyploidy, aneuploidy, and loss of heterozygosity have large impacts on the TE load. We characterized 18 de novo TE insertions, indicating that transposition only has a minor role in shaping the TE landscape in MA lines. Because the scarcity of TE mobilization in MA lines provided insufficient resolution to confidently dissect transposition rate variation in hybrids, we adapted an in vivo assay to measure transposition rates in various S. paradoxus hybrid backgrounds. We found that transposition rates are not increased by hybridization, but are modulated by many genotype-specific factors including initial TE load, TE sequence variants, and mitochondrial DNA inheritance. Our results show the multiple scales at which TE load is shaped in hybrid genomes, being highly impacted by SV dynamics and finely modulated by genotype-specific variation in transposition rates.
Collapse
Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| |
Collapse
|
34
|
Wang R, Yang Y, Tian H, Yi H, Xu L, Lv Y, Ge J, Zhao Y, Wang L, Zhou S, Wang F. A Scalable and Robust Chloroplast Genotyping Solution: Development and Application of SNP and InDel Markers in the Maize Chloroplast Genome. Genes (Basel) 2024; 15:293. [PMID: 38540352 PMCID: PMC10970264 DOI: 10.3390/genes15030293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.
Collapse
Affiliation(s)
- Rui Wang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Yang Yang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Hongli Tian
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Hongmei Yi
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Liwen Xu
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Yuanda Lv
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Jianrong Ge
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Yikun Zhao
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Lu Wang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany (LSEB), Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Fengge Wang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| |
Collapse
|
35
|
Liu L, Du J, Liu Z, Zuo W, Wang Z, Li J, Zeng Y. Comparative and phylogenetic analyses of nine complete chloroplast genomes of Orchidaceae. Sci Rep 2023; 13:21403. [PMID: 38049440 PMCID: PMC10696064 DOI: 10.1038/s41598-023-48043-2] [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: 06/02/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023] Open
Abstract
The orchid family has 200,000 species and 700 genera, and it is found worldwide in the tropics and subtropics. In China, there are 1247 species and subspecies of orchids belonging to the Orchidaceae family. Orchidaceae is one of the most diverse plant families in the world, known for their lush look, remarkable ecological tolerance, and capability for reproduction. It has significant decorative and therapeutic value. In terms of evolution, the orchid family is one of the more complicated groups, but up until now, little has been known about its affinities. This study examined the properties of 19 chloroplast (cp) genomes, of which 11 had previously been published and nine had only recently been revealed. Following that, topics such as analysis of selection pressure, codon usage, amino acid frequencies, repeated sequences, and reverse repeat contraction and expansion are covered. The Orchidaceae share similar cp chromosomal characteristics, and we have conducted a preliminary analysis of their evolutionary connections. The cp genome of this family has a typical tepartite structure and a high degree of consistency across species. Platanthera urceolata with more tandem repeats of the cp genome. Similar cp chromosomal traits can be seen in the orchidaceae. Galearis roborowskyi, Neottianthe cucullata, Neottianthe monophylla, Platanthera urceolata and Ponerorchis compacta are the closest cousins, according to phylogenetic study.
Collapse
Affiliation(s)
- Likuan Liu
- College of Life Sciences, Qinghai Normal University, Xining, China
- Academy of Plateau Science Sustainability, Xining, China
| | - Jingxuan Du
- College of Life Sciences, Qinghai Normal University, Xining, China
| | - Zhihua Liu
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Wuhan, China
| | - Wenming Zuo
- College of Geosciences, Qinghai Normal University, Xining, China
| | - Zhenglei Wang
- College of Life Sciences, Qinghai Normal University, Xining, China
| | - Jinping Li
- College of Life Sciences, Qinghai Normal University, Xining, China.
- Academy of Plateau Science Sustainability, Xining, China.
| | - Yang Zeng
- College of Life Sciences, Qinghai Normal University, Xining, China.
