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Zuo W, Li H. Assemble and comparative analysis of the mitochondrial genome of Rhododendron delavayi: Insights into phylogenetic relationships and genomic variations. Gene 2024; 927:148741. [PMID: 38969246 DOI: 10.1016/j.gene.2024.148741] [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: 12/26/2023] [Revised: 04/07/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
Rhododendron delavayi, a notable ornamental plant primarily found in regions of China like Yunnan and Guizhou provinces, holds substantial horticultural value. To elucidate the systematic phylogenetic relationships and organelle genomic differences within R. delavayi and related Rhododendron species, we conducted sequencing and assembly of the complete mitochondrial genome of R. delavayi. The full-length mitochondrial genome of it was a singular circular molecule spanning 1,009,263 bp, comprising 53 protein-coding genes, including 18 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 32 protein-coding genes. A total of 1,182 simple sequence repeats (SSRs) loci were identified in the R. delavayi mitochondrial genome, primarily consisting of single nucleotide, dinucleotide, and trinucleotide repeats. Nucleotide diversity analysis highlighted five genes (atp6, atp9, cox2, nad1, and rpl10) with the highest diversity within the mitochondrial genomes of Rhododendron genus. Comparative analysis of the mitochondrial genome of R. delavayi with those of four other Rhododendron species indicated complex rearrangements in 21 genes, including rps4, nad6, rps3, atp6, cob, atp9, nad7, among others. The mitochondrial phylogenetic tree revealed a close relationship between R. delavayi and R. decorum, forming a sister clade to R. × pulchrum and R. simsii. Furthermore, 126 plastid-to-mitochondrial gene transfers in R. delavayi were identified, ranging from 30 bp to 19,385 bp. These fragments collectively constituted 47.54 % and 9.52 % of the chloroplast and mitochondrial genomes (202,169 bp), respectively. Complex mitochondrial-to-mitochondrial transfers were also observed, with 843 identified fragments totaling 312,036 bp (30.92 % of the mitochondrial genome). Segments exceeding 10 kb may mediate homologous recombination within the mitochondrial molecules. Remarkably, our study underscores that the mitochondrial genome of R. delavayi was the largest reported within the Rhododendron genus to date. The intricate rearrangements observed in the mitochondrial genomes of Rhododendron species, alone with the identification of five potential molecular marker sites, provided valuable insights for species classification and parentage identification within the Rhododendron genus.
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Affiliation(s)
- Weiwei Zuo
- College of Agriculture, Guizhou University, Guiyang 550025, China.
| | - Huie Li
- College of Agriculture, Guizhou University, Guiyang 550025, China.
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2
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Veeraragavan S, Johansen M, Johnston IG. Evolution and maintenance of mtDNA gene content across eukaryotes. Biochem J 2024; 481:1015-1042. [PMID: 39101615 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] [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.
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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
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3
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Moreira D, Blaz J, Kim E, Eme L. A gene-rich mitochondrion with a unique ancestral protein transport system. Curr Biol 2024:S0960-9822(24)00920-5. [PMID: 39084221 DOI: 10.1016/j.cub.2024.07.017] [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: 11/26/2023] [Revised: 05/03/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024]
Abstract
Mitochondria originated from an ancient endosymbiosis involving an alphaproteobacterium.1,2,3 Over time, these organelles reduced their gene content massively, with most genes being transferred to the host nucleus before the last eukaryotic common ancestor (LECA).4 This process has yielded varying gene compositions in modern mitogenomes, including the complete loss of this organellar genome in some extreme cases.5,6,7,8,9,10,11,12,13,14 At the other end of the spectrum, jakobids harbor the most gene-rich mitogenomes, encoding 60-66 proteins.8 Here, we introduce the mitogenome of Mantamonas sphyraenae, a protist from the deep-branching CRuMs supergroup.15,16 Remarkably, it boasts the most gene-rich mitogenome outside of jakobids, by housing 91 genes, including 62 protein-coding ones. These include rare homologs of the four subunits of the bacterial-type cytochrome c maturation system I (CcmA, CcmB, CcmC, and CcmF) alongside a unique ribosomal protein S6. During the early evolution of mitochondria, gene transfer from the proto-mitochondrial endosymbiont to the nucleus became possible thanks to systems facilitating the transport of proteins synthesized in the host cytoplasm back to the mitochondrion. In addition to the universally found eukaryotic protein import systems, jakobid mitogenomes were reported to uniquely encode the SecY transmembrane protein of the Sec general secretory pathway, whose evolutionary origin was however unclear. The Mantamonas mitogenome not only encodes SecY but also SecA, SecE, and SecG, making it the sole eukaryote known to house a complete mitochondrial Sec translocation system. Furthermore, our phylogenetic and comparative genomic analyses provide compelling evidence for the alphaproteobacterial origin of this system, establishing its presence in LECA.
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Affiliation(s)
- David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91190 Gif-sur-Yvette, France.
| | - Jazmin Blaz
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91190 Gif-sur-Yvette, France
| | - Eunsoo Kim
- Division of EcoScience, Ewha Womans University, Seoul, South Korea; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Laura Eme
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91190 Gif-sur-Yvette, France.
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4
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Sanita Lima M, Silva Domingues D, Rossi Paschoal A, Smith DR. Long-read RNA sequencing can probe organelle genome pervasive transcription. Brief Funct Genomics 2024:elae026. [PMID: 38880995 DOI: 10.1093/bfgp/elae026] [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: 03/28/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate - organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.
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Affiliation(s)
- Matheus Sanita Lima
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Douglas Silva Domingues
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Padua Dias 11, Piracicaba, SP 13418-900, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group (BIOINFO-CP), Federal University of Technology - Paraná - UTFPR, Avenida Alberto Carazzai 1640, Cornélio Procópio, PR 86300000, Brazil
| | - David Roy Smith
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
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Song X, Geng Y, Xu C, Li J, Guo Y, Shi Y, Ma Q, Li Q, Zhang M. The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny. IMA Fungus 2024; 15:15. [PMID: 38863028 PMCID: PMC11167856 DOI: 10.1186/s43008-024-00149-6] [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: 11/13/2023] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
In the present study, three mitogenomes from the Bipolaris genus (Bipolaris maydis, B. zeicola, and B. oryzae) were assembled and compared with the other two reported Bipolaris mitogenomes (B. oryzae and B. sorokiniana). The five mitogenomes were all circular DNA molecules, with lengths ranging from 106,403 bp to 135,790 bp. The mitogenomes of the five Bipolaris species mainly comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 13 PCGs in the five mitogenomes. Across the 13 core PCGs tested, nad6 had the least genetic distance among the 16 Pleosporales species we investigated, indicating that this gene was highly conserved. In addition, the Ka/Ks values for all 12 core PCGs (excluding rps3) were < 1, suggesting that these genes were subject to purifying selection. Comparative mitogenomic analyses indicate that introns were the main factor contributing to the size variation of Bipolaris mitogenomes. The introns of the cox1 gene experienced frequent gain/loss events in Pleosporales species. The gene arrangement and collinearity in the mitogenomes of the five Bipolaris species were almost highly conserved within the genus. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the five Bipolaris species formed well-supported topologies. This study is the first report on the mitogenomes of B. maydis and B. zeicola, as well as the first comparison of mitogenomes among Bipolaris species. The findings of this study will further advance investigations into the population genetics, evolution, and genomics of Bipolaris species.
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Affiliation(s)
- Xinzheng Song
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuehua Geng
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chao Xu
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiaxin Li
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yashuang Guo
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yan Shi
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qingzhou Ma
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
| | - Meng Zhang
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
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Malik M, Malik F, Fatma T, Qasim Hayat M, Jamal A, Gul A, Faraz Bhatti M. The complete mitochondrial genome of Penicillium expansum: Insights into the fungal evolution and phylogeny. Gene 2024; 910:148315. [PMID: 38417689 DOI: 10.1016/j.gene.2024.148315] [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: 12/26/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Penicillium expansum is an important phytopathogenic fungus that causes blue mold disease. In this study, the novel mitochondrial genome of P. expansum was sequenced, assembled, annotated, and compared with the previously published Penicillium mitogenomes. P. expansum mitogenome is composed of circular DNA molecules with a genome size of 25,496 bp. It encodes 16 protein-encoding genes (PCGs), two rRNA genes, and 25 tRNA genes. Comparative analysis with six other Penicillium species revealed that gene length, GC content, AT skew, and GC skew were variable among the core protein-coding genes. The Penicillium species' gene synteny analysis identified several gene rearrangements. Among the core 15 PCGs, atp8 had the lowest K2P genetic distance, which shows that this gene is highly conserved. The Ka/Ks value of most PCGs was less than 1, which shows that these genes have undergone purifying selection. Phylogenetic analysis based on 14 concatenated core mitochondrial genes revealed that P. expansum shares a close relationship with P. solitum. This study served as a first report on the complete mitochondrial genome of P. expansum and its comparative analysis that will contribute to population genetics and rapid evolutionary studies among Penicillium species.
