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Bueno VM, Trevisan B, Caira JN. Phylogeny of the cestode family Escherbothriidae (Cestoda: Rhinebothriidea) reveals unexpected patterns of association with skate hosts. INVERTEBR SYST 2024; 38:IS23056. [PMID: 38744525 DOI: 10.1071/is23056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/17/2024] [Indexed: 05/16/2024]
Abstract
The rhinebothriidean tapeworm family Escherbothriidae has recently been expanded to include the genus Ivanovcestus , species of which parasitise arhynchobatid skates. Similarities in morphology and host associations between Ivanovcestus and Semiorbiseptum - a genus yet to be assigned to one of the families in the order Rhinebothriidea - led us to explore the possibility that Semiorbiseptum might also belong in the Escherbothriidae. Morphological similarities with Scalithrium ivanovae , Scalithrium kirchneri and Rhinebothrium scobinae , all of which also parasitise arhynchobatid skates, raised questions regarding the generic placements of these species. In addition, new collections from the skate Sympterygia brevicaudata revealed two new species that morphologically resemble species of Ivanovcestus . A combination of morphological and molecular data were used to assess the generic placement of the newly discovered species and refine our understanding of the membership of the family Escherbothriidae. Sequence data for the D1-D3 region of the 28S rDNA gene were generated de novo for 14 specimens of 7 rhinebothriidean species and combined with comparable published data to represent all 6 families in the Rhinebothriidea in the analysis. The phylogenetic tree resulting from maximum likelihood analysis strongly supports the inclusion of the genus Semiorbiseptum in the family Escherbothriidae. Our work also suggests that the skate-hosted species previously assigned to Scalithrium and Rhinebothrium are also members of Semiorbiseptum and that Ivanovcestus is a junior synonym of Semiorbiseptum . Six species are transferred to Semiorbiseptum , bringing the total number of species in the genus to ten. The diagnosis of Semiorbiseptum is amended to accommodate the additional species. A second species in the previously monotypic type genus of the family, Escherbothrium , is described. The diagnosis of the Escherbothriidae is amended to include the new and transferred species. This study underscores the importance of integrating morphological and molecular data in bringing resolution to cestode systematics. We believe our findings provide a robust foundation for future research into the evolutionary history and host associations of cestodes within the order Rhinebothriidea and beyond. These also highlight the importance of expanding our understanding of skate-hosted cestodes. ZooBank: urn:lsid:zoobank.org:pub:8052AFCA-5FBD-4430-95F4-0E5E368DEA3D.
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Affiliation(s)
- V M Bueno
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, 75 N. Eagleville Road, Storrs, CT 006269-3043, USA
| | - B Trevisan
- Department of Zoology, Universidade de São Paulo, Rua do Matão, Travessa 14 número 101, São Paulo, SP, CEP 05508-090, Brazil
| | - J N Caira
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, 75 N. Eagleville Road, Storrs, CT 006269-3043, USA
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Zheng X, Huang X, Yang J, Yang H, Zhang X. The complete mitochondrial genome of Nycteribia formosana (Diptera, Nycteribiidae). Mitochondrial DNA B Resour 2023; 8:1406-1410. [PMID: 38130733 PMCID: PMC10732201 DOI: 10.1080/23802359.2023.2290127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The family Hippoboscidae is an ectoparasite that primarily inhabits bats and relies on the host's blood for sustenance. This research provides the first complete mitochondrial genome of Nycteribia formosana, which shares similar characteristics with other dipteran insects. The circularized mitochondrial genome, spanning 15,107 bp, encompasses 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), two ribosomal RNA genes, and a control region. The nucleotide composition of A, C, G, and T is 40.4%, 10.9%, 6.7%, and 42.0%, respectively. The findings from the phylogenetic analysis suggest that the species under investigation forms a cluster with other species belonging to the family Nycteribiidae. Consequently, this study provides valuable insights for the identification of N. formosana.