- Academy of Plateau Science Sustainability, Xining, China.
| |
Collapse
|
36
|
Hitchcock TJ, Gardner A. Sexual antagonism in sequential hermaphrodites. Proc Biol Sci 2023; 290:20232222. [PMID: 37989243 PMCID: PMC10688264 DOI: 10.1098/rspb.2023.2222] [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: 09/30/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Females and males may have distinct phenotypic optima, but share essentially the same complement of genes, potentially leading to trade-offs between attaining high fitness through female versus male reproductive success. Such sexual antagonism may be particularly acute in hermaphrodites, where both reproductive strategies are housed within a single individual. While previous models have focused on simultaneous hermaphroditism, we lack theory for how sexual antagonism may play out under sequential hermaphroditism, which has the additional complexities of age-structure. Here, we develop a formal theory of sexual antagonism in sequential hermaphrodites. First, we construct a general theoretical overview of the problem, then consider different types of sexually antagonistic and life-history trade-offs, under different modes of genetic inheritance (autosomal or cytoplasmic), and different forms of sequential hermaphroditism (protogynous, protoandrous or bidirectional). Finally, we provide a concrete illustration of these general patterns by developing a two-stage two-sex model, which yields conditions for both invasion of sexually antagonistic alleles and maintenance of sexually antagonistic polymorphisms.
Collapse
Affiliation(s)
- Thomas J. Hitchcock
- RIKEN Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako, Saitama 351-0198, Japan
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
| | - Andy Gardner
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
| |
Collapse
|
37
|
Yan S, Ma P, Zuo C, Zhu Y, Ma X, Zhang Z. Genetic Analysis Based on Mitochondrial nad2 Gene Reveals a Recent Population Expansion of the Invasive Mussel, Mytella strigata, in China. Genes (Basel) 2023; 14:2038. [PMID: 38002981 PMCID: PMC10671778 DOI: 10.3390/genes14112038] [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: 09/27/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Mytella strigata is a highly adaptable invasive alien species that has been established in coastal China since 2014. Mitochondrial DNA (mtDNA) is an important tool for studying the evolution and population genetics of invasive species. In this study, the mitochondrial genome of M. strigata from China was sequenced by Illumina high-throughput sequencing and characterized with 13 protein-coding genes (PCGs). By assessing the selective pressure of 13 PCGs, the nad2 gene had the fastest evolutionary rate and was finally selected for population genetic analysis. A total of 285 nad2 sequences from seven M. strigata populations in China were analyzed and showed obviously T-rich and C-rich characteristics. According to population genetic diversity analysis, all the seven populations had haplotype (gene) diversity (Hd) ≥ 0.5 and nucleotide diversity (Pi) < 0.005. Haplotype networks showed a "star" distribution. Population historical dynamic analyses showed that Fu's Fs and Tajima's D values of all populations were negative except the Qukou (QK) and Beihai (BH) populations. The Zhangzhou (ZJ) and Xiamen (XM) populations were unimodal while the other populations were multimodal. These results suggested that the population of M. strigata in China may have passed the bottleneck period and is currently in a state of population expansion.
Collapse
Affiliation(s)
- Shaojing Yan
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
| | - Peizhen Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Chenxia Zuo
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- College of Life Sciences, Qingdao University, Qingdao 266000, China
| | - Yi Zhu
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojie Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
38
|
Nieto-Panqueva F, Rubalcava-Gracia D, Hamel PP, González-Halphen D. The constraints of allotopic expression. Mitochondrion 2023; 73:30-50. [PMID: 37739243 DOI: 10.1016/j.mito.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Allotopic expression is the functional transfer of an organellar gene to the nucleus, followed by synthesis of the gene product in the cytosol and import into the appropriate organellar sub compartment. Here, we focus on mitochondrial genes encoding OXPHOS subunits that were naturally transferred to the nucleus, and critically review experimental evidence that claim their allotopic expression. We emphasize aspects that may have been overlooked before, i.e., when modifying a mitochondrial gene for allotopic expression━besides adapting the codon usage and including sequences encoding mitochondrial targeting signals━three additional constraints should be considered: (i) the average apparent free energy of membrane insertion (μΔGapp) of the transmembrane stretches (TMS) in proteins earmarked for the inner mitochondrial membrane, (ii) the final, functional topology attained by each membrane-bound OXPHOS subunit; and (iii) the defined mechanism by which the protein translocator TIM23 sorts cytosol-synthesized precursors. The mechanistic constraints imposed by TIM23 dictate the operation of two pathways through which alpha-helices in TMS are sorted, that eventually determine the final topology of membrane proteins. We used the biological hydrophobicity scale to assign an average apparent free energy of membrane insertion (μΔGapp) and a "traffic light" color code to all TMS of OXPHOS membrane proteins, thereby predicting which are more likely to be internalized into mitochondria if allotopically produced. We propose that the design of proteins for allotopic expression must make allowance for μΔGapp maximization of highly hydrophobic TMS in polypeptides whose corresponding genes have not been transferred to the nucleus in some organisms.