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Affiliation(s)
- Mahnoor Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Fatima Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Muhammad Qasim Hayat
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
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7
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Hu Y, Jia F, Hu L, Wu C, Tian T, Li T, Chen B. Comparative mitogenome research revealed the phylogenetics and evolution of the superfamily Tenebrionoidea (Coleoptera: Polyphage). Ecol Evol 2024; 14:e11520. [PMID: 38932962 PMCID: PMC11199344 DOI: 10.1002/ece3.11520] [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: 11/30/2023] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Despite the worldwide distribution and rich diversity of the superfamily Tenebrionoidea, the knowledge of the mitochondrial genomes (mtgenome) characteristics of the superfamily is still very limited, and its phylogenetics and evolution remain unresolved. In the present study, we newly sequenced mtgenomes from 19 species belonging to Tenebrionoidea, and a total of 90 mitochondrial genomes from 16 families of Tenebrionoidea were used for phylogenetic analysis. There exist 37 genes for all 82 species of complete mtgenomes of 16 families investigated, and their characteristics are identical as reported mtgenomes of other Tenebrionoids. The Ka/Ks analysis suggests that all 13 PCGs have undergone a strong purifying selection. The phylogenetic analysis suggests the monophyly of Mordellidae, Meloidae, Oedemeridae, Pyrochroidae, Salpingidae, Scraptiidae, Lagriidae, and Tenebrionidae, and the Mordellidae is close to the Ripiphoridae. The "Tenebrionidae clade" and "Meloidae clade" are monophyletic, and both of them are sister groups. In the "Meloidae clade," Meloidae is close to Anthicidae. In the "Tenebrionidae clade," the family Lagriidae and Tenebrionidae are sister groups. The divergence time analysis suggests that Tenebrionoidea originated in the late Jurassic, Meloidae Mordellidae, Lagriidae, and Tenebrionidae in the Cretaceous, Oedemeridae in Paleogene. The work lays a base for the study of mtgenome, phylogenetics, and evolution of the superfamily Tenebrionoidea.
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Affiliation(s)
- Yun‐Jian Hu
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Feng‐Fan Jia
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Li Hu
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Chuan Wu
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Tian Tian
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Ting‐Jing Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Bin Chen
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life SciencesChongqing Normal UniversityChongqingChina
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Zeb U, Aziz T, Azizullah A, Zan XY, Khan AA, Bacha SAS, Cui FJ. Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny. PHYSIOLOGIA PLANTARUM 2024; 176:e14363. [PMID: 38837786 DOI: 10.1111/ppl.14363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 06/07/2024]
Abstract
Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.
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Affiliation(s)
- Umar Zeb
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
- Faculty of Biological and Biomedical Science, Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Tariq Aziz
- Faculty of Civil Engineering and Mechanics, Jiangsu University, Zhenjiang, PR China
| | - Azizullah Azizullah
- Faculty of Biological and Biomedical Science, Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Xin-Yi Zan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Asif Ali Khan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Syed Asim Shah Bacha
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Feng-Jie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
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Ma X, Niu M, Ni HM, Ding WX. Mitochondrial dynamics, quality control, and mtDNA in alcohol-associated liver disease and liver cancer. Hepatology 2024:01515467-990000000-00861. [PMID: 38683546 DOI: 10.1097/hep.0000000000000910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024]
Abstract
Mitochondria are intracellular organelles responsible for energy production, glucose and lipid metabolism, cell death, cell proliferation, and innate immune response. Mitochondria are highly dynamic organelles that constantly undergo fission, fusion, and intracellular trafficking, as well as degradation and biogenesis. Mitochondrial dysfunction has been implicated in a variety of chronic liver diseases including alcohol-associated liver disease, metabolic dysfunction-associated steatohepatitis, and HCC. In this review, we provide a detailed overview of mitochondrial dynamics, mitophagy, and mitochondrial DNA-mediated innate immune response, and how dysregulation of these mitochondrial processes affects the pathogenesis of alcohol-associated liver disease and HCC. Mitochondrial dynamics and mitochondrial DNA-mediated innate immune response may thereby represent an attractive therapeutic target for ameliorating alcohol-associated liver disease and alcohol-associated HCC.
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Affiliation(s)
- Xiaowen Ma
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Mengwei Niu
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Hong-Min Ni
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Internal Medicine, Division of Gastroenterology, Hepatology and Mobility, University of Kansas Medical Center, Kansas City, Kansas, USA
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10
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Cheng Q, Liu QQ, Lu CA. A state-of-the-science review of using mitochondrial DNA copy number as a biomarker for environmental exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123642. [PMID: 38402934 DOI: 10.1016/j.envpol.2024.123642] [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: 12/17/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Mitochondria are bioenergetic, biosynthetic, and signaling organelles in eukaryotes, and contain their own genomes, mitochondrial DNA (mtDNA), to supply energy to cells by generating ATP via oxidative phosphorylation. Therefore, the threat to mitochondria' integrity and health resulting from environmental exposure could induce adverse health effects in organisms. In this review, we summarized the association between mtDNA copy number (mtDNAcn), and environmental exposures as reported in the literature. We conducted a literature search in the Web of Science using [Mitochondrial DNA copy number] and [Exposure] as two keywords and employed three selection criteria for the final inclusion of 97 papers for review. The consensus of data was that mtDNAcn could be used as a plausible biomarker for cumulative exposures to environmental chemical and physical agents. In order to furtherly expand the application of mtDNAcn in ecological and environmental health research, we suggested a series of algorithms aiming to standardize the calculation of mtDNAcn based on the PCR results in this review. We also discussed the pitfalls of using whole blood/plasma samples for mtDNAcn measurements and regard buccal cells a plausible and practical alternative. Finally, we recognized the importance of better understanding the mechanistic analysis and regulatory mechanism of mtDNAcn, in particular the signals release and regulation pathways. We believe that the development of using mtDNAcn as an exposure biomarker will revolutionize the evaluation of chronic sub-lethal toxicity of chemicals to organisms in ecological and environmental health research that has not yet been implemented.
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Affiliation(s)
- Qing Cheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Qing Qing Liu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chensheng Alex Lu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China; School of Public Health, University of Washington, Seattle, WA, 98195, USA.
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11
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Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024; 25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [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: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.
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Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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Zhang Y, Li Z, Deng Y, Liu B, Huang M, Chen Z. Characterization of the complete mitochondrial genome of Paecilomyces variotii and comparative evolutionary mitochondriomics of 36 fungi. Mol Biol Rep 2024; 51:390. [PMID: 38446255 DOI: 10.1007/s11033-024-09330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUD Paecilomyces variotii has important economic value in stimulating crop growth, biodegradation, and other aspects. Up to now, there are no research reports on its mitochondrial genome. METHODS AND RESULTS The mitochondrial genome of Paecilomyces variotii was determined with the next-generation sequencing method (Illumina, NovaSeq), and its characteristics were analyzed using various bioinformatics approaches. The length of complete mitochondrial genome sequence of P. variotii is 40,965 bp and consists of 14 protein-coding genes, 2 ribosomal RNA genes, 1 ribosomal protein S3 gene, 26 transport RNA genes. The results of phylogenetics analysis using Bayesian inference and Maximum likelihood methods showed that P. variotii belongs to the Eurotiales order in the Thermoascaceae family, and 9 genera within the Eurotiomycetes class were effectively distinguished with high support rates (bootstrap value > 92% and posterior probabilities > 99%). The analysis of synonymous substitution rates and nonsynonymous substitution rates indicated that the Ka/Ks values of the 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class ranged from 0 to 0.4333. CONCLUSIONS This study revealed the structural and sequence information characteristics of the mitochondrial genome of P. variotii, and the phylogenetic results strongly support its classification within the family Thermoascaceae, consistent with traditional morphological taxonomy studies. The 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class are subject to strong purifying (negative) selection. The results of this research provides an important molecular basis for the development of genomics, evolutionary genetics and molecular markers of P. variotii in the future.
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Affiliation(s)
- Yujie Zhang
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Zhengyi Li
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Yijia Deng
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Bin Liu
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Minyi Huang
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Zhiyin Chen
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China.