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Affiliation(s)
- Xiaoyan Zheng
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xiaobin Huang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Jinting Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Huijuan Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xianzheng Zhang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
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Dziedzic E, Sidlauskas B, Cronn R, Anthony J, Cornwell T, Friesen TA, Konstantinidis P, Penaluna BE, Stein S, Levi T. Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA. Mol Ecol Resour 2023; 23:1880-1904. [PMID: 37602732 DOI: 10.1111/1755-0998.13855] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
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Affiliation(s)
- Emily Dziedzic
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brian Sidlauskas
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Cronn
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - James Anthony
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Trevan Cornwell
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Thomas A Friesen
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Peter Konstantinidis
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brooke E Penaluna
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - Staci Stein
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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4
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McCowin MF, Collins PC, Rouse GW. Updated phylogeny of Vestimentifera (Siboglinidae, Polychaeta, Annelida) based on mitochondrial genomes, with a new species. Mol Phylogenet Evol 2023; 187:107872. [PMID: 37451325 DOI: 10.1016/j.ympev.2023.107872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Siboglinid tubeworms are found at chemosynthetic environments worldwide and the Vestimentifera clade is particularly well known for their reliance on chemoautotrophic bacterial symbionts for nutrition. The mitochondrial genomes have been published for nine vestimentiferan species to date. This study provides new complete mitochondrial genomes for ten further Vestimentifera, including the first mitochondrial genomes sequenced for Alaysia spiralis, Arcovestia ivanovi, Lamellibrachia barhami, Lamellibrachia columna, Lamellibrachia donwalshi, and unnamed species of Alaysia and Oasisia. Phylogenetic analyses combining fifteen mitochondrial genes and the nuclear 18S rRNA gene recovered Lamellibrachia as sister to the remaining Vestimentifera and Riftia pachyptila as separate from the other vent-endemic taxa. Implications and auxiliary analyses regarding differing phylogenetic tree topologies, substitution saturation, ancestral state reconstruction, and divergence estimates are also discussed. Additionally, a new species of Alaysia is described from the Manus Basin.
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Affiliation(s)
- Marina F McCowin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA.
| | - Patrick C Collins
- Queen's University Belfast, Belfast, Co. Antrim, BT9 5DL, Northern Ireland
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA; South Australian Museum, North Terrace, Adelaide, SA 5000, Australia.
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Pouchon C, Boluda CG. REFMAKER: make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae. Mol Phylogenet Evol 2023:107826. [PMID: 37257798 DOI: 10.1016/j.ympev.2023.107826] [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: 01/18/2023] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10% of the produced libraries, and the low coverage associated with these libraries (< 3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can next be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.
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Affiliation(s)
- Charles Pouchon
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland.
| | - Carlos G Boluda
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland
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Huynh S, Cloutier A, Sin SYW. Museomics and phylogenomics of lovebirds (Psittaciformes, Psittaculidae, Agapornis) using low-coverage whole-genome sequencing. Mol Phylogenet Evol 2023; 185:107822. [PMID: 37220800 DOI: 10.1016/j.ympev.2023.107822] [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: 01/12/2023] [Revised: 05/07/2023] [Accepted: 05/19/2023] [Indexed: 05/25/2023]
Abstract
Natural history collections contain specimens that provide important insights into studies of ecology and evolution. With the advancement of high-throughput sequencing, historical DNA (hDNA) from museum specimens has become a valuable source of genomic data to study the evolutionary history of organisms. Low-coverage whole genome sequencing (WGS) has been increasingly applied to museum specimens for analyzing organelle genomes, but is still uncommon for genotyping the nuclear DNA fraction. In this study, we applied low-coverage WGS to phylogenomic analyses of parrots in the genus Agapornis by including both modern samples and historical specimens of ∼100-year-old. Agapornis are small-sized African and Malagasy parrots with diverse characters. Earlier phylogenetic studies failed to resolve the positions of some key lineages, prohibiting a robust interpretation of the biogeography and evolution of these African parrots. Here, we demonstrated the use of low-coverage WGS for generating both mitochondrial and nuclear genomic data, and evaluated data quality differences between modern and historical samples. Our resolved Agapornis phylogeny indicates the ancestor of Agapornis likely colonized Madagascar from Australasia by trans-oceanic dispersal events before dispersing to the African continent. Genome-wide SNPs also allowed us to identify the parental origins of hybrid Agapornis individuals. This study demonstrates the potential of applying low-coverage WGS to phylogenomics and population genomics analyses and illustrates how including historical museum specimens can address outstanding questions regarding the evolutionary history of contemporary lineages.