Collapse
Affiliation(s)
- Felipe Nieto-Panqueva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico; Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrice P Hamel
- Department of Molecular Genetics and Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA; Vellore Institute of Technology (VIT), School of BioScience and Technology, Vellore, Tamil Nadu, India
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| |
Collapse
|
39
|
Wang Y, Zhu X, Gu Y, Liu Z, Mao Y, Liu X, Bai Z, Wang G, Li J. Study on the Role of Mitophagy Receptor PHB2 in Doubly Uniparental Inheritance of Hyriopsis cumingii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:790-799. [PMID: 37594541 DOI: 10.1007/s10126-023-10240-5] [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: 03/05/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023]
Abstract
In bivalves, the heterogeneity of mitochondrial DNA and its unique mode of transmission have been the focus of attention, which is called doubly uniparental inheritance (DUI). Prohibitin-2 (phb2) is a mitochondrial inner membrane protein that is a key mitophagy receptor for parental mitochondrial removal. Hyriopsis cumingii is a freshwater bivalve in China, the full-length cDNA of H. cumingii phb2 (named Hcphb2) is 2917 bp and encodes a total of 300 amino acids, a highly conserved sequence. Hcphb2 was highly expressed in the ovary. In the gonadal tissues of 5- to 8-month-old female mussels, the expression level of Hcphb2 continued to significantly increase. After Hcphb2 siRNA interference in 6-month-old female mussels, the expression of M-COII, a marker gene on M-type mitochondria, showed a considerable increase (p < 0.05). In contrast, the expression of autophagosome formation and maturation-related genes, atg4b, atg5, atg12, and atg16l, in the ATG family genes was significantly decreased (p < 0.01). Subcellular localization showed that Hcphb2 appeared in spermatogonia, spermatocyte, spermatid, and sperm, and its location changes synchronize with the behavior of M-type mitochondria location changes in DUI species. And it was found that miR-184 negatively regulated Hcphb2. The above results suggest that the mitochondrial autophagy receptor gene Hcphb2 may be associated with the degradation of M-type mitochondria in the freshwater mussel. This process requires multiple genes to participate, of which Hcphb2 and autophagy genes are only some of those that may play a role.
Collapse
Affiliation(s)
- Yayu Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, 314000, China
| | - Xiaoyue Zhu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Yang Gu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Zongyu Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Yingrui Mao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Xiaojun Liu
- Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, 314000, China
- Taizhou Innovation Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, 318000, China
| | - Zhiyi Bai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Guiling Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| |
Collapse
|
40
|
Bhatti JS, Kaur S, Mishra J, Dibbanti H, Singh A, Reddy AP, Bhatti GK, Reddy PH. Targeting dynamin-related protein-1 as a potential therapeutic approach for mitochondrial dysfunction in Alzheimer's disease. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166798. [PMID: 37392948 DOI: 10.1016/j.bbadis.2023.166798] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that manifests its pathology through synaptic damage, mitochondrial abnormalities, microRNA deregulation, hormonal imbalance, increased astrocytes & microglia, accumulation of amyloid β (Aβ) and phosphorylated Tau in the brains of AD patients. Despite extensive research, the effective treatment of AD is still unknown. Tau hyperphosphorylation and mitochondrial abnormalities are involved in the loss of synapses, defective axonal transport and cognitive decline in patients with AD. Mitochondrial dysfunction is evidenced by enhanced mitochondrial fragmentation, impaired mitochondrial dynamics, mitochondrial biogenesis and defective mitophagy in AD. Hence, targeting mitochondrial proteins might be a promising therapeutic strategy in treating AD. Recently, dynamin-related protein 1 (Drp1), a mitochondrial fission protein, has gained attention due to its interactions with Aβ and hyperphosphorylated Tau, altering mitochondrial morphology, dynamics, and bioenergetics. These interactions affect ATP production in mitochondria. A reduction in Drp1 GTPase activity protects against neurodegeneration in AD models. This article provides a comprehensive overview of Drp1's involvement in oxidative damage, apoptosis, mitophagy, and axonal transport of mitochondria. We also highlighted the interaction of Drp1 with Aβ and Tau, which may contribute to AD progression. In conclusion, targeting Drp1 could be a potential therapeutic approach for preventing AD pathology.
Collapse
Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India.
| | - Satinder Kaur
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Jayapriya Mishra
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | | | - Arti Singh
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Arubala P Reddy
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA.
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - P Hemachandra Reddy
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA; Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| |
Collapse
|
41
|
Liu L, Chen M, Folk RA, Wang M, Zhao T, Shang F, Soltis DE, Li P. Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids. Mol Ecol Resour 2023; 23:1673-1688. [PMID: 37449554 DOI: 10.1111/1755-0998.13833] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an "expanded" malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.