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Breton S. Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species. Mol Biol Rep 2024; 51:298. [PMID: 38341808 DOI: 10.1007/s11033-024-09270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. METHODS AND RESULTS The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes. CONCLUSION The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada.
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Xu H, Zhu Z, Tian Z, Wei C, Fan Q, Wang Y, Shen S, Deng G, Ding M. The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae. Genes (Basel) 2024; 15:111. [PMID: 38255000 PMCID: PMC10815617 DOI: 10.3390/genes15010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.
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Affiliation(s)
- Hui Xu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ziyi Zhu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zeyuan Tian
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Cuiyuan Wei
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qi Fan
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanbing Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Shikang Shen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Gang Deng
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
| | - Mingliang Ding
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Food Crops Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650200, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100083, China
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Chen SC, Jiang HY, Liao SR, Chen TX, Wang XQ. Complete mitochondrial genome of Stethoconus japonicus (Hemiptera: Miridae): Insights into the evolutionary traits within the family Miridae. Gene 2024; 891:147830. [PMID: 37758005 DOI: 10.1016/j.gene.2023.147830] [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: 05/31/2023] [Revised: 09/12/2023] [Accepted: 09/23/2023] [Indexed: 09/29/2023]
Abstract
The mitochondrial (mt) genome sequence of insects possesses numerous evolutionary traits. To better understand the evolution of mt genomes within the family Miridae, the complete mt genome of the predatory Japanese plant bug Stethoconus japonicus Schumacher was sequenced before undertaking a comparative analysis of all reported plant bug mt genomes. The mt genome of S. japonicus is a closed-circular and double-stranded DNA molecule of 16,274 bp (GenBank: MK341530), which consists of 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and a putative control region (CR). Consistent with other plant bugs, the mt genome of S. japonicus is strongly AT-biased (73.49 %) with A-skewed (0.202) and C-skewed (-0.248). All 13 PCGs initiate translation using ATN codons and TAA served as complete stop codons for eight PCGs, which as incomplete stop codon "T-" for cox1, nad1, nad5-6 and "TA-" for cox2. Regarding other features, all 22 tRNAs could be folded into typical cloverleaf secondary structures. The control region is 1,717 bp and contains a long tandem repeat sequence of a 165 bp unit repeated six times. Similar sequence with variable number of tandemly repeated units from intra-genus CRs is a distinct characteristic of plant bug mt genomes. Phylogenetic relationships of 15 bugs were eventually analyzed based on Maximum likelihood (ML) and Bayesian inference (BI) methods using 17 mt genome sequences. In the phylogenetic trees, species from a same genus or subfamily are clustered into a branch with high supporting values.and the result suggest that Deraeocorinae is more closely related to Mirinae than Bryocorinae. Finally, this study revealed that mutation of tRNA anticodon is a useful phylogenetic marker that could be of significance for studies of evolutionary patterns.
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Affiliation(s)
- Shi-Chun Chen
- Tea Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, PR China.
| | - Hong-Yan Jiang
- Tea Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, PR China.
| | - Shu-Ran Liao
- Tea Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, PR China.
| | - Ting-Xu Chen
- Tea Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, PR China.
| | - Xiao-Qing Wang
- Tea Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, PR China.
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Kabtani J, Ranque S. A Comparative Description of Dermatophyte Genomes: A State-of-the-Art Review. Mycopathologia 2023; 188:1007-1025. [PMID: 37812320 DOI: 10.1007/s11046-023-00802-5] [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: 05/11/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
The nomenclature and phylogeny of dermatophytes is currently based on the nucleotide sequence polymorphisms of a few genomic regions. However, the limitations of this multilocus sequence-based approach makes dermatophyte species identification difficult. Variation and adaptation are key to the persistence of species. Nevertheless, this heterogeneity poses a genuine problem for the classification and nomenclature of dermatophytes. The relatively high intra-species and low inter-species polymorphisms of this keratinophilic group of fungi hampers both species delineation and identification. Establishing the taxonomic boundaries of dermatophyte species complexes remains controversial. Furthermore, until recently, knowledge of molecular biology, genetics and genomics remained limited. This systematic review highlights the added value of whole genome sequencing and analysis data in dermatophyte classification that might enhance identification and, consequently, the diagnosis and management of dermatophytoses. Our approach consisted in describing and comparing the dermatophyte mitochondrial genomes, secretomes (Adhesins, LysM domains, proteases) and metabolic pathways, with the aim to provide new insights and a better understanding of the phylogeny and evolution of dermatophytes.
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Affiliation(s)
- J Kabtani
- IHU Méditerranée Infection, 13005, Marseille, France
| | - S Ranque
- IHU Méditerranée Infection, 13005, Marseille, France.
- AP-HM, IRD, SSA, VITROME, Aix-Marseille Université, 13005, Marseille, France.
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Li J, Chen Y, Liu Y, Wang C, Li L, Chao Y. Complete mitochondrial genome of Agrostis stolonifera: insights into structure, Codon usage, repeats, and RNA editing. BMC Genomics 2023; 24:466. [PMID: 37596544 PMCID: PMC10439588 DOI: 10.1186/s12864-023-09573-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Plants possess mitochondrial genomes that are large and complex compared to animals. Despite their size, plant mitochondrial genomes do not contain significantly more genes than their animal counterparts. Studies into the sequence and structure of plant mitochondrial genomes heavily imply that the main mechanism driving replication of plant mtDNA, and offer valuable insights into plant evolution, energy production, and environmental adaptation. RESULTS This study presents the first comprehensive analysis of Agrostis stolonifera's mitochondrial genome, characterized by a branched structure comprising three contiguous chromosomes, totaling 560,800 bp with a GC content of 44.07%. Annotations reveal 33 unique protein-coding genes (PCGs), 19 tRNA genes, and 3 rRNA genes. The predominant codons for alanine and glutamine are GCU and CAA, respectively, while cysteine and phenylalanine exhibit weaker codon usage biases. The mitogenome contains 73, 34, and 23 simple sequence repeats (SSRs) on chromosomes 1, 2, and 3, respectively. Chromosome 1 exhibits the most frequent A-repeat monomeric SSR, whereas chromosome 2 displays the most common U-repeat monomeric SSR. DNA transformation analysis identifies 48 homologous fragments between the mitogenome and chloroplast genome, representing 3.41% of the mitogenome's total length. The PREP suite detects 460 C-U RNA editing events across 33 mitochondrial PCGs, with the highest count in the ccmFn gene and the lowest in the rps7 gene. Phylogenetic analysis confirms A. stolonifera's placement within the Pooideae subfamily, showing a close relationship to Lolium perenne, consistent with the APG IV classification system. Numerous homologous co-linear blocks are observed in A. stolonifera's mitogenomes and those of related species, while certain regions lack homology. CONCLUSIONS The unique features and complexities of the A. stolonifera mitochondrial genome, along with its similarities and differences to related species, provide valuable insights into plant evolution, energy production, and environmental adaptation. The findings from this study significantly contribute to the growing body of knowledge on plant mitochondrial genomes and their role in plant biology.
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Affiliation(s)
- Jiaxing Li
- School of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Yinglong Chen
- UWA School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Yaling Liu
- Inner Mongolia M-Grass Ecology And Environment (Group) Co., Ltd, Hohhot, 010010, China
| | - Chen Wang
- Mentougou District Bureau of Ecological and Environment of Beijing Municipality, Beijing, 102300, China
| | - Ling Li
- Mentougou District Bureau of Ecological and Environment of Beijing Municipality, Beijing, 102300, China
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
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Shan Y, Li J, Zhang X, Yu J. The complete mitochondrial genome of Amorphophallus albus and development of molecular markers for five Amorphophallus species based on mitochondrial DNA. FRONTIERS IN PLANT SCIENCE 2023; 14:1180417. [PMID: 37416891 PMCID: PMC10322194 DOI: 10.3389/fpls.2023.1180417] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Introduction Amorphophallus albus is an herbaceous, cormous, perennial plant used as a food source and traditional medicine in Asia. Methods In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. albus. Then we analyzed the repeated elements and mitochondrial plastid sequences (MTPTs), predicted RNA editing sites in mitochondrial protein-coding genes (PCGs). Lastly, we inferred the phylogenetic relationships of A. albus and other angiosperms based on mitochondrial PCGs, and designed two molecular markers based on mitochondrial DNA. Results and discussion The complete mitogenome of A. albus consists of 19 circular chromosomes. And the total length of A. albus mitogenome is 537,044 bp, with the longest chromosome measuring 56,458 bp and the shortest measuring 12,040 bp. We identified and annotated a total of 36 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes in the mitogenome. Additionally, we analyzed mitochondrial plastid DNAs (MTPTs) and identified 20 MTPTs between the two organelle genomes, with a combined length of 22,421 bp, accounting for 12.76% of the plastome. Besides, we predicted a total of 676 C to U RNA editing sites on 36 protein-coding genes of high confidence using Deepred-mt. Furthermore, extensive genomic rearrangement was observed between A. albus and the related mitogenomes. We conducted phylogenetic analyses based on mitochondrial PCGs to determine the evolutionary relationships between A. albus and other angiosperms. Finally, we developed and validated two molecular markers, Ai156 and Ai976, based on two intron regions (nad2i156 and nad4i976) respectively. The discrimination success rate was 100 % in validation experiments for five widely grown konjac species. Our results reveal the multi-chromosome mitogenome of A. albus, and the developed markers will facilitate molecular identification of this genus.