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Affiliation(s)
- Stella Huynh
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Mueum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
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Yang J, Huang X, Yang H, Wang Y, Zhang X, Zheng X. The complete mitochondrial genome of Nycteribia parvula Speiser, 1901 (Diptera, Nycteribiidae). Mitochondrial DNA B Resour 2023; 8:276-280. [PMID: 36860476 PMCID: PMC9970243 DOI: 10.1080/23802359.2023.2169573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Species of the family Nycteribiidae are blood-sucking ectoparasites that parasitize bats. To further enrich the molecular data of species in the family Nycteribiidae, the complete mitochondrial genome of Nycteribia parvula was sequenced for the first time in this study. The complete mitochondrial genome of N. parvula is 16,060 base pairs (bp) in size, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The nucleotide contents of A, T, G, and C are respectively 40.86%, 42.19%, 6.51%, and 10.44%. The phylogenetic analysis based on 13 PCGs supports the monophyly of the family Nycteribiidae, and N. parvula is the closest relative to Phthiridium szechuanum.
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Affiliation(s)
- Jinting Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xiaobin Huang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China,CONTACT Xiaobin Huang Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, Yunnan, China
| | - Huijuan Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Yujuan Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Xianzheng Zhang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xiaoyan Zheng
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
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Sosale MS, Songsasen N, İbiş O, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica). Gene 2023; 866:147303. [PMID: 36854348 DOI: 10.1016/j.gene.2023.147303] [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: 11/15/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023]
Abstract
The golden jackal (Canis aureus) is a canid species found across southern Eurasia. Several subspecies of this animal have been genetically studied in regions such as Europe, the Middle East, and India. However, one subspecies that lacks current research is the Indochinese jackal (Canis aureus cruesemanni), which is primarily found in Southeast Asia. Using a genome skimming approach, we assembled the first complete mitochondrial genome for an Indochinese jackal from Thailand. To expand the number of available Canis aureus mitogenomes, we also assembled and sequenced the first complete mitochondrial genome of a golden jackal from Turkey, representing the C. a. moreotica subspecies. The mitogenomes contained 37 annotated genes and are 16,729 bps (C. a. cruesemanni) and 16,669 bps (C. a. moreotica) in length. Phylogenetic analysis with 26 additional canid mitogenomes and analyses of a cytochrome b gene-only data set together support the Indochinese jackal as a distinct and early-branching lineage among golden jackals, thereby supporting its recognition as a possible subspecies. These analyses also demonstrate that the golden jackal from Turkey is likely not a distinct lineage due to close genetic relationships with golden jackals from India and Israel.
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Affiliation(s)
- Medhini S Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA.
| | - Nucharin Songsasen
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA
| | - Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey; Vectors and Vector-Borne Diseases Implementation and Research Center, Erciyes University, Kayseri, Turkey
| | - Cody W Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA.
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Zhang X, Huang X, Wang Y, Yang H, Yang J, Zheng X. The complete mitochondrial genome of Phthiridium szechuanum (Nycteribiidae, Diptera). Mitochondrial DNA B Resour 2023; 8:211-214. [PMID: 36761103 PMCID: PMC9904301 DOI: 10.1080/23802359.2023.2171245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Phthiridium szechuanum is a bat surface parasite under the family Nycteribiidae that prefers to roost in the hair of bats to feed on their blood. In this study, the complete mitochondrial genome of P. szechuanum was studied for the first time using Illumina sequencing technology. The mitochondrial genome was 14,896 bp in size and was predicted to encode 37 genes including 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic trees were constructed using the IQ-TREE web server and phylogenetic analysis was performed using the maximum likelihood method, and P. szechuanum was found to be phylogenetically closest to Basilia ansifera. These data will provide a molecular biological approach to the species identification of P. szechuanum and provide a new reference for further studies on the population genetics and phylogeny of the family Nycteribiidae.
