1
|
Islam S, Peart C, Kehlmaier C, Sun YH, Lei F, Dahl A, Klemroth S, Alexopoulou D, Del Mar Delgado M, Laiolo P, Carlos Illera J, Dirren S, Hille S, Lkhagvasuren D, Töpfer T, Kaiser M, Gebauer A, Martens J, Paetzold C, Päckert M. Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies). Mol Phylogenet Evol 2024; 198:108135. [PMID: 38925425 DOI: 10.1016/j.ympev.2024.108135] [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: 06/01/2023] [Revised: 03/25/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.
Collapse
Affiliation(s)
- Safiqul Islam
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany; Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany; Division of Systematic Zoology, Faculty of Biology, LMU Munich, Biocenter, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Claire Peart
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Biocenter, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Christian Kehlmaier
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andreas Dahl
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Sylvia Klemroth
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Dimitra Alexopoulou
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Maria Del Mar Delgado
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Paola Laiolo
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Juan Carlos Illera
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | | | - Sabine Hille
- University of Natural Resources and Life Sciences, Vienna, Gregor Mendel-Strasse 33, 1180 Vienna, Austria
| | - Davaa Lkhagvasuren
- Department of Biology, School of Arts and Sciences, National University of Mongolia, P.O.Box 46A-546, Ulaanbaatar 210646, Mongolia
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity Change, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee, Bonn, Germany
| | | | | | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University, 55099 Mainz, Germany
| | - Claudia Paetzold
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Martin Päckert
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany.
| |
Collapse
|
2
|
Molina M, Oliveira G, Oliveira RRM, Nunes GL, Pires ES, Prous X, Ribeiro M, Vasconcelos S. Complete mitochondrial genomes of three vulnerable cave bat species and their phylogenetic relationships within the order Chiroptera. PLoS One 2024; 19:e0308741. [PMID: 39172941 PMCID: PMC11340975 DOI: 10.1371/journal.pone.0308741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
The IUCN Red List of Threatened Species contains 175 Brazilian bat species that are threatened by extinction in some degree. From this perspective, it is essential to expand the knowledge about the genetic diversity of vulnerable bats. Genomic sequencing can be useful to generate robust and informative genetic references, increasing resolution when analyzing relationships among populations, species, or higher taxonomic levels. In this study, we sequenced and characterized in detail the first complete mitochondrial genomes of Furipterus horrens, Lonchorhina aurita, and Natalus macrourus, and investigated their phylogenetic position based on amino acid sequences of protein-coding genes (PCGs). The mitogenomes of these species are 16,516, 16,697, and 16,668 bp in length, respectively, and each comprises 13 PCGs, 22 tRNA genes, two rRNA genes, and a putative control region (CR). In the three species, genes were arranged similarly to all other previously described bat mitogenomes, and nucleotide composition was also consistent with the reported range. The length and arrangement of rrnS and rrnL were also consistent with those of other bat species, showing a positive AT-skew and a negative GC-skew. Except for trnS1, for which we did not observe the DHU arm, all other tRNAs showed the cloverleaf secondary structure in the three species. In addition, the mitogenomes showed minor differences in start and stop codons, and in all PCGs, codons ending in adenine were more common compared to those ending in guanine. We found that PCGs of the three species use multiple codons to encode each amino acid, following the previously documented pattern. Furthermore, all PCGs are under purifying selection, with atp8 experiencing the most relaxed purifying selection. Considering the phylogenetic reconstruction, F. horrens was recovered as sister to Noctilio leporinus, L. aurita and Tonatia bidens shared a node within Phyllostomidae, and N. macrourus appeared as sister to Molossidae and Vespertilionidae.