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Castrillo ML, Bich GÁ, Amerio NS, Barengo MP, Zapata PD, Saparrat MCN, Villalba LL. Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma. Front Microbiol 2023; 14:1141087. [PMID: 37383640 PMCID: PMC10294050 DOI: 10.3389/fmicb.2023.1141087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/24/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. Methods The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. Results T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. Discussion The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.
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Affiliation(s)
- María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Soledad Amerio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcela Paola Barengo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mario Carlos Nazareno Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Instituto de Botánica Carlos Spegazzini, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
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Fan X, Zhang D, Hou T, Zhang Q, Wang Z. Insight into the health risk implicated in mitochondrial toxicity of dibutyl phthalate exposure on zebrafish (Danio rerio) cells. CHEMOSPHERE 2023; 326:138510. [PMID: 36966926 DOI: 10.1016/j.chemosphere.2023.138510] [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: 12/14/2022] [Revised: 03/06/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
Dibutyl phthalate (DBP) is commonly applied plasticizer in plastic products such as face masks, easily leaches or migrates into environment and its widespread contamination posed profound health risks. Further concerns rise regarding to the toxicity of DBP at subcellular level, while little is known about the ranging effects on mitochondrial susceptibility. Present study investigated the mitochondrial impairments with implicated cell death upon DBP exposure on zebrafish cells. Elevated mitochondrial oxidative stress reduced its membrane potential and count, enhanced fragmentation, and impaired ultrastructure that showed smaller size and cristae rupture. Afterwards, the critical function of ATP synthesis was damaged and the stabilized binding capacity between DBP with mitochondrial respiratory complexes was simulated by the molecular docking. And the top pathways enrichment of mitochondrion and metabolism by transcriptome analyses verified the mitochondrial dysfunction that indicated the human diseases risks. The mitochondrial DNA (mtDNA) replication and transcription with DNA methylation modifications were also disrupted, reflecting the genotoxicity on mtDNA. Moreover, the activated autophagy and apoptosis underlying mitochondrial susceptibility integrated into cellular homeostasis changes. These findings provide the first systemic evidence broadening and illustrating the mitochondrial toxicity of DBP exposure on zebrafish model that raise concern on phthalates contamination and ecotoxicological evaluation.
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Affiliation(s)
- Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dingfu Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qianqing Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å. Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Front Microbiol 2023; 14:1159811. [PMID: 37275157 PMCID: PMC10234125 DOI: 10.3389/fmicb.2023.1159811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. Methods In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and Discussion Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
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22
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Christinaki AC, Theelen B, Zania A, Coutinho SDA, Cabañes JF, Boekhout T, Kouvelis VN. Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia. Sci Rep 2023; 13:6308. [PMID: 37072481 PMCID: PMC10113387 DOI: 10.1038/s41598-023-33486-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Mitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. In this study, the comparative analysis of Malassezia mitogenomes contributed to phylogenetic tree construction for all species. The mitogenomes presented significant size and gene order diversity which correlates to their phylogeny. Most importantly, they showed the inclusion of large inverted repeats (LIRs) and G-quadruplex (G4) DNA elements, rendering Malassezia mitogenomes a valuable test case for elucidating the evolutionary mechanisms responsible for this genome diversity. Both LIRs and G4s coexist and convergently evolved to provide genome stability through recombination. This mechanism is common in chloroplasts but, hitherto, rarely found in mitogenomes.
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Affiliation(s)
- Anastasia C Christinaki
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Alkmini Zania
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | | | - Javier F Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Vassili N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece.
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23
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Fatma T, Ahmed Khan H, Ahmed A, Adnan F, Zeshan, Virk N, Faraz Bhatti M. Functional annotation and comparative analysis of four Botrytis cinerea mitogenomes reported from Punjab, Pakistan. Saudi J Biol Sci 2023; 30:103605. [PMID: 36950365 PMCID: PMC10025148 DOI: 10.1016/j.sjbs.2023.103605] [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: 09/12/2022] [Revised: 02/02/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Botrytis cinerea is one of the top phytopathogenic fungus which ubiquitously cause grey mold on a variety of horticultural plants. The mechanism of respiration in the fungus occurs within the mitochondria. Mitogenomes serve as a key molecular marker for the investigation of fungal evolutionary patterns. This study aimed at the complete assembly, characterization, and comparative relationship of four mitogenomes of Botrytis cinerea strains including Kst5C, Kst14A, Kst32B, Kst33A, respectively. High throughput sequencing of four mitogenomes allowed the full assembly and annotation of these sequences. The total genome length of these 4 isolates Kst5C Kst14A, Kst32B, Kst33A was 69,986 bp, 77,303 bp, 76,204 bp and 55, 226 bp respectively. The distribution of features represented 2 ribosomal RNA genes,14 respiration encoding proteins, 1 mitochondrial ribosomal protein-encoding gene, along with varying numbers of transfer RNA genes, protein-coding genes, mobile intronic regions and homing endonuclease genes including LAGLIDADG and GIY-YIG domains were found in all four mitogenomes. The comparative analyses performed also decipher significant results for four mitogenomes among fungal isolates included in the study. This is the first report on the detailed annotation of mitogenomes as a proof for investigation of variation patterns present with in the B. cinerea causing grey mold on strawberries in Pakistan. This study will also contribute to the rapid evolutionary analysis and population patterns present among Botrytis cinerea.
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Affiliation(s)
- Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Fazal Adnan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Zeshan
- Institute of Environmental Sciences and Engineering (IESE), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
- Corresponding author.
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24
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Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria). mBio 2023; 14:e0030223. [PMID: 36939357 PMCID: PMC10127745 DOI: 10.1128/mbio.00302-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria-the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1, -3, -4, -4L, -5, and -7, cob, cox1, -2, and -3, and atp1, -6, and -9, with forams and radiolarians additionally carrying nad2 and nad6, respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.
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25
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Gao JW, Yuan XP, Jakovlić I, Wu H, Xiang CY, Xie M, Song R, Xie ZG, Wu YA, Ou DS. The mitochondrial genome of Heterosentis pseudobagri (Wang & Zhang, 1987) Pichelin & Cribb, 1999 reveals novel aspects of tRNA genes evolution in Acanthocephala. BMC Genomics 2023; 24:95. [PMID: 36864372 PMCID: PMC9979467 DOI: 10.1186/s12864-023-09177-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/10/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Acanthocephala is a clade of obligate endoparasites whose mitochondrial genomes (mitogenomes) and evolution remain relatively poorly understood. Previous studies reported that atp8 is lacking from acanthocephalan mitogenomes, and that tRNA genes often have nonstandard structures. Heterosentis pseudobagri (Arhythmacanthidae) is an acanthocephalan fish endoparasite for which no molecular data are currently available, and biological information is unavailable in the English language. Furthermore, there are currently no mitogenomes available for Arhythmacanthidae. METHODS We sequenced its mitogenome and transcriptome, and conducted comparative mitogenomic analyses with almost all available acanthocephalan mitogenomes. RESULTS The mitogenome had all genes encoded on the same strand and unique gene order in the dataset. Among the 12 protein-coding genes, several genes were highly divergent and annotated with difficulty. Moreover, several tRNA genes could not be identified automatically, so we had to identify them manually via a detailed comparison with orthologues. As common in acanthocephalans, some tRNAs lacked either the TWC arm or the DHU arm, but in several cases, we annotated tRNA genes only on the basis of the conserved narrow central segment comprising the anticodon, while the flanking 5' and 3' ends did not exhibit any resemblance to orthologues and they could not be folded into a tRNA secondary structure. We corroborated that these are not sequencing artefacts by assembling the mitogenome from transcriptomic data. Although this phenomenon was not observed in previous studies, our comparative analyses revealed the existence of highly divergent tRNAs in multiple acanthocephalan lineages. CONCLUSIONS These findings indicate either that multiple tRNA genes are non-functional or that (some) tRNA genes in (some) acanthocephalans might undergo extensive posttranscriptional tRNA processing which restores them to more conventional structures. It is necessary to sequence mitogenomes from yet unrepresented lineages and further explore the unusual patterns of tRNA evolution in Acanthocephala.
