1
|
Dhorne-Pollet S, Barrey E, Pollet N. A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants. BMC Genomics 2020; 21:785. [PMID: 33176683 PMCID: PMC7661214 DOI: 10.1186/s12864-020-07183-9] [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: 12/20/2019] [Accepted: 10/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step. RESULTS We optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3 kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. We evaluated SNPs identified using these long-reads by Sanger sequencing as ground truth and found a precision of 100.0%; a recall of 93.1% and a F1-score of 0.964 using the Twilight horse mtDNA reference. The choice of the mtDNA reference impacted variant calling efficiency with F1-scores varying between 0.947 and 0.964. CONCLUSIONS Our method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.
Collapse
Affiliation(s)
- Sophie Dhorne-Pollet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Eric Barrey
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Nicolas Pollet
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.
| |
Collapse
|
2
|
The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian. BMC Evol Biol 2020; 20:110. [PMID: 32847507 PMCID: PMC7448330 DOI: 10.1186/s12862-020-01673-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
Background Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancient oceanic archipelagos. Here, we focus on the granitic islands of the Seychelles, which are unusual among island systems because they have been isolated for a long time and are home to a monophyletic radiation of caecilian amphibians that has been separated from its extant sister lineage for ca. 65–62 Ma. We selected the most widespread Seychelles caecilian species, Hypogeophis rostratus, to investigate intraspecific morphological and genetic (mitochondrial and nuclear) variation across the archipelago (782 samples from nine islands) to identify patterns and test processes that shaped their evolutionary history within the Seychelles. Results Overall a signal of strong geographic structuring with distinct northern- and southern-island clusters were identified across all datasets. We suggest that these distinct groups have been isolated for ca. 1.26 Ma years without subsequent migration between them. Populations from the somewhat geographically isolated island of Frégate showed contrasting relationships to other islands based on genetic and morphological data, clustering alternatively with northern-island (genetic) and southern-island (morphological) populations. Conclusions Although variation in H. rostratus across the Seychelles is explained more by isolation-by-distance than by adaptation, the genetic-morphological incongruence for affinities of Frégate H. rostratus might be caused by local adaptation over-riding the signal from their vicariant history. Our findings highlight the need of integrative approaches to investigate fine-scale geographic structuring to uncover underlying diversity and to better understand evolutionary processes on ancient, continental islands.
Collapse
|
3
|
Pons J, Bover P, Bidegaray-Batista L, Arnedo MA. Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders. BMC Genomics 2019; 20:665. [PMID: 31438844 PMCID: PMC6706885 DOI: 10.1186/s12864-019-6026-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In recent years, Next Generation Sequencing (NGS) has accelerated the generation of full mitogenomes, providing abundant material for studying different aspects of molecular evolution. Some mitogenomes have been observed to harbor atypical sequences with bizarre secondary structures, which origins and significance could only be fully understood in an evolutionary framework. RESULTS Here we report and analyze the mitochondrial sequences and gene arrangements of six closely related spiders in the sister genera Parachtes and Harpactocrates, which belong to the nocturnal, ground dwelling family Dysderidae. Species of both genera have compacted mitogenomes with many overlapping genes and strikingly reduced tRNAs that are among the shortest described within metazoans. Thanks to the conservation of the gene order and the nucleotide identity across close relatives, we were able to predict the secondary structures even on arm-less tRNAs, which would be otherwise unattainable for a single species. They exhibit aberrant secondary structures with the lack of either DHU or TΨC arms and many miss-pairings in the acceptor arm but this degeneracy trend goes even further since at least four tRNAs are arm-less in the six spider species studied. CONCLUSIONS The conservation of at least four arm-less tRNA genes in two sister spider genera for about 30 myr suggest that these genes are still encoding fully functional tRNAs though they may be post-transcriptionally edited to be fully functional as previously described in other species. We suggest that the presence of overlapping and truncated tRNA genes may be related and explains why spider mitogenomes are smaller than those of other invertebrates.
Collapse
Affiliation(s)
- Joan Pons
- Departamento de Biodiversidad y Conservación, Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB), Miquel Marquès, 21, 07190 Esporles, Illes Balears Spain
| | - Pere Bover
- ARAID Foundation – IUCA Grupo-Aragosaurus, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12 -, 50009 Zaragoza, Spain
| | - Leticia Bidegaray-Batista
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Miquel A. Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-8028 Barcelona, Catalonia Spain
| |
Collapse
|
4
|
Zhang D, Zou H, Hua CJ, Li WX, Mahboob S, Al-Ghanim KA, Al-Misned F, Jakovlić I, Wang GT. Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda. Genome Biol Evol 2019; 11:1797-1812. [PMID: 31192351 PMCID: PMC6601869 DOI: 10.1093/gbe/evz121] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2019] [Indexed: 01/04/2023] Open
Abstract
The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.