Collapse
Affiliation(s)
- Michele Molina
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Guilherme Oliveira
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | | | - Xavier Prous
- Gerência de Espeleologia, Vale, Nova Lima, Minas Gerais, Brazil
| | - Mariane Ribeiro
- Gerência de Espeleologia, Vale, Nova Lima, Minas Gerais, Brazil
| | - Santelmo Vasconcelos
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| |
Collapse
|
3
|
Sterling-Montealegre RA, Prada CF. Variability and evolution of gene order rearrangement in mitochondrial genomes of arthropods (except Hexapoda). Gene 2024; 892:147906. [PMID: 37844850 DOI: 10.1016/j.gene.2023.147906] [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: 06/07/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
In the species-rich Phylum Arthropoda, the mitochondrial genome is relatively well conserved both in terms of number and order of genes. However, specific clades have a 'typical' gene order that differs from the putative arthropod ancestral arrangement. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter- and intra-taxonomic levels in the Arthropoda and to postulate the most parsimonious ancestral orders representing the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of arthropod mitochondrial genomes available in the NCBI database. Using a combination of bioinformatics methods that examined mitochondrial gene rearrangements in 464 species of arthropods from three subphyla (Chelicerata, Myriapoda, and Crustacea [except Hexapoda, previously analyzed]), we observed differences in the rate of rearrangement within major lineages. A higher rate of mitochondrial genome rearrangement was observed in Crustacea and Chelicerata compared to Myriapoda. Likewise, early branching clades exhibit less variability in mitochondrial genome order than late branching clades, within each subphylum. We identified 'hot regions' in the mitochondrial genome of each studied subphylum, and postulated the most likely ancestral gene order in each subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics of mitochondrial genome gene order in arthropods and new mitochondrial genome architectures in different taxonomic divisions within each major lineage of arthropods.
Collapse
Affiliation(s)
| | - Carlos Fernando Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
| |
Collapse
|
4
|
Complete mitochondrial genome of Phoneutria depilata (Araneae, Ctenidae): New Insights into the Phylogeny and Evolution of Spiders. Gene 2022; 850:146925. [PMID: 36191823 DOI: 10.1016/j.gene.2022.146925] [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: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/25/2022] [Indexed: 11/20/2022]
Abstract
Spiders (Araneae) are the most abundant terrestrial predators and megadiverse on earth. In recent years, the mitochondrial genome of a great diversity of species has been sequenced, mainly for ecological and commercial purposes. These studies have uncovered the existence of a variety of mitochondrial genome rearrangements. However, there is poor genetic information in several taxonomic families of spiders. We have sequenced the complete genome of Phoneutria depilata (Ctenidae) and, based on this, extract the mitogenomes of other ctenid species from published transcriptomes to perform a comparative study among spider species to determine the relationship between the level of mitochondrial rearrangements and its possible relationship with molecular variability in spiders. Complete mitochondrial genomes of eighteen spiders (including eight Ctenidae species) were obtained by two different methodologies (sequencing and transcriptome extraction). Fifty-eight spider mitochondrial genomes were downloaded from the NCBI database for gene order analysis. After verifying the annotation of each mitochondrial gene, a phylogenetic and a gene order analysis from 76 spider mitochondrial genomes were carried out. Our results show a high rate of annotation error in the published spider mitochondrial genomes, which could lead to errors in phylogenetic inference. Moreover, to provide new mitochondrial genomes in spiders by two different methodologies to obtain them, our analysis identifies six different mitochondrial architectures among all spiders. Translocation or tandem duplication random loss (TDRL) events in tRNA genes were identified to explain the evolution of the spider mitochondrial genome. In addition, our findings provide new insights into spider mitochondrial evolution.
Collapse
|
5
|
Prada CF, Casadiego MA, Freire CCM. Evolution of Helicobacter spp: variability of virulence factors and their relationship to pathogenicity. PeerJ 2022; 10:e13120. [PMID: 36061745 PMCID: PMC9435515 DOI: 10.7717/peerj.13120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/24/2022] [Indexed: 01/12/2023] Open
Abstract
Background Virulence factors (VF) are bacteria-associated molecules that assist to colonize the host at the cellular level. Bacterial virulence is highly dynamic and specific pathogens have a broad array of VFs. The genus Helicobacter is gram-negative, microaerobic, flagellated, and mucus-inhabiting bacteria associated with gastrointestinal inflammation. To investigate about their pathogenicity, several Helicobacter species have been characterized and sequenced. Since the variability and possible origin of VF in the genus are not clear, our goal was to perform a comparative analysis of Helicobacter species in order to investigate VF variability and their evolutionary origin. Methods The complete genomes of 22 Helicobacter species available in NCBI were analyzed, using computational tools. We identifyed gain and loss events in VF genes, which were categorized in seven functional groups to determine their most parsimonious evolutionary origin. After verifying the annotation of all VF genes, a phylogeny from conserved VF organized by Helicobacter species according to gastric Helicobacter species (GHS) or enterohepatic (EHS) classification was obtained. Results Gain and loss analysis of VF orthologous in Helicobacter ssp revealed the most possible evolutionary origin for each gene set. Microevolutionary events in urease and flagella genes were detected during the evolution of the genus. Our results pointed that acquisition of ureases and adherence genes and deletion of cytotoxins in some lineages, as well as variation in VF genes copy number, would be related to host adaptation during evolution of the Helicobacter genus. Our findings provided new insights about the genetic differences between GHS and EHS and their relationship with pathogenicity.