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Affiliation(s)
- Jin-Wei Gao
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153 Hunan China
| | - Xi-Ping Yuan
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153 Hunan China
| | - Ivan Jakovlić
- grid.32566.340000 0000 8571 0482State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000 China
| | - Hao Wu
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153 Hunan China
| | - Chuan-Yu Xiang
- grid.32566.340000 0000 8571 0482State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000 China
| | - Min Xie
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153 Hunan China
| | - Rui Song
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China.
| | - Zhong-Gui Xie
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153 Hunan China
| | - Yuan-An Wu
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153 Hunan China
| | - Dong-Sheng Ou
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153 Hunan China
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26
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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: 0] [Impact Index Per Article: 0] [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.
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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
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27
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Szafranski P. New Dielis species and structural dichotomy of the mitochondrial cox2 gene in Scoliidae wasps. Sci Rep 2023; 13:1950. [PMID: 36732536 PMCID: PMC9895450 DOI: 10.1038/s41598-023-27806-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
Some mitochondrial protein-coding genes of protists and land plants have split over the course of evolution into complementary genes whose products can form heteromeric complexes that likely substitute for the undivided proteins. One of these genes, cox2, has also been found to have split in animals, specifically in Scoliidae wasps (Hymenoptera: Apocrita) of the genus Dielis (Campsomerini), while maintaining the conventional structure in related Scolia (Scoliini). Here, a hitherto unrecognized Nearctic species of Dielis, D. tejensis, is described based on its phenotype and mtDNA. The mitogenome of D. tejensis sp. nov. differs from that of the sympatric sibling species Dielis plumipes fossulana by the reduced size of the cox2-dividing insert, which, however, still constitutes the fifth part of the mtDNA; an enlarged nad2-trnW intergenic region; the presence of two trnKttt paralogues; and other features. Both species of Dielis have a unique insertion of a threonine in COXIIA, predicted to be involved in COXIIA-COXIIB docking, and substitutions of two hydrophobic residues with redox-active cysteines around the CuA centre in COXIIB. Importantly, the analysis of mtDNA from another Campsomerini genus, Megacampsomeris, shows that its cox2 gene is also split. The presented data highlight evolutionary processes taking place in hymenopteran mitogenomes that do not fall within the mainstream of animal mitochondrion evolution.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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28
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Zhang N, Li Y, Halanych KM, Kong L, Li Q. A comparative analysis of mitochondrial ORFs provides new insights on expansion of mitochondrial genome size in Arcidae. BMC Genomics 2022; 23:809. [PMID: 36474182 PMCID: PMC9727918 DOI: 10.1186/s12864-022-09040-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arcidae, comprising about 260 species of ark shells, is an ecologically and economically important lineage of bivalve mollusks. Interestingly, mitochondrial genomes of several Arcidae species are 2-3 times larger than those of most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. The large mitochondrial genome size is mainly due to expansion of unassigned regions (regions that are functionally unassigned). Previous work on unassigned regions of Arcidae mtDNA genomes has focused on nucleotide-level analyses to observe sequence characteristics, however the origin of expansion remains unclear. RESULTS We assembled six new mitogenomes and sequenced six transcriptomes of Scapharca broughtonii to identify conserved functional ORFs that are transcribed in unassigned regions. Sixteen lineage-specific ORFs with different copy numbers were identified from seven Arcidae species, and 11 of 16 ORFs were expressed and likely biologically active. Unassigned regions of 32 Arcidae mitogenomes were compared to verify the presence of these novel mitochondrial ORFs and their distribution. Strikingly, multiple structural analyses and functional prediction suggested that these additional mtDNA-encoded proteins have potential functional significance. In addition, our results also revealed that the ORFs have a strong connection to the expansion of Arcidae mitochondrial genomes and their large-scale duplication play an important role in multiple expansion events. We discussed the possible origin of ORFs and hypothesized that these ORFs may originate from duplication of mitochondrial genes. CONCLUSIONS The presence of lineage-specific mitochondrial ORFs with transcriptional activity and potential functional significance supports novel features for Arcidae mitochondrial genomes. Given our observation and analyses, these ORFs may be products of mitochondrial gene duplication. These findings shed light on the origin and function of novel mitochondrial genes in bivalves and provide new insights into evolution of mitochondrial genome size in metazoans.
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Affiliation(s)
- Ning Zhang
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yuanning Li
- grid.27255.370000 0004 1761 1174Shandong University, Qingdao, China
| | - Kenneth M. Halanych
- grid.217197.b0000 0000 9813 0452Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28409 USA
| | - Lingfeng Kong
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qi Li
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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De Novo Hybrid Assembly of the Salvia miltiorrhiza Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of Salvia Species. Int J Mol Sci 2022; 23:ijms232214267. [PMID: 36430747 PMCID: PMC9694629 DOI: 10.3390/ijms232214267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Salvia miltiorrhiza has been an economically important medicinal plant. Previously, an S. miltiorrhiza mitochondrial genome (mitogenome) assembled from Illumina short reads, appearing to be a single circular molecule, has been published. Based on the recent reports on the plant mitogenome structure, we suspected that this conformation does not accurately represent the complexity of the S. miltiorrhiza mitogenome. In the current study, we assembled the mitogenome of S. miltiorrhiza using the PacBio and Illumina sequencing technologies. The primary structure of the mitogenome contained two mitochondrial chromosomes (MC1 and MC2), which corresponded to two major conformations, namely, Mac1 and Mac2, respectively. Using two approaches, including (1) long reads mapping and (2) polymerase chain reaction amplification followed by Sanger sequencing, we observed nine repeats that can mediate recombination. We predicted 55 genes, including 33 mitochondrial protein-coding genes (PCGs), 3 rRNA genes, and 19 tRNA genes. Repeat analysis identified 112 microsatellite repeats and 3 long-tandem repeats. Phylogenetic analysis using the 26 shared PCGs resulted in a tree that was congruent with the phylogeny of Lamiales species in the APG IV system. The analysis of mitochondrial plastid DNA (MTPT) identified 16 MTPTs in the mitogenome. Moreover, the analysis of nucleotide substitution rates in Lamiales showed that the genes atp4, ccmB, ccmFc, and mttB might have been positively selected. The results lay the foundation for future studies on the evolution of the Salvia mitogenome and the molecular breeding of S. miltiorrhiza.
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30
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Hugaboom M, Hatmaker EA, LaBella AL, Rokas A. Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi. G3 (BETHESDA, MD.) 2022; 13:6777267. [PMID: 36305682 PMCID: PMC9836360 DOI: 10.1093/g3journal/jkac285] [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: 08/23/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.
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Affiliation(s)
- Miya Hugaboom
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Elizabeth Anne Hatmaker
- Corresponding author: Department of Biological Sciences, Vanderbilt University, VU Station B 35-1364, Nashville, TN 37235, USA. (AH)
| | - Abigail L LaBella
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Antonis Rokas
- Corresponding author: Department of Biological Sciences, Vanderbilt University, VU Station B 35-1364, Nashville, TN 37235, USA. (AR)
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31
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Gornik SG, Flores V, Reinhardt F, Erber L, Salas-Leiva DE, Douvropoulou O, Lassadi I, Einarsson E, Mörl M, Git A, Stadler PF, Pain A, Waller RF. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes. Mol Biol Evol 2022; 39:6701636. [PMID: 36108082 PMCID: PMC9550989 DOI: 10.1093/molbev/msac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.
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Affiliation(s)
| | - Victor Flores
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Franziska Reinhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Dayana E Salas-Leiva
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Olga Douvropoulou
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany,Discrete Biomathematics, Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany,Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währinger Str. 17, Alsergrund, Vienna 1090, Austria,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Arnab Pain
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,International Institute for Zoonosis Control, Hokkaido University, 001-0020 North 20, West 10 Kita-ku, Sapporo 001-0020, Japan
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Schalamun M, Schmoll M. Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1002161. [PMID: 37746224 PMCID: PMC10512326 DOI: 10.3389/ffunb.2022.1002161] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/25/2022] [Indexed: 09/26/2023]
Abstract
The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.
