1
|
Mokhtar MM, Alsamman AM, El Allali A. MegaSSR: a web server for large scale microsatellite identification, classification, and marker development. FRONTIERS IN PLANT SCIENCE 2023; 14:1219055. [PMID: 38162302 PMCID: PMC10757629 DOI: 10.3389/fpls.2023.1219055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 01/03/2024]
Abstract
Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.
Collapse
Affiliation(s)
- Morad M. Mokhtar
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Benguerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Alsamman M. Alsamman
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Benguerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Benguerir, Morocco
| |
Collapse
|
2
|
Shamanskiy V, Mikhailova AA, Tretiakov EO, Ushakova K, Mikhailova AG, Oreshkov S, Knorre DA, Ree N, Overdevest JB, Lukowski SW, Gostimskaya I, Yurov V, Liou CW, Lin TK, Kunz WS, Reymond A, Mazunin I, Bazykin GA, Fellay J, Tanaka M, Khrapko K, Gunbin K, Popadin K. Secondary structure of the human mitochondrial genome affects formation of deletions. BMC Biol 2023; 21:103. [PMID: 37158879 PMCID: PMC10166460 DOI: 10.1186/s12915-023-01606-1] [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: 06/17/2022] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions. RESULTS By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9 kb and another within 13-16 kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11 kb and contacting regions between 6-9 kb and 13-16 kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482 bp (base pair) and a second arm at 13,447-13,459 bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging. CONCLUSIONS Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.
Collapse
Affiliation(s)
- Victor Shamanskiy
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina A Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Evgenii O Tretiakov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Kristina Ushakova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina G Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Sergei Oreshkov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia Ree
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Jonathan B Overdevest
- Department of Otolaryngology, Columbia University Irving Medical Center, New York, USA
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Australia
| | - Irina Gostimskaya
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Valerian Yurov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Tsu-Kung Lin
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Wolfram S Kunz
- Division of Neurochemistry, Department of Experimental Epileptology and Cognition Research, University Bonn, Bonn, Germany
- Department of Epileptology, University Hospital of Bonn, Bonn, Germany
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Georgii A Bazykin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Laboratory of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia
| | - Jacques Fellay
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Masashi Tanaka
- Department for Health and Longevity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8636, Japan
- Department of Neurology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Department of Clinical Laboratory, IMS Miyoshi General Hospital, Fujikubo, Miyoshi-Machi, Iruma, Saitama Prefecture, 974-3354-0041, Japan
| | | | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
3
|
Pabis K. Triplex and other DNA motifs show motif-specific associations with mitochondrial DNA deletions and species lifespan. Mech Ageing Dev 2021; 194:111429. [PMID: 33422563 DOI: 10.1016/j.mad.2021.111429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 11/20/2022]
Abstract
The "theory of resistant biomolecules" posits that long-lived species show resistance to molecular damage at the level of their biomolecules. Here, we test this hypothesis in the context of mitochondrial DNA (mtDNA) as it implies that predicted mutagenic DNA motifs should be inversely correlated with species maximum lifespan (MLS). First, we confirmed that guanine-quadruplex and direct repeat (DR) motifs are mutagenic, as they associate with mtDNA deletions in the human major arc of mtDNA, while also adding mirror repeat (MR) and intramolecular triplex motifs to a growing list of potentially mutagenic features. What is more, triplex motifs showed disease-specific associations with deletions and an apparent interaction with guanine-quadruplex motifs. Surprisingly, even though DR, MR and guanine-quadruplex motifs were associated with mtDNA deletions, their correlation with MLS was explained by the biased base composition of mtDNA. Only triplex motifs negatively correlated with MLS even after adjusting for body mass, phylogeny, mtDNA base composition and effective number of codons. Taken together, our work highlights the importance of base composition for the comparative biogerontology of mtDNA and suggests that future research on mitochondrial triplex motifs is warranted.
Collapse
Affiliation(s)
- Kamil Pabis
- Georg August University of Göttingen, Göttingen, Germany.
| |
Collapse
|
4
|
Miyazawa H, Osigus HJ, Rolfes S, Kamm K, Schierwater B, Nakano H. Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions. Genome Biol Evol 2020; 13:5919586. [PMID: 33031489 PMCID: PMC7813641 DOI: 10.1093/gbe/evaa213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2020] [Indexed: 12/16/2022] Open
Abstract
Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32–43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon–intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.
Collapse
Affiliation(s)
- Hideyuki Miyazawa
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan.,Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Hans-Jürgen Osigus
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Sarah Rolfes
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Kai Kamm
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Bernd Schierwater
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| |
Collapse
|
5
|
Cabañas N, Becerra A, Romero D, Govezensky T, Espinosa-Aguirre JJ, Camacho-Carranza R. Repetitive DNA profile of the amphibian mitogenome. BMC Bioinformatics 2020; 21:197. [PMID: 32429835 PMCID: PMC7236288 DOI: 10.1186/s12859-020-3532-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Background Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians. Results This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry. Conclusions Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.
Collapse
Affiliation(s)
- Noel Cabañas
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Tzipe Govezensky
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Jesús Javier Espinosa-Aguirre
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Rafael Camacho-Carranza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico. .,Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico.
| |
Collapse
|
6
|
Shamanskiy VA, Timonina VN, Popadin KY, Gunbin KV. Correction to: ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation. BMC Genomics 2019; 20:556. [PMID: 31286882 PMCID: PMC6613262 DOI: 10.1186/s12864-019-5950-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 11/10/2022] Open
Affiliation(s)
- Viktor A Shamanskiy
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Valeria N Timonina
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Konstantin Yu Popadin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Konstantin V Gunbin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.
- Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
| |
Collapse
|
7
|
Orlov YL, Kochetov AV, Li G, Kolchanov NA. Genomics research at Bioinformatics of Genome Regulation and Structure\ Systems Biology (BGRS\SB) conferences in Novosibirsk. BMC Genomics 2019; 20:322. [PMID: 32039700 PMCID: PMC7227187 DOI: 10.1186/s12864-019-5707-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia. .,Novosibirsk State University, 630090, Novosibirsk, Russia. .,A.O.Kovalevsky Institute of Marine Biological Research of RAS, 119334, Moscow, Russia.
| | - Alex V Kochetov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
| | - Guoliang Li
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.,Novosibirsk State University, 630090, Novosibirsk, Russia
| |
Collapse
|