Collapse
Affiliation(s)
- Carlos F. Prada
- Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos, Sao Paulo, Brazil,Grupo de Investigación de Biología y Ecología de Artrópodos. Facultad de Ciencias., Universidad del Tolima, Tolima, Colombia
| | - Maria A. Casadiego
- Grupo de Investigación de Biología y Ecología de Artrópodos. Facultad de Ciencias., Universidad del Tolima, Tolima, Colombia
| | - Caio CM Freire
- Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos, Sao Paulo, Brazil
| |
Collapse
|
6
|
Homchan S, Gupta YM. The complete mitochondrial genome of giant cricket, Tarbinskiellus portentosus (Orthoptera: Gryllidae) and its curation. Mitochondrial DNA B Resour 2022; 7:1427-1431. [PMID: 35958061 PMCID: PMC9359167 DOI: 10.1080/23802359.2022.2107441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Tarbinskiellus portentosus, commonly known as giant cricket one of the important edible cricket species. However, the genetic information of these species is still limited. Therefore, we have assembled and annotated the first mitochondrial genome of T. portentosus. The mitogenome is 15710 bp long and has GC content of 27.19%. The nucleotide composition is similar with other insect mitogenomes (A 40.6%; T 32.2%; C 17.3%; G 9.9%). The gene organization in the mitogenome of T. portentosus is identical to the mitogenome of other cricket species. The complete mitogenome of T. portentosus consisted 37 genes including 13 protein coding genes, 22 tRNA genes, and two rRNA genes. The newly assembled mitogenome will help molecular biology research on edible crickets. Since mitogenome genes are traditionally used for DNA barcoding and phylogenetic analysis, comparative analysis of T. portentosus mitogenome with other related cricket species will also aid researchers in developing universal primers for species identification toward food security. Apart from the main goal of providing full mitogenome of T. portentosus, paper also provides conceptual workflow based on de novo assembly and its correction for final mitogenome construction.
Collapse
Affiliation(s)
- Somjit Homchan
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Yash Munnalal Gupta
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| |
Collapse
|
7
|
Mitogenome of the extinct Desert 'rat-kangaroo' times the adaptation to aridity in macropodoids. Sci Rep 2022; 12:5829. [PMID: 35388060 PMCID: PMC8987032 DOI: 10.1038/s41598-022-09568-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/25/2022] [Indexed: 01/31/2023] Open
Abstract
The evolution of Australia's distinctive marsupial fauna has long been linked to the onset of continent-wide aridity. However, how this profound climate change event affected the diversification of extant lineages is still hotly debated. Here, we assemble a DNA sequence dataset of Macropodoidea-the clade comprising kangaroos and their relatives-that incorporates a complete mitogenome for the Desert 'rat-kangaroo', Caloprymnus campestris. This enigmatic species went extinct nearly 90 years ago and is known from a handful of museum specimens. Caloprymnus is significant because it was the only macropodoid restricted to extreme desert environments, and therefore calibrates the group's specialisation for increasingly arid conditions. Our robustly supported phylogenies nest Caloprymnus amongst the bettongs Aepyprymnus and Bettongia. Dated ancestral range estimations further reveal that the Caloprymnus-Bettongia lineage originated in nascent xeric settings during the middle to late Miocene, ~ 12 million years ago (Ma), but subsequently radiated into fragmenting mesic habitats after the Pliocene to mid-Pleistocene. This timeframe parallels the ancestral divergences of kangaroos in woodlands and forests, but predates their adaptive dispersal into proliferating dry shrublands and grasslands from the late Miocene to mid-Pleistocene, after ~ 7 Ma. We thus demonstrate that protracted changes in both climate and vegetation likely staged the emergence of modern arid zone macropodoids.