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Affiliation(s)
- Miriam Schalamun
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Monika Schmoll
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
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Intraspecific comparison of mitochondrial genomes reveals the evolution in medicinal fungus Ganoderma lingzhi. J Biosci Bioeng 2022; 134:374-383. [PMID: 36075811 DOI: 10.1016/j.jbiosc.2022.07.003] [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: 09/25/2021] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/21/2022]
Abstract
Several mitogenomes of the genus Ganoderma have been assembled, but intraspecific comparisons of mitogenomes in Ganoderma lingzhi have not been reported. In this study, 19 G. lingzhi mitogenomes were assembled and analyzed combined with three mitogenomes of G. lingzhi from GenBank in term of the characteristics, evolution, and phylogeny. The results showed that the mitogenomes of the G. lingzhi strains are closed circular ranging from 49.23 kb to 68.37 kb. The genetic distance, selective pressure, and base variation indicate that the 14 common protein coding genes were highly conserved. The differences in introns, open reading frames, and repetitive sequences in the mitogenome were the main factors leaded to the variations in mitogenome. The introns were horizontally transferred in mitogenomes, and the differences between introns in the same insertion, which were primarily caused by the repetitive sequence, showed that the introns may be under degeneration. Besides, the frequent insertion and deletion of introns showed an evolutionary rate faster than protein coding genes. Phylogenetic analysis showed that the G. lingzhi strains gathered with high support, and those with the same intron distribution law had closer clustering relationships.
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Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2205041119. [PMID: 35994648 PMCID: PMC9436333 DOI: 10.1073/pnas.2205041119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.
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Zhang H, Lu C, Liu Q, Zou T, Qiao G, Huang X. Insights into the Evolution of Aphid Mitogenome Features from New Data and Comparative Analysis. Animals (Basel) 2022; 12:ani12151970. [PMID: 35953959 PMCID: PMC9367533 DOI: 10.3390/ani12151970] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genomes and their rearrangement patterns can provide useful information for inferring evolutionary history of organisms. Aphids are one of the insect groups with some unique mitogenome features. In this study, to examine whether some features in aphid mitogenomes are independent species-specific evolutionary events or clade-specific events at certain taxonomic levels, we sequenced three new aphid mitogenomes (Hormaphidinae: Ceratovacuna keduensis, Pseudoregma panicola; Lachninae: Nippolachnus piri) and compared them with all known aphid mitogenomes. The three mitogenomes are 16,059–17,033 bp in length, with a set of 37 typical mitochondrial genes, a non-coding control region and a tandem repeat region. The gene orders of them are all highly rearranged. Within the subfamily Hormaphidinae, the presence of repeat region and mitogenome rearrangement in Cerataphidini species but not in the other two tribes indicate that these may be Cerataphidini-specific features. The same gene rearrangement pattern in the two Lachninae species, N. piri (Tuberolachnini) and Stomaphis sinisalicis (Stomaphidini), supports that this feature should be at least derived from the common ancestor of two tribes. Overall, our data and analyses provide new insights into the evolutionary patterns of gene rearrangement and repeat region in aphid mitogenomes, and further corroborate the potential role of gene rearrangement in elucidating the evolutionary history of different insect lineages.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Congcong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Tianmin Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- Correspondence: (G.Q.); (X.H.)
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.L.); (Q.L.); (T.Z.)
- Correspondence: (G.Q.); (X.H.)
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Bénit P, Goncalves J, El Khoury R, Rak M, Favier J, Gimenez-Roqueplo AP, Rustin P. Succinate Dehydrogenase, Succinate, and Superoxides: A Genetic, Epigenetic, Metabolic, Environmental Explosive Crossroad. Biomedicines 2022; 10:biomedicines10081788. [PMID: 35892689 PMCID: PMC9394281 DOI: 10.3390/biomedicines10081788] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
Research focused on succinate dehydrogenase (SDH) and its substrate, succinate, culminated in the 1950s accompanying the rapid development of research dedicated to bioenergetics and intermediary metabolism. This allowed researchers to uncover the implication of SDH in both the mitochondrial respiratory chain and the Krebs cycle. Nowadays, this theme is experiencing a real revival following the discovery of the role of SDH and succinate in a subset of tumors and cancers in humans. The aim of this review is to enlighten the many questions yet unanswered, ranging from fundamental to clinically oriented aspects, up to the danger of the current use of SDH as a target for a subclass of pesticides.
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Affiliation(s)
- Paule Bénit
- NeuroDiderot, Inserm, Université Paris Cité, F-75019 Paris, France; (P.B.); (M.R.)
| | - Judith Goncalves
- Paris Centre de Recherche Cardiovasculaire (PARCC), Inserm, Université Paris Cité, F-75015 Paris, France; (J.G.); (J.F.)
| | - Riyad El Khoury
- Department of Pathology and Laboratory Medicine, Neuromuscular Diagnostic Laboratory, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon;
| | - Malgorzata Rak
- NeuroDiderot, Inserm, Université Paris Cité, F-75019 Paris, France; (P.B.); (M.R.)
| | - Judith Favier
- Paris Centre de Recherche Cardiovasculaire (PARCC), Inserm, Université Paris Cité, F-75015 Paris, France; (J.G.); (J.F.)
| | - Anne-Paule Gimenez-Roqueplo
- Département de Médecine Génomique des Tumeurs et des Cancers, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, F-75015 Paris, France;
| | - Pierre Rustin
- NeuroDiderot, Inserm, Université Paris Cité, F-75019 Paris, France; (P.B.); (M.R.)
- Correspondence:
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Complex Physical Structure of Complete Mitochondrial Genome of Quercus acutissima (Fagaceae): A Significant Energy Plant. Genes (Basel) 2022; 13:genes13081321. [PMID: 35893058 PMCID: PMC9331829 DOI: 10.3390/genes13081321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/06/2023] Open
Abstract
Quercus acutissima Carruth. is a Chinese important energy plant with high ecological and economic values. While the species chloroplast genome has been reported, its mitochondrial genome (mitogenome) is still unexplored. Here, we assembled and annotated the Q. acutissima mitogenome, and we compared its characteristic differences with several closely related species. The Q. acutissima mitogenome’s main structure is branched with three distinguished contigs (linear molecule 1, circular molecule 2, and circular molecule 3) with 448,982 bp total length and 45.72% GC content. The mitogenome contained 51 genes, including 32 protein-coding, 16 tRNA and 3 rRNA genes. We examined codon usage, repeated sequences, genome recombination, chloroplast to mitochondrion DNA transformation, RNA editing, and synteny in the Q. acutissima mitogenome. Phylogenetic trees based on 29 species mitogenomes clarified the species classification. Our results provided comprehensive information of Q. acutissima mitogenome, and they are expected to provide valuable information for Fagaceae evolutionary biology and to promote the species germplasm utilization.
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38
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Ellena V, Steiger MG. The importance of complete and high-quality genome sequences in Aspergillus niger research. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:935993. [PMID: 37746178 PMCID: PMC10512394 DOI: 10.3389/ffunb.2022.935993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/27/2022] [Indexed: 09/26/2023]
Abstract
The possibility to sequence the entire genome of an organism revolutionized the fields of biology and biotechnology. The first genome sequence of the important filamentous fungus Aspergillus niger was obtained in 2007, 11 years after the release of the first eukaryotic genome sequence. From that moment, genomics of A. niger has seen major progresses, facilitated by the advances in the sequencing technologies and in the methodologies for gene function prediction. However, there are still challenges to face when trying to obtain complete genomes, equipped with all the repetitive sequences that they contain and without omitting the mitochondrial sequences. The aim of this perspective article is to discuss the current status of A. niger genomics and draw attention to the open challenges that the fungal community should address to move research of this important fungus forward.
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Affiliation(s)
- Valeria Ellena
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
| | - Matthias G. Steiger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
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Yan L, Hou Z, Ma J, Wang H, Gao J, Zeng C, Chen Q, Yue B, Zhang X. Complete mitochondrial genome of Episymploce splendens (Blattodea: Ectobiidae): A large intergenic spacer and lacking of two tRNA genes. PLoS One 2022; 17:e0268064. [PMID: 35653382 PMCID: PMC9162313 DOI: 10.1371/journal.pone.0268064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
The complete mitochondrial genome of Episymploce splendens, 15,802 bp in length, was determined and annotated in this study. The mito-genome included 13 PCGs, 20 tRNAs and 2 rRNAs. Unlike most typical mito-genomes with conservative gene arrangement and exceptional economic organization, E. splendens mito-genome has two tRNAs (tRNA-Gln and tRNA-Met) absence and a long intergenic spacer sequence (93 bp) between tRNA-Val and srRNA, showing the diversified features of insect mito-genomes. This is the first report of the tRNAs deletion in blattarian mito-genomes and we supported the duplication/random loss model as the origin mechanism of the long intergenic spacer. Two Numts, Numt-1 (557 bp) and Numt-2 (975 bp) transferred to the nucleus at about 14.15 Ma to 22.34 Ma, and 19.19 Ma to 24.06 Ma respectively, were found in E. splendens. They can be used as molecular fossils in insect phylogenetic relationship inference. Our study provided useful data for further studies on the evolution of insect mito-genome.