Collapse
Affiliation(s)
- Luxian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengzhen Chen
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Meizhen Wang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fude Shang
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, Henan, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
42
|
Debelli A, Kienzle L, Khorami HH, Angers A, Breton S. Validation of the male-specific ORF of the paternally-transmitted mtDNA in Mytilus edulis as a protein-coding gene. Gene 2023; 879:147586. [PMID: 37356740 DOI: 10.1016/j.gene.2023.147586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
There appears to be an additional set of sex-specific mtDNA-encoded proteins in bivalve species with doubly uniparental mitochondrial inheritance that may be involved in the transmission of the female and male mitogenomes. In the marine mussel Mytilus edulis, the translation of the female-specific open reading frame (F-ORF) was demonstrated but the translation of the male-specific ORF (M-ORF) remains to be shown. Here we validate the male-specific ORF of the paternal mitogenome in M. edulis as a protein-coding gene. The M-ORF protein was detected only in male gonads and localized in sperm mitochondria and acrosome, suggesting that it is involved in a key sperm function in Mytilus edulis.
Collapse
Affiliation(s)
- Alizée Debelli
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Laura Kienzle
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Hajar Hosseini Khorami
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Annie Angers
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada.
| |
Collapse
|
43
|
Sun Z, Wu Y, Fan P, Guo D, Zhang S, Song C. Assembly and analysis of the mitochondrial genome of Prunella vulgaris. FRONTIERS IN PLANT SCIENCE 2023; 14:1237822. [PMID: 37600185 PMCID: PMC10433383 DOI: 10.3389/fpls.2023.1237822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Prunella vulgaris (Lamiaceae) is widely distributed in Eurasia. Former studies have demonstrated that P. vulgaris has a wide range of pharmacological effects. Nevertheless, no complete P. vulgaris mitochondrial genome has been reported, which limits further understanding of the biology of P. vulgaris. Here, we assembled the first complete mitochondrial genome of P. vulgaris using a hybrid assembly strategy based on sequencing data from both Nanopore and Illumina platforms. Then, the mitochondrial genome of P. vulgaris was analyzed comprehensively in terms of gene content, codon preference, intercellular gene transfer, phylogeny, and RNA editing. The mitochondrial genome of P. vulgaris has two circular structures. It has a total length of 297, 777 bp, a GC content of 43.92%, and 29 unique protein-coding genes (PCGs). There are 76 simple sequence repeats (SSRs) in the mitochondrial genome, of which tetrameric accounts for a large percentage (43.4%). A comparative analysis between the mitochondrial and chloroplast genomes revealed that 36 homologous fragments exist in them, with a total length of 28, 895 bp. The phylogenetic analysis showed that P. vulgaris belongs to the Lamiales family Lamiaceae and P. vulgaris is closely related to Salvia miltiorrhiza. In addition, the mitochondrial genome sequences of seven species of Lamiaceae are unconservative in their alignments and undergo frequent genome reorganization. This work reports for the first time the complete mitochondrial genome of P. vulgaris, which provides useful genetic information for further Prunella studies.
Collapse
Affiliation(s)
- Zhihao Sun
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ya Wu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pengyu Fan
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei, China
| | - Dengli Guo
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei, China
| | - Sanyin Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| |
Collapse
|
44
|
van der Walt D, Steenkamp ET, Wingfield BD, Wilken PM. Evidence of Biparental Mitochondrial Inheritance from Self-Fertile Crosses between Closely Related Species of Ceratocystis. J Fungi (Basel) 2023; 9:686. [PMID: 37367622 DOI: 10.3390/jof9060686] [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: 04/26/2023] [Revised: 06/07/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Hybridization is recognized as a notable driver of evolution and adaptation, which closely related species may exploit in the form of incomplete reproductive barriers. Three closely related species of Ceratocystis (i.e., C. fimbriata, C. manginecans and C. eucalypticola) have previously been shown to hybridize. In such studies, naturally occurring self-sterile strains were mated with an unusual laboratory-generated sterile isolate type, which could have impacted conclusions regarding the prevalence of hybridization and inheritance of mitochondria. In the current study, we investigated whether interspecific crosses between fertile isolates of these three species are possible and, if so, how mitochondria are inherited by the progeny. For this purpose, a PCR-RFLP method and a mitochondrial DNA-specific PCR technique were custom-made. These were applied in a novel approach of typing complete ascospore drops collected from the fruiting bodies in each cross to distinguish between self-fertilizations and potential hybridization. These markers showed hybridization between C. fimbriata and C. eucalypticola and between C. fimbriata and C. manginecans, while no hybridization was detected in the crosses involving C. manginecans and C. eucalypticola. In both sets of hybrid progeny, we detected biparental inheritance of mitochondria. This study was the first to successfully produce hybrids from a cross involving self-fertile isolates of Ceratocystis and also provided the first direct evidence of biparental mitochondrial inheritance in the Ceratocystidaceae. This work lays the foundation for further research focused on investigating the role of hybridization in the speciation of Ceratocystis species and if mitochondrial conflict could have influenced the process.