Collapse
|
8
|
Montaña-Lozano P, Moreno-Carmona M, Ochoa-Capera M, Medina NS, Boore JL, Prada CF. Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class. Sci Rep 2022; 12:5479. [PMID: 35361853 PMCID: PMC8971445 DOI: 10.1038/s41598-022-09512-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
Vertebrate mitochondrial genomes have been extensively studied for genetic and evolutionary purposes, these are normally believed to be extremely conserved, however, different cases of gene rearrangements have been reported. To verify the level of rearrangement and the mitogenome evolution, we performed a comparative genomic analysis of the 2831 vertebrate mitochondrial genomes representing 12 classes available in the NCBI database. Using a combination of bioinformatics methods, we determined there is a high number of errors in the annotation of mitochondrial genes, especially in tRNAs. We determined there is a large variation in the proportion of rearrangements per gene and per taxonomic class, with higher values observed in Actinopteri, Amphibia and Reptilia. We highlight that these are results for currently available vertebrate sequences, so an increase in sequence representativeness in some groups may alter the rearrangement rates, so in a few years it would be interesting to see if these rates are maintained or altered with the new mitogenome sequences. In addition, within each vertebrate class, different patterns in rearrangement proportion with distinct hotspots in the mitochondrial genome were found. We also determined that there are eleven convergence events in gene rearrangement, nine of which are new reports to the scientific community.
Collapse
Affiliation(s)
- Paula Montaña-Lozano
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Manuela Moreno-Carmona
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Mauricio Ochoa-Capera
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Natalia S Medina
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia.
| |
Collapse
|
9
|
Westerman M, Loke S, Tan MH. Molecular relationships of the red-bellied dasyure (Phascolosorex doriae) – a rare marsupial from western New Guinea. AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am21011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mitochondrial genome of the rare endemic New Guinean dasyurid Phascolosorex doriae (Thomas 1886) has been used to clarify relationships within ‘phascolosoricinae’. The mitochondrial genome has the typical gene arrangement seen in other marsupials. Molecular analyses using complete mitogenomes of other dasyurids resolve the red-bellied dasyure as sister to the narrow-striped dasyure Phascolosorex dorsalis and show that these two species diverged in the early Pliocene. The invasion of emergent New Guinean rainforest habitats (in the late Miocene) by the common ancestor of Ph. doriae, Ph. dorsalis and Neophascogale lorentzii represents one of three separate such invasions by dasyurid lineages.
Collapse
|
10
|
Rodriguez AM, Urrea DA, Prada CF. Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin. PeerJ 2021; 9:e12272. [PMID: 34900406 PMCID: PMC8628625 DOI: 10.7717/peerj.12272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023] Open
Abstract
Background Helicobacter pylori is a pathogenic bacteria that colonize the gastrointestinal tract from human stomachs and causes diseases including gastritis, peptic ulcers, gastric lymphoma (MALT), and gastric cancer, with a higher prevalence in developing countries. Its high genetic diversity among strains is caused by a high mutation rate, observing virulence factors (VFs) variations in different geographic lineages. This study aimed to postulate the genetic variability associated with virulence factors present in the Helicobacter pylori strains, to identify the relationship of these genes with their phylogeographic origin. Methods The complete genomes of 135 strains available in NCBI, from different population origins, were analyzed using bioinformatics tools, identifying a high rate; as well as reorganization events in 87 virulence factor genes, divided into seven functional groups, to determine changes in position, number of copies, nucleotide identity and size, contrasting them with their geographical lineage and pathogenic phenotype. Results Bioinformatics analyses show a high rate of gene annotation errors in VF. Analysis of genetic variability of VFs shown that there is not a direct relationship between the reorganization and geographic lineage. However, regarding the pathogenic phenotype demonstrated in the analysis of many copies, size, and similarity when dividing the strains that possess and not the cag pathogenicity island (cagPAI), having a higher risk of developing gastritis and peptic ulcer was evidenced. Our data has shown that the analysis of the overall genetic variability of all VFs present in each strain of H. pylori is key information in understanding its pathogenic behavior.