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Affiliation(s)
- Lin Yan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhenzhen Hou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jinnan Ma
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongmei Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jie Gao
- Sichuan Key Laboratory of Medicinal Periplaneta Americana, Sichuan Gooddoctor Pharmaceutical Group, Chengdu, China
| | - Chenjuan Zeng
- Sichuan Key Laboratory of Medicinal Periplaneta Americana, Sichuan Gooddoctor Pharmaceutical Group, Chengdu, China
| | - Qin Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- * E-mail:
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40
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Christinaki AC, Kanellopoulos SG, Kortsinoglou AM, Andrikopoulos MΑ, Theelen B, Boekhout T, Kouvelis VN. Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts. Genome Biol Evol 2022; 14:6586520. [PMID: 35576568 PMCID: PMC9154068 DOI: 10.1093/gbe/evac073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Saccharomycotina yeasts belong to diverse clades within the kingdom of fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 155 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions’ diversity, genetic code alterations, and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process, mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout the evolution of Saccharomycotina. Overall, this work shows that phylogenetic studies based on the mt genome of yeasts highlight major evolutionary events.
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Affiliation(s)
- Anastasia C Christinaki
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Spyros G Kanellopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Alexandra M Kortsinoglou
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Marios Α Andrikopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
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Varassas SP, Kouvelis VN. Mitochondrial Transcription of Entomopathogenic Fungi Reveals Evolutionary Aspects of Mitogenomes. Front Microbiol 2022; 13:821638. [PMID: 35387072 PMCID: PMC8979003 DOI: 10.3389/fmicb.2022.821638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Entomopathogenic fungi and more specifically genera Beauveria and Metarhizium have been exploited for the biological control of pests. Genome analyses are important to understand better their mode of action and thus, improve their efficacy against their hosts. Until now, the sequences of their mitochondrial genomes were studied, but not at the level of transcription. Except of yeasts and Neurospora crassa, whose mt gene transcription is well described, in all other Ascomycota, i.e., Pezizomycotina, related information is extremely scarce. In this work, mt transcription and key enzymes of this function were studied. RT-PCR experiments and Northern hybridizations reveal the transcriptional map of the mt genomes of B. bassiana and M. brunneum species. The mt genes are transcribed in six main transcripts and undergo post-transcriptional modifications to create single gene transcripts. Promoters were determined in both mt genomes with a comparative in silico analysis, including all known information from other fungal mt genomes. The promoter consensus sequence is 5'-ATAGTTATTAT-3' which is in accordance with the definition of the polycistronic transcripts determined with the experiments described above. Moreover, 5'-RACE experiments in the case of premature polycistronic transcript nad1-nad4-atp8-atp6 revealed the 5' end of the RNA transcript immediately after the in silico determined promoter, as also found in other fungal species. Since several conserved elements were retrieved from these analyses compared to the already known data from yeasts and N. crassa, the phylogenetic analyses of mt RNA polymerase (Rpo41) and its transcriptional factor (Mtf1) were performed in order to define their evolution. As expected, it was found that fungal Rpo41 originate from the respective polymerase of T7/T3 phages, while the ancestor of Mtf1 is of alpha-proteobacterial origin. Therefore, this study presents insights about the fidelity of the mt single-subunit phage-like RNA polymerase during transcription, since the correct identification of mt promoters from Rpo41 requires an ortholog to bacterial sigma factor, i.e., Mtf1. Thus, a previously proposed hypothesis of a phage infected alpha-proteobacterium as the endosymbiotic progenitor of mitochondrion is confirmed in this study and further upgraded by the co-evolution of the bacterial (Mtf1) and viral (Rpo41) originated components in one functional unit.
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Affiliation(s)
| | - Vassili N. Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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Prince S, Munoz C, Filion-Bienvenue F, Rioux P, Sarrasin M, Lang BF. Refining Mitochondrial Intron Classification With ERPIN: Identification Based on Conservation of Sequence Plus Secondary Structure Motifs. Front Microbiol 2022; 13:866187. [PMID: 35369492 PMCID: PMC8971849 DOI: 10.3389/fmicb.2022.866187] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Mitochondrial genomes—in particular those of fungi—often encode genes with a large number of Group I and Group II introns that are conserved at both the sequence and the RNA structure level. They provide a rich resource for the investigation of intron and gene structure, self- and protein-guided splicing mechanisms, and intron evolution. Yet, the degree of sequence conservation of introns is limited, and the primary sequence differs considerably among the distinct intron sub-groups. It makes intron identification, classification, structural modeling, and the inference of gene models a most challenging and error-prone task—frequently passed on to an “expert” for manual intervention. To reduce the need for manual curation of intron structures and mitochondrial gene models, computational methods using ERPIN sequence profiles were initially developed in 2007. Here we present a refinement of search models and alignments using the now abundant publicly available fungal mtDNA sequences. In addition, we have tested in how far members of the originally proposed sub-groups are clearly distinguished and validated by our computational approach. We confirm clearly distinct mitochondrial Group I sub-groups IA1, IA3, IB3, IC1, IC2, and ID. Yet, IB1, IB2, and IB4 ERPIN models are overlapping substantially in predictions, and are therefore combined and reported as IB. We have further explored the conversion of our ERPIN profiles into covariance models (CM). Current limitations and prospects of the CM approach will be discussed.
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Rosolen RR, Aono AH, Almeida DA, Ferreira Filho JA, Horta MAC, De Souza AP. Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1. Front Genet 2022; 13:807243. [PMID: 35281818 PMCID: PMC8912865 DOI: 10.3389/fgene.2022.807243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/04/2022] [Indexed: 12/24/2022] Open
Abstract
Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis of T. harzianum IOC-3844 and T. harzianum CBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences among Trichoderma spp. The results of the T. harzianum strains were compared with those of Trichoderma atroviride CBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed with cre1 or xyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of the cre1 and xyr1 groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts in cre1 and xyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluated T. harzianum strains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related to xyr1 and cre1 differed, suggesting that each T. harzianum strain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluated T. harzianum strains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.
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Affiliation(s)
- Rafaela Rossi Rosolen
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Déborah Aires Almeida
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Jaire Alves Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Anete Pereira De Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Anete Pereira De Souza,
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44
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Lin WC, Chen YH, Gu SY, Shen HL, Huang KC, Lin WD, Chang MC, Chang IF, Hong CY, Cheng WH. CFM6 is an Essential CRM Protein Required for the Splicing of nad5 Transcript in Arabidopsis Mitochondria. PLANT & CELL PHYSIOLOGY 2022; 63:217-233. [PMID: 34752612 DOI: 10.1093/pcp/pcab161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 05/21/2023]
Abstract
Plant chloroplast RNA splicing and ribosome maturation (CRM)-domain-containing proteins are capable of binding RNA to facilitate the splicing of group I or II introns in chloroplasts, but their functions in mitochondria are less clear. In the present study, Arabidopsis thaliana CFM6, a protein with a single CRM domain, was expressed in most plant tissues, particularly in flower tissues, and restricted to mitochondria. Mutation of CFM6 causes severe growth defects, including stunted growth, curled leaves, delayed embryogenesis and pollen development. CFM6 functions specifically in the splicing of group II intron 4 of nad5, which encodes a subunit of mitochondrial complex I, as evidenced by the loss of nad5 intron 4 splicing and high accumulation of its pretranscripts in cfm6 mutants. The phenotypic and splicing defects of cfm6 were rescued in transgenic plants overexpressing 35S::CFM6-YFP. Splicing failure in cfm6 also led to the loss of complex I activity and to its improper assembly. Moreover, dysfunction of complex I induced the expression of proteins or genes involved in alternative respiratory pathways in cfm6. Collectively, CFM6, a previously uncharacterized CRM domain-containing protein, is specifically involved in the cis-splicing of nad5 intron 4 and plays a pivotal role in mitochondrial complex I biogenesis and normal plant growth.