Collapse
Affiliation(s)
- Daniella van der Walt
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| |
Collapse
|
45
|
Niu Y, Zhang T, Chen M, Chen G, Liu Z, Yu R, Han X, Chen K, Huang A, Chen C, Yang Y. Analysis of the Complete Mitochondrial Genome of the Bitter Gourd ( Momordica charantia). PLANTS (BASEL, SWITZERLAND) 2023; 12:1686. [PMID: 37111909 PMCID: PMC10143269 DOI: 10.3390/plants12081686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/16/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Bitter gourd (Momordica charantia L.) is a significant vegetable. Although it has a special bitter taste, it is still popular with the public. The industrialization of bitter gourd could be hampered by a lack of genetic resources. The bitter gourd's mitochondrial and chloroplast genomes have not been extensively studied. In the present study, the mitochondrial genome of bitter gourd was sequenced and assembled, and its substructure was investigated. The mitochondrial genome of bitter gourd is 331,440 bp with 24 unique core genes, 16 variable genes, 3 rRNAs, and 23 tRNAs. We identified 134 SSRs and 15 tandem repeats in the entire mitochondrial genome of bitter gourd. Moreover, 402 pairs of repeats with a length greater than or equal to 30 were observed in total. The longest palindromic repeat was 523 bp, and the longest forward repeat was 342 bp. We found 20 homologous DNA fragments in bitter gourd, and the summary insert length was 19,427 bp, accounting for 5.86% of the mitochondrial genome. We predicted a total of 447 potential RNA editing sites in 39 unique PCGs and also discovered that the ccmFN gene has been edited the most often, at 38 times. This study provides a basis for a better understanding and analysis of differences in the evolution and inheritance patterns of cucurbit mitochondrial genomes.
Collapse
Affiliation(s)
- Yu Niu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Muxi Chen
- Guangdong Helinong Biological Seeds Co., Ltd., Shantou 515800, China
- Guangdong Helinong Agricultural Research Institute Co., Ltd., Shantou 515800, China
| | - Guoju Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhaohua Liu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Renbo Yu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Xu Han
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Kunhao Chen
- Guangdong Helinong Biological Seeds Co., Ltd., Shantou 515800, China
- Guangdong Helinong Agricultural Research Institute Co., Ltd., Shantou 515800, China
| | - Aizheng Huang
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yan Yang
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| |
Collapse
|
46
|
Wang YW, Elmore H, Pringle A. Uniparental Inheritance and Recombination as Strategies to Avoid Competition and Combat Muller's Ratchet among Mitochondria in Natural Populations of the Fungus Amanita phalloides. J Fungi (Basel) 2023; 9:476. [PMID: 37108928 PMCID: PMC10142858 DOI: 10.3390/jof9040476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Uniparental inheritance of mitochondria enables organisms to avoid the costs of intracellular competition among potentially selfish organelles. By preventing recombination, uniparental inheritance may also render a mitochondrial lineage effectively asexual and expose mitochondria to the deleterious effects of Muller's ratchet. Even among animals and plants, the evolutionary dynamics of mitochondria remain obscure, and less is known about mitochondrial inheritance among fungi. To understand mitochondrial inheritance and test for mitochondrial recombination in one species of filamentous fungus, we took a population genomics approach. We assembled and analyzed 88 mitochondrial genomes from natural populations of the invasive death cap Amanita phalloides, sampling from both California (an invaded range) and Europe (its native range). The mitochondrial genomes clustered into two distinct groups made up of 57 and 31 mushrooms, but both mitochondrial types are geographically widespread. Multiple lines of evidence, including negative correlations between linkage disequilibrium and distances between sites and coalescent analysis, suggest low rates of recombination among the mitochondria (ρ = 3.54 × 10-4). Recombination requires genetically distinct mitochondria to inhabit a cell, and recombination among A. phalloides mitochondria provides evidence for heteroplasmy as a feature of the death cap life cycle. However, no mushroom houses more than one mitochondrial genome, suggesting that heteroplasmy is rare or transient. Uniparental inheritance emerges as the primary mode of mitochondrial inheritance, even as recombination appears as a strategy to alleviate Muller's ratchet.