Collapse
Affiliation(s)
- Aura M Rodriguez
- Grupo de Investigación de Biología y Ecología de Artrópodos. Facultad de Ciencias, Universidad del Tolima, Ibague, Tolima, Colombia
| | - Daniel A Urrea
- Laboratorio de Investigaciones en Parasitología Tropical. Facultad de Ciencias, Universidad del Tolima, Ibague, Tolima, Colombia
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos. Facultad de Ciencias, Universidad del Tolima, Ibague, Tolima, Colombia
| |
Collapse
|
11
|
Pons J, Ensenyat JJ, Bover P, Serra M, Nardi F. Aln2tbl: building a mitochondrial features table from a assembly alignment in fasta format. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2732-2735. [PMID: 34447886 PMCID: PMC8386716 DOI: 10.1080/23802359.2021.1966334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The sequencing, annotation and analysis of complete mitochondrial genomes is an important research tool in phylogeny and evolution. Starting with the primary sequence, genes/features are generally annotated automatically to obtain preliminary annotations in the form of a feature table. Further manual curation in a graphic alignment editor is nevertheless necessary to revise annotations. As such, the automatically generated feature table is invalidated and has to be modified manually before submission to data banks. We developed aln2tbl.py, a python script that recreates a feature table from a manually refined alignment of genes mapped on the mitochondrial genome in fasta format. The feature table is populated with notes and annotations specific to mitochondrial genomes. The table can be used to create a sqn file to be submitted directly to data banks. In summary, our scripts fills one gap in the available toolbox and, combined with other software, allows the automation of the entire process, from primary sequence to annotated genome submission, even if a manual curation step is conducted in a visual sequence editor.
Collapse
Affiliation(s)
- Joan Pons
- Departament de Biodiversitat Animal i Microbiana, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Juan José Ensenyat
- Tecnologies de la informació i la comunicació, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Pere Bover
- Instituto Universitario de Investigación en Ciencias Ambientales (IUCA), Grupo Aragosaurus - Departamento de Ciencias de la Tierra, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Miquel Serra
- Tecnologies de la informació i la comunicació, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Francesco Nardi
- Department of Life Sciences, University of Siena, Siena, Italy
| |
Collapse
|
12
|
Mehl T, Gruenstaeudl M. airpg: automatically accessing the inverted repeats of archived plastid genomes. BMC Bioinformatics 2021; 22:413. [PMID: 34418956 PMCID: PMC8379869 DOI: 10.1186/s12859-021-04309-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 07/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations. RESULTS We introduce airpg, a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using airpg, followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations. CONCLUSION The number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. airpg enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index at http://pypi.python.org/pypi/airpg .
Collapse
Affiliation(s)
- Tilman Mehl
- Institut für Bioinformatik, Freie Universität Berlin, 14195 Berlin, Germany
| | | |
Collapse
|
13
|
Moreno-Carmona M, Cameron SL, Prada Quiroga CF. How are the mitochondrial genomes reorganized in Hexapoda? Differential evolution and the first report of convergences within Hexapoda. Gene 2021; 791:145719. [PMID: 33991648 DOI: 10.1016/j.gene.2021.145719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022]
Abstract
The evolution of the Hexapoda mitochondrial genome has been the focus of several genetic and evolutionary studies over the last decades. However, they have concentrated on certain taxonomic orders of economic or health importance. The recent increase of mitochondrial genomes sequencing of diverse taxonomic orders generates an important opportunity to clarify the evolution of this group of organisms. However, there is no comparative study that investigates the evolution of the Hexapoda mitochondrial genome. In order to verify the level of rearrangement and the mitochondrial genome evolution, we performed a comparative genomic analysis of the Hexapoda mitochondrial genome available in the NCBI database. Using a combination of bioinformatics methods to carefully examine the mitochondrial gene rearrangements in 1198 Hexapoda species belonging to 32 taxonomic orders, we determined that there is a great variation in the rate of rearrangement by gene and by taxonomic order. A higher rate of genetic reassortment is observed in Phthiraptera, Thysanoptera, Protura, and Hymenoptera; compared to other taxonomic orders. Twenty-four events of convergence in the genetic order between different taxonomic orders were determined, most of them not previously reported; which proves the great evolutionary dynamics within Hexapoda.
Collapse
Affiliation(s)
- Manuela Moreno-Carmona
- Grupo de investigación de Biología y ecología de artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia
| | - Stephen L Cameron
- Department of Entomology, Purdue University, 901 West State Street, West Lafayette, IN 47907, USA
| | - Carlos Fernando Prada Quiroga
- Grupo de investigación de Biología y ecología de artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
| |
Collapse
|
14
|
Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Collapse
Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
| |
Collapse
|
15
|
Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes. Int J Mol Sci 2021; 22:ijms22041811. [PMID: 33670420 PMCID: PMC7918261 DOI: 10.3390/ijms22041811] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 01/06/2023] Open
Abstract
Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.