Collapse
Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Cong-Jie Hua
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| |
Collapse
|
5
|
Gueuning M, Ganser D, Blaser S, Albrecht M, Knop E, Praz C, Frey JE. Evaluating next-generation sequencing (NGS) methods for routine monitoring of wild bees: Metabarcoding, mitogenomics or NGS barcoding. Mol Ecol Resour 2019; 19:847-862. [PMID: 30912868 PMCID: PMC6850489 DOI: 10.1111/1755-0998.13013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/15/2019] [Indexed: 12/26/2022]
Abstract
Implementing cost‐effective monitoring programs for wild bees remains challenging due to the high costs of sampling and specimen identification. To reduce costs, next‐generation sequencing (NGS)‐based methods have lately been suggested as alternatives to morphology‐based identifications. To provide a comprehensive presentation of the advantages and weaknesses of different NGS‐based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Using a regular monitoring data set (723 specimens identified using morphology), we found that NGS barcoding performed best for both species presence/absence and abundance data, producing only few false positives (3.4%) and no false negatives. In contrast, the proportion of false positives and false negatives was higher using metabarcoding and mitogenomics. Although strong correlations were found between biomass and read numbers, abundance estimates significantly skewed the communities' composition in these two techniques. NGS barcoding recovered the same ecological patterns as morphology. Ecological conclusions based on metabarcoding and mitogenomics were similar to those based on morphology when using presence/absence data, but different when using abundance data. In terms of workload and cost, we show that metabarcoding and NGS barcoding can compete with morphology, but not mitogenomics which was consistently more expensive. Based on these results, we advocate that NGS barcoding is currently the seemliest NGS method for monitoring of wild bees. Furthermore, this method has the advantage of potentially linking DNA sequences with preserved voucher specimens, which enable morphological re‐examination and will thus produce verifiable records which can be fed into faunistic databases.
Collapse
Affiliation(s)
- Morgan Gueuning
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland.,Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Dominik Ganser
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Simon Blaser
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | | | - Eva Knop
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Christophe Praz
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Juerg E Frey
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
| |
Collapse
|
6
|
Labisko J, Griffiths RA, Chong-Seng L, Bunbury N, Maddock ST, Bradfield KS, Taylor ML, Groombridge JJ. Endemic, endangered and evolutionarily significant: cryptic lineages in Seychelles’ frogs (Anura: Sooglossidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
| | - Richard A Griffiths
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | | | - Nancy Bunbury
- Seychelles Islands Foundation, Victoria, Mahé, Seychelles
- Centre for Ecology and Conservation, University of Exeter, UK
| | - Simon T Maddock
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
- School of Biology, Chemistry and Forensic Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
- Department of Life Sciences, The Natural History Museum, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Michelle L Taylor
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| |
Collapse
|
7
|
Liu ZQ, Liu YF, Kuermanali N, Wang DF, Chen SJ, Guo HL, Zhao L, Wang JW, Han T, Wang YZ, Wang J, Shen CF, Zhang ZZ, Chen CF. Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae. PLoS One 2018; 13:e0197524. [PMID: 29768482 PMCID: PMC5955544 DOI: 10.1371/journal.pone.0197524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/03/2018] [Indexed: 02/07/2023] Open
Abstract
Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1. sequence the first Hyalomma mitogenome; 2. scrutinise the proposed synonymization using molecular data, i.e. complete mitogenomes of both subspecies: H. a. asiaticum and kozlovi; 3. conduct phylogenomic and comparative analyses of all available Ixodidae mitogenomes. Results corroborate the proposed synonymization: the two mitogenomes are almost identical (99.6%). Genomic features of both mitogenomes are standard for Metastriata; which includes the presence of two control regions and all three "Tick-Box" motifs. Gene order and strand distribution are perfectly conserved for the entire Metastriata group. Suspecting compositional biases, we conducted phylogenetic analyses (29 almost complete mitogenomes) using homogeneous and heterogeneous (CAT) models of substitution. The results were congruent, apart from the deep-level topology of prostriate ticks (Ixodes): the homogeneous model produced a monophyletic Ixodes, but the CAT model produced a paraphyletic Ixodes (and thereby Prostriata), divided into Australasian and non-Australasian clades. This topology implies that all metastriate ticks have evolved from the ancestor of the non-Australian branch of prostriate ticks. Metastriata was divided into three clades: 1. Amblyomminae and Rhipicephalinae (Rhipicephalus, Hyalomma, Dermacentor); 2. Haemaphysalinae and Bothriocrotoninae, plus Amblyomma sphenodonti; 3. Amblyomma elaphense, basal to all Metastriata. We conclude that mitogenomes have the potential to resolve the long-standing debate about the evolutionary history of ticks, but heterogeneous evolutionary models should be used to alleviate the effects of compositional heterogeneity on deep-level relationships.
Collapse
Affiliation(s)
- Zhi-Qiang Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Yan-Feng Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| | - Nuer Kuermanali
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Deng-Feng Wang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Shi-Jun Chen
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Hui-Ling Guo
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Li Zhao
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Jun-Wei Wang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Tao Han
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Yuan-Zhi Wang
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| | - Jie Wang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Chen-Feng Shen
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Zhuang-Zhi Zhang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Chuang-Fu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| |
Collapse
|
8
|
Adamson EAS, Saha A, Maddock ST, Nussbaum RA, Gower DJ, Streicher JW. Microsatellite discovery in an insular amphibian (Grandisonia alternans) with comments on cross-species utility and the accuracy of locus identification from unassembled Illumina data. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0580-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|