Collapse
Affiliation(s)
- Yen-Wen Wang
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Holly Elmore
- Rethink Priorities, San Francisco, CA 94117, USA
| | - Anne Pringle
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
47
|
Silva SR, Miranda VFO, Michael TP, Płachno BJ, Matos RG, Adamec L, Pond SLK, Lucaci AG, Pinheiro DG, Varani AM. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae). Mol Phylogenet Evol 2023; 181:107711. [PMID: 36693533 DOI: 10.1016/j.ympev.2023.107711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.
Collapse
Affiliation(s)
- Saura R Silva
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Vitor F O Miranda
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St., 30-387 Cracow, Poland.
| | - Ramon G Matos
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Lubomir Adamec
- Department of Experimental and Functional Morphology, Institute of Botany CAS, Dukelská 135, CZ-379 01 Třeboň, Czech Republic.
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Daniel G Pinheiro
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Alessandro M Varani
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| |
Collapse
|
48
|
Frangedakis E, Marron AO, Waller M, Neubauer A, Tse SW, Yue Y, Ruaud S, Waser L, Sakakibara K, Szövényi P. What can hornworts teach us? FRONTIERS IN PLANT SCIENCE 2023; 14:1108027. [PMID: 36968370 PMCID: PMC10030945 DOI: 10.3389/fpls.2023.1108027] [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: 11/25/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.
Collapse
Affiliation(s)
| | - Alan O. Marron
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Sze Wai Tse
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Yuling Yue
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Stephanie Ruaud
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Lucas Waser
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| |
Collapse
|
49
|
Yao YL, Ma XY, Wang TY, Yan JY, Chen NF, Hong JS, Liu BQ, Xu ZQ, Zhang N, Lv C, Sun X, Luan JB. A bacteriocyte symbiont determines whitefly sex ratio by regulating mitochondrial function. Cell Rep 2023; 42:112102. [PMID: 36774548 DOI: 10.1016/j.celrep.2023.112102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 02/13/2023] Open
Abstract
Nutritional symbionts influence host reproduction, but the underlying molecular mechanisms are largely unclear. We previously found that the bacteriocyte symbiont Hamiltonella impacts the sex ratio of the whitefly Bemisia tabaci. Hamiltonella synthesizes folate by cooperation with the whitefly. Folate deficiency by Hamiltonella elimination or whitefly gene silencing distorted whitefly sex ratio, and folate supplementation restored the sex ratio. Hamiltonella deficiency or gene silencing altered histone H3 lysine 9 trimethylation (H3K9me3) level, which was restored by folate supplementation. Genome-wide chromatin immunoprecipitation-seq analysis of H3K9me3 indicated mitochondrial dysfunction in symbiont-deficient whiteflies. Hamiltonella deficiency compromised mitochondrial quality of whitefly ovaries. Repressing ovary mitochondrial function led to distorted whitefly sex ratio. These findings indicate that the symbiont-derived folate regulates host histone methylation modifications, which thereby impacts ovary mitochondrial function, and finally determines host sex ratio. Our study suggests that a nutritional symbiont can regulate animal reproduction in a way that differs from reproductive manipulators.
Collapse
Affiliation(s)
- Ya-Lin Yao
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xin-Yu Ma
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Tian-Yu Wang
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Jin-Yang Yan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nai-Fei Chen
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Ji-Sheng Hong
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Bing-Qi Liu
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zi-Qi Xu
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nuo Zhang
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Chao Lv
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiang Sun
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Jun-Bo Luan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
| |
Collapse
|
50
|
Cao P, Huang Y, Zong M, Xu Z. De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers. Genes (Basel) 2023; 14:526. [PMID: 36833452 PMCID: PMC9957484 DOI: 10.3390/genes14020526] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
As a valuable Chinese traditional medicinal species, Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of C. speciosa was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The C. speciosa mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of C. speciosa and closely related species. This work is the first to report the C. speciosa mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism.
Collapse
Affiliation(s)
- Pei Cao
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuan Huang
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Mei Zong
- College of Life Sciences, Anqing Normal University, Anqing 246133, China
| | - Zilong Xu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| |
Collapse
|