Collapse
|
16
|
The evolutionary history of manatees told by their mitogenomes. Sci Rep 2021; 11:3564. [PMID: 33574363 PMCID: PMC7878490 DOI: 10.1038/s41598-021-82390-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/18/2021] [Indexed: 12/24/2022] Open
Abstract
The manatee family encompasses three extant congeneric species: Trichechus senegalensis (African manatee), T. inunguis (Amazonian manatee), and T. manatus (West Indian manatee). The fossil record for manatees is scant, and few phylogenetic studies have focused on their evolutionary history. We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes. The complete mitochondrial genomes of T. inunguis (16,851 bp), T. senegalensis (16,882 bp), and T. manatus (16,882 bp), comprise 13 protein-coding genes, 2 ribosomal RNA genes (rRNA - 12S and 16S), and 22 transfer RNA genes (tRNA), and (D-loop/CR). Our analyses show that the first split within Trichechus occurred during the Late Miocene (posterior mean 6.56 Ma and 95% HPD 3.81–10.66 Ma), followed by a diversification event in the Plio-Pleistocene (posterior mean 1.34 Ma, 95% HPD 0.1–4.23) in the clade composed by T. inunguis and T. manatus; T. senegalensis is the sister group of this clade with higher support values (pp > 0.90). The branch-site test identified positive selection on T. inunguis in the 181st position of the ND4 amino acid gene (LRT = 6.06, p = 0.0069, BEB posterior probability = 0.96). The ND4 gene encodes one subunit of the NADH dehydrogenase complex, part of the oxidative phosphorylation machinery. In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.
Collapse
|
17
|
Zhang J, Miao G, Hu S, Sun Q, Ding H, Ji Z, Guo P, Yan S, Wang C, Kan X, Nie L. Quantification and evolution of mitochondrial genome rearrangement in Amphibians. BMC Ecol Evol 2021; 21:19. [PMID: 33563214 PMCID: PMC7871395 DOI: 10.1186/s12862-021-01755-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.
Collapse
Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
- Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China.
- Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China.
| | - Guopen Miao
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Shunjie Hu
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Qi Sun
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Hengwu Ding
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhicheng Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Pen Guo
- Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Xianzhao Kan
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| |
Collapse
|
18
|
Cucini C, Fanciulli PP, Frati F, Convey P, Nardi F, Carapelli A. Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data. Genes (Basel) 2020; 12:genes12010044. [PMID: 33396901 PMCID: PMC7824276 DOI: 10.3390/genes12010044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/16/2020] [Accepted: 12/27/2020] [Indexed: 01/01/2023] Open
Abstract
Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition.
Collapse
Affiliation(s)
- Claudio Cucini
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (C.C.); (P.P.F.); (F.F.); (F.N.)
| | - Pietro P. Fanciulli
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (C.C.); (P.P.F.); (F.F.); (F.N.)
| | - Francesco Frati
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (C.C.); (P.P.F.); (F.F.); (F.N.)
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK;
| | - Francesco Nardi
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (C.C.); (P.P.F.); (F.F.); (F.N.)
| | - Antonio Carapelli
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (C.C.); (P.P.F.); (F.F.); (F.N.)
- Correspondence:
| |
Collapse
|
19
|
van den Burg MP, Herrando-Pérez S, Vieites DR. ACDC, a global database of amphibian cytochrome-b sequences using reproducible curation for GenBank records. Sci Data 2020; 7:268. [PMID: 32792559 PMCID: PMC7426930 DOI: 10.1038/s41597-020-00598-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 06/29/2020] [Indexed: 11/09/2022] Open
Abstract
Genetic data are a crucial and exponentially growing resource across all biological sciences, yet curated databases are scarce. The widespread occurrence of sequence and (meta)data errors in public repositories calls for comprehensive improvements of curation protocols leading to robust research and downstream analyses. We collated and curated all available GenBank cytochrome-b sequences for amphibians, a benchmark marker in this globally declining vertebrate clade. The Amphibia's Curated Database of Cytochrome-b (ACDC) consists of 36,514 sequences representing 2,309 species from 398 genera (median = 2 with 50% interquartile ranges of 1-7 species/genus). We updated the taxonomic identity of >4,800 sequences (ca. 13%) and found 2,359 (6%) conflicting sequences with 84% of the errors originating from taxonomic misidentifications. The database (accessible at https://doi.org/10.6084/m9.figshare.9944759 ) also includes an R script to replicate our study for other loci and taxonomic groups. We provide recommendations to improve genetic-data quality in public repositories and flag species for which there is a need for taxonomic refinement in the face of increased rate of amphibian extinctions in the Anthropocene.