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Affiliation(s)
- Wei-Chih Lin
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Ya-Huei Chen
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei 114, Taiwan
| | - Shin-Yuan Gu
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hwei-Ling Shen
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Chau Huang
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Ing-Feng Chang
- Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chwan-Yang Hong
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei 114, Taiwan
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45
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Valenti I, Degradi L, Kunova A, Cortesi P, Pasquali M, Saracchi M. The First Mitochondrial Genome of Ciborinia camelliae and Its Position in the Sclerotiniaceae Family. FRONTIERS IN FUNGAL BIOLOGY 2022; 2:802511. [PMID: 37744111 PMCID: PMC10512376 DOI: 10.3389/ffunb.2021.802511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 09/26/2023]
Abstract
Ciborinia camelliae is the causal agent of camellia flower blight (CFB). It is a hemibiotrophic pathogen, inoperculate Discomycete of the family Sclerotiniaceae. It shows host and organ specificity infecting only flowers of species belonging to the genus Camellia, causing serious damage to the ornamental component of the plant. In this work, the first mitochondrial genome of Ciborinia camellia is reported. The mitogenome was obtained by combining Illumina short read and Nanopore long read technology. To resolve repetitive elements, specific primers were designed and used for Sanger sequencing. The manually curated mitochondrial DNA (mtDNA) of the Italian strain DSM 112729 is a circular sequence of 114,660 bp, with 29.6% of GC content. It contains two ribosomal RNA genes, 33 transfer RNAs, one RNase P gene, and 62 protein-coding genes. The latter include one gene coding for a ribosomal protein (rps3) and the 14 typical proteins involved in the oxidative metabolism. Moreover, a partial mtDNA assembled from a contig list was obtained from the deposited genome assembly of a New Zealand strain of C. camelliae. The present study contributes to understanding the mitogenome arrangement and the evolution of this phytopathogenic fungus in comparison to other Sclerotiniaceae species and confirms the usefulness of mitochondrial analysis to define phylogenetic positioning of this newly sequenced species.
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Affiliation(s)
| | | | | | | | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
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46
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Hao W. From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes? Front Microbiol 2022; 13:806575. [PMID: 35126340 PMCID: PMC8811140 DOI: 10.3389/fmicb.2022.806575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/03/2022] [Indexed: 11/26/2022] Open
Abstract
Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies.
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47
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Pearman WS, Wells SJ, Dale J, Silander OK, Freed NE. Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211550. [PMID: 35242350 PMCID: PMC8753154 DOI: 10.1098/rsos.211550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/29/2021] [Indexed: 05/03/2023]
Abstract
Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda, species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod, Isocladus armatus. Data from long- and short-read DNA sequencing suggest that I. armatus has two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda. Additionally, we find that an asymmetrical site previously observed across many species within Isopoda is absent in I. armatus, but confirm the presence of two asymmetrical sites recently reported in two other isopod species.
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Affiliation(s)
- William S. Pearman
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
| | - Sarah J. Wells
- School of Environmental and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
| | - James Dale
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
| | - Olin K. Silander
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
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48
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Deng S, Ma X, Chen Y, Feng H, Zhou D, Wang X, Zhang Y, Zhao M, Zhang J, Daly P, Wei L. LAMP Assay for Distinguishing Fusarium oxysporum and Fusarium commune in Lotus ( Nelumbo nucifera) Rhizomes. PLANT DISEASE 2022; 106:231-246. [PMID: 34494867 DOI: 10.1094/pdis-06-21-1223-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yields of edible rhizome from cultivation of the perennial hydrophyte lotus (Nelumbo nucifera) can be severely reduced by rhizome rot disease caused by Fusarium species. There is a lack of rapid field-applicable methods for detection of these pathogens on lotus plants displaying symptoms of rhizome rot. Fusarium commune (91%) and Fusarium oxysporum (9%) were identified at different frequencies from lotus samples showing symptoms of rhizome rot. Because these two species can cause different severity of disease and their morphology is similar, molecular diagnostic-based methods to detect these two species were developed. Based on the comparison of the mitochondrial genome of the two species, three specific DNA loci targets were found. The designed primer sets for conventional PCR, quantitative PCR, and loop-mediated isothermal amplification (LAMP) precisely distinguished the above two species when isolated from lotus and other plants. The LAMP detection limits were 10 pg/μl and 1 pg/μl of total DNA for F. commune and F. oxysporum, respectively. We also carried out field-mimicked experiments on lotus seedlings and rhizomes (including inoculated samples and field-diseased samples), and the results indicated that the LAMP primer sets and the supporting portable methods are suitable for rapid diagnosis of the lotus disease in the field. The LAMP-based detection method will aid in the rapid identification of whether F. oxysporum or F. commune is infecting lotus plants with symptoms of rhizome rot and can facilitate efficient pesticide use and prevent disease spread through vegetative propagation of Fusarium-infected lotus rhizomes.
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Affiliation(s)
- Sheng Deng
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Xin Ma
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yifan Chen
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu Province, P.R. China
| | - Hui Feng
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Dongmei Zhou
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Xiaoyu Wang
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Yong Zhang
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, U.S.A
| | - Min Zhao
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Jinfeng Zhang
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Paul Daly
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - Lihui Wei
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R. China
- School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu Province, P.R. China
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49
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Clergeot PH, Olson Å. Mitonuclear Genetic Interactions in the Basidiomycete Heterobasidion parviporum Involve a Non-conserved Mitochondrial Open Reading Frame. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:779337. [PMID: 37744141 PMCID: PMC10512249 DOI: 10.3389/ffunb.2021.779337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/19/2021] [Indexed: 09/26/2023]
Abstract
The mitochondrial and nuclear genomes of Eukaryotes are inherited separately and consequently follow distinct evolutionary paths. Nevertheless, the encoding of many mitochondrial proteins by the nuclear genome shows the high level of integration they have reached, which makes mitonuclear genetic interactions all the more conceivable. For each species, natural selection has fostered the evolution of coadapted alleles in both genomes, but a population-wise divergence of such alleles could lead to important phenotypic variation, and, ultimately, to speciation. In this study in the Basidiomycete Heterobasidion parviporum, we have investigated the genetic basis of phenotypic variation among laboratory-designed heterokaryons carrying the same pair of haploid nuclei, but a different mitochondrial genome. Radial growth rate data of thirteen unrelated homokaryotic parents and of their heterokaryotic offspring were combined with SNP data extracted from parental genome sequences to identify nuclear and mitochondrial loci involved in mitonuclear interactions. Two nuclear loci encoding mitochondrial proteins appeared as best candidates to engage in a genetic interaction affecting radial growth rate with a non-conserved mitochondrial open reading frame of unknown function and not reported apart from the Russulales order of Basidiomycete fungi. We believe our approach could be useful to investigate several important traits of fungal biology where mitonuclear interactions play a role, including virulence of fungal pathogens.
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Affiliation(s)
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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50
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Yang J, Yang X, Su T, Hu Z, Zhang M. The Development of Mitochondrial Gene Editing Tools and Their Possible Roles in Crop Improvement for Future Agriculture. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 3:2100019. [PMID: 36619350 PMCID: PMC9744482 DOI: 10.1002/ggn2.202100019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Indexed: 01/11/2023]
Abstract
We are living in the era of genome editing. Nowadays, targeted editing of the plant nuclear DNA is prevalent in basic biological research and crop improvement since its first establishment a decade ago. However, achieving the same accomplishment for the plant mitochondrial genome has long been deemed impossible. Recently, the pioneer studies on editing plant mitogenome have been done using the mitochondria-targeted transcription activator-like effector nucleases (mitoTALENs) in rice, rapeseed, and Arabidopsis. It is well documented that mitochondria play essential roles in plant development and stress tolerance, particularly, in cytoplasmic male sterility widely used in production of hybrids. The success of mitochondrial genome editing enables studying the fundamentals of mitochondrial genome. Furthermore, mitochondrial RNA editing (mostly by nuclear-encoded pentatricopeptide repeat (PPR) proteins) in a sequence-specific manner can simultaneously change the production of translatable mitochondrial mRNA. Moreover, direct editing of the nuclear-encoding mitochondria-targeted factors required for plant mitochondrial genome dynamics and recombination may facilitate genetic manipulation of plant mitochondria. Here, the present state of knowledge on editing the plant mitochondrial genome is reviewed.
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Affiliation(s)
- Jinghua Yang
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanya572025China,Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhou310058China
| | - Xiaodong Yang
- Departments of Biology and Plant ScienceThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Tongbing Su
- Beijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijing100097China
| | - Zhongyuan Hu
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanya572025China,Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhou310058China
| | - Mingfang Zhang
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanya572025China,Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhou310058China
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