Collapse
Affiliation(s)
- Matthijs P van den Burg
- Department of Biogeography and Global Change. Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), C/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
| | - Salvador Herrando-Pérez
- Department of Biogeography and Global Change. Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), C/José Gutiérrez Abascal 2, 28006, Madrid, Spain
- School of Biological Sciences, The University of Adelaide, 5005, South Australia, Australia
| | - David R Vieites
- Department of Biogeography and Global Change. Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), C/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| |
Collapse
|
20
|
Donath A, Jühling F, Al-Arab M, Bernhart SH, Reinhardt F, Stadler PF, Middendorf M, Bernt M. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Res 2020; 47:10543-10552. [PMID: 31584075 PMCID: PMC6847864 DOI: 10.1093/nar/gkz833] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 08/30/2019] [Accepted: 09/29/2019] [Indexed: 11/13/2022] Open
Abstract
With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.
Collapse
Affiliation(s)
- Alexander Donath
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, D-53113 Bonn, Germany
| | - Frank Jühling
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 3 Rue Koeberlé, F-67000 Strasbourg, France.,Université de Strasbourg, 4 Rue Blaise Pascal, F-67081 Strasbourg, France
| | - Marwa Al-Arab
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon
| | - Stephan H Bernhart
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Franziska Reinhardt
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.,Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems, Department of Computer Science, Universität Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany
| | - Matthias Bernt
- Swarm Intelligence and Complex Systems, Department of Computer Science, Universität Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.,Helmholtz Centre for Environmental Research - UFZ, Young Investigators Group Bioinformatics and Transcriptomics Permoserstraße 15, D-04318 Leipzig, Germany
| |
Collapse
|
21
|
qMGR: A new approach for quantifying mitochondrial genome rearrangement. Mitochondrion 2020; 52:20-23. [DOI: 10.1016/j.mito.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/26/2019] [Accepted: 02/07/2020] [Indexed: 11/20/2022]
|
22
|
Monnahan PJ, Michno JM, O'Connor C, Brohammer AB, Springer NM, McGaugh SE, Hirsch CN. Using multiple reference genomes to identify and resolve annotation inconsistencies. BMC Genomics 2020; 21:281. [PMID: 32264824 DOI: 10.1101/651984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 03/24/2020] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can differ. Of particular concern are split-gene misannotations, in which a single gene is incorrectly annotated as two distinct genes or two genes are incorrectly annotated as a single gene. These misannotations can have major impacts on functional prediction, estimates of expression, and many downstream analyses. RESULTS We developed a high-throughput method based on pairwise comparisons of annotations that detect potential split-gene misannotations and quantifies support for whether the genes should be merged into a single gene model. We demonstrated the utility of our method using gene annotations of three reference genomes from maize (B73, PH207, and W22), a difficult system from an annotation perspective due to the size and complexity of the genome. On average, we found several hundred of these potential split-gene misannotations in each pairwise comparison, corresponding to 3-5% of gene models across annotations. To determine which state (i.e. one gene or multiple genes) is biologically supported, we utilized RNAseq data from 10 tissues throughout development along with a novel metric and simulation framework. The methods we have developed require minimal human interaction and can be applied to future assemblies to aid in annotation efforts. CONCLUSIONS Split-gene misannotations occur at appreciable frequency in maize annotations. We have developed a method to easily identify and correct these misannotations. Importantly, this method is generic in that it can utilize any type of short-read expression data. Failure to account for split-gene misannotations has serious consequences for biological inference, particularly for expression-based analyses.
Collapse
Affiliation(s)
- Patrick J Monnahan
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Christine O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| |
Collapse
|
23
|
Monnahan PJ, Michno JM, O'Connor C, Brohammer AB, Springer NM, McGaugh SE, Hirsch CN. Using multiple reference genomes to identify and resolve annotation inconsistencies. BMC Genomics 2020; 21:281. [PMID: 32264824 PMCID: PMC7140576 DOI: 10.1186/s12864-020-6696-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 03/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can differ. Of particular concern are split-gene misannotations, in which a single gene is incorrectly annotated as two distinct genes or two genes are incorrectly annotated as a single gene. These misannotations can have major impacts on functional prediction, estimates of expression, and many downstream analyses. RESULTS We developed a high-throughput method based on pairwise comparisons of annotations that detect potential split-gene misannotations and quantifies support for whether the genes should be merged into a single gene model. We demonstrated the utility of our method using gene annotations of three reference genomes from maize (B73, PH207, and W22), a difficult system from an annotation perspective due to the size and complexity of the genome. On average, we found several hundred of these potential split-gene misannotations in each pairwise comparison, corresponding to 3-5% of gene models across annotations. To determine which state (i.e. one gene or multiple genes) is biologically supported, we utilized RNAseq data from 10 tissues throughout development along with a novel metric and simulation framework. The methods we have developed require minimal human interaction and can be applied to future assemblies to aid in annotation efforts. CONCLUSIONS Split-gene misannotations occur at appreciable frequency in maize annotations. We have developed a method to easily identify and correct these misannotations. Importantly, this method is generic in that it can utilize any type of short-read expression data. Failure to account for split-gene misannotations has serious consequences for biological inference, particularly for expression-based analyses.
Collapse
Affiliation(s)
- Patrick J Monnahan
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Christine O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| |
Collapse
|
24
|
Tyagi K, Kumar V, Poddar N, Prasad P, Tyagi I, Kundu S, Chandra K. The gene arrangement and phylogeny using mitochondrial genomes in spiders (Arachnida: Araneae). Int J Biol Macromol 2020; 146:488-496. [PMID: 31923488 DOI: 10.1016/j.ijbiomac.2020.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 01/04/2023]
Abstract
The complete mitochondrial genome (mitogenome) of Cheiracanthium triviale was sequenced for the first time. The 14,595 bp C. triviale mitogenome contained 37 genes (13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs) and one control region. The mitogenome of Dysdera silvatica which was available at NCBI GenBank was annotated. The mitogenome of C. triviale was compared with 43 previously sequenced spider species to observe the gene arrangements, control region and phylogeny. TreeREx analysis identified 19 mitochondrial gene rearrangements (11 transposition, 6 inversion, 2 inverse transposition) in spiders as compared with the putative ancestral gene order and lead to form new gene boundaries: trnQ-trnA, trnA-trnM for Loxosceles similis; nad3-trnS1, trnE-trnL2, trnL2-trnA, trnN-trnF for Agelena silvatica; trnN-trnE, trnE-trnA, trnR-trnF, nad4L-trnW, trnW-trnP for Carrhotus xanthogramma; trnQ-trnW, trnW-trnG, trnG-trnM for Tetragnatha nitens. Our study revealed that the gene rearrangement in spiders with putative ancestor is accelerated in Araneomorphae as compared to Mygalomorphae. Phylogenetic analysis of spiders using mitochondrial sequence data supports the monophyly of two infraorders, and sister relationship of Cheiracanthiidae with Selenopidae and Salticidae. The systematic position of the Cheiracanthium species always a controversial issue as this taxa was placed in different families by different authors.
Collapse
Affiliation(s)
- Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India.
| | - Nikita Poddar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Priya Prasad
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| |
Collapse
|
25
|
Bouda E, Stapon A, Garcia-Diaz M. Mechanisms of mammalian mitochondrial transcription. Protein Sci 2019; 28:1594-1605. [PMID: 31309618 DOI: 10.1002/pro.3688] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 01/06/2023]
Abstract
Numerous age-related human diseases have been associated with deficiencies in cellular energy production. Moreover, genetic alterations resulting in mitochondrial dysfunction are the cause of inheritable disorders commonly known as mitochondrial diseases. Many of these deficiencies have been directly or indirectly linked to deficits in mitochondrial gene expression. Transcription is an essential step in gene expression and elucidating the molecular mechanisms involved in this process is critical for understanding defects in energy production. For the past five decades, substantial efforts have been invested in the field of mitochondrial transcription. These efforts have led to the discovery of the main protein factors responsible for transcription as well as to a basic mechanistic understanding of the transcription process. They have also revealed various mechanisms of transcriptional regulation as well as the links that exist between the transcription process and downstream processes of RNA maturation. Here, we review the knowledge gathered in early mitochondrial transcription studies and focus on recent findings that shape our current understanding of mitochondrial transcription, posttranscriptional processing, as well as transcriptional regulation in mammalian systems.
Collapse
Affiliation(s)
- Emilie Bouda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Anthony Stapon
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| |
Collapse
|