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Affiliation(s)
- Xianzheng Zhang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xiaobin Huang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China,CONTACT Xiaobin Huang Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Yujuan Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Huijuan Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Jinting Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xiaoyan Zheng
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
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Papaiakovou M, Fraija-Fernández N, James K, Briscoe AG, Hall A, Jenkins TP, Dunn J, Levecke B, Mekonnen Z, Cools P, Doyle SR, Cantacessi C, Littlewood DTJ. Evaluation of genome skimming to detect and characterise human and livestock helminths. Int J Parasitol 2023; 53:69-79. [PMID: 36641060 DOI: 10.1016/j.ijpara.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023]
Abstract
The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples.
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Affiliation(s)
- Marina Papaiakovou
- Natural History Museum, Cromwell Road, London, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Natalia Fraija-Fernández
- Natural History Museum, Cromwell Road, London, UK; Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain
| | - Katherine James
- Natural History Museum, Cromwell Road, London, UK; Interdisciplinary Computing and Complex BioSystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew G Briscoe
- Natural History Museum, Cromwell Road, London, UK; NatureMetrics, Surrey Research Park, Guildford, UK
| | - Andie Hall
- Natural History Museum, Cromwell Road, London, UK
| | - Timothy P Jenkins
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Dunn
- Department of Infectious Disease Epidemiology, Imperial College, London W2 1PG, UK
| | - Bruno Levecke
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | - Zeleke Mekonnen
- Jimma University Institute of Health (JUIH), Jimma, Ethiopia
| | - Piet Cools
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | | | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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11
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Poon ESK, Chen G, Tsang HY, Shek CT, Tsui WC, Zhao H, Guénard B, Sin SYW. Species richness of bat flies and their associations with host bats in a subtropical East Asian region. Parasit Vectors 2023; 16:37. [PMID: 36707856 PMCID: PMC9881358 DOI: 10.1186/s13071-023-05663-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Understanding the interactions between bat flies and host bats offer us fundamental insights into the coevolutionary and ecological processes in host-parasite relationships. Here, we investigated the identities, host specificity, and patterns of host association of bat flies in a subtropical region in East Asia, which is an understudied region for bat fly research. METHODS We used both morphological characteristics and DNA barcoding to identify the bat fly species found on 11 cavernicolous bat species from five bat families inhabiting Hong Kong. We first determined the phylogenetic relationships among bat fly species. Then, we elucidated the patterns of bat-bat fly associations and calculated the host specificity of each bat fly species. Furthermore, we assembled the mitogenomes of three bat fly species from two families (Nycteribiidae and Streblidae) to contribute to the limited bat fly genetic resources available. RESULTS We examined 641 individuals of bat flies and found 20 species, of which many appeared to be new to science. Species of Nycteribiidae included five Nycteribia spp., three Penicillidia spp., two Phthiridium spp., one Basilia sp., and one species from a hitherto unknown genus, whereas Streblidae included Brachytarsina amboinensis, three Raymondia spp., and four additional Brachytarsina spp. Our bat-bat fly association network shows that certain closely related bat flies within Nycteribiidae and Streblidae only parasitized host bat species that are phylogenetically more closely related. For example, congenerics of Raymondia only parasitized hosts in Rhinolophus and Hipposideros, which are in two closely related families in Rhinolophoidea, but not other distantly related co-roosting species. A wide spectrum of host specificity of these bat fly species was also revealed, with some bat fly species being strictly monoxenous, e.g. nycteribiid Nycteribia sp. A, Phthiridium sp. A, and streblid Raymondia sp. A, while streblid B. amboinensis is polyxenous. CONCLUSIONS The bat fly diversity and specificity uncovered in this study have shed light on the complex bat-bat fly ecology in the region, but more bat-parasite association studies are still needed in East Asian regions like China as a huge number of unknown species likely exists. We highly recommend the use of DNA barcoding to support morphological identification to reveal accurate host-ectoparasite relationships for future studies.
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Affiliation(s)
- Emily Shui Kei Poon
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Guoling Chen
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Hiu Yu Tsang
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Chung Tong Shek
- grid.484292.10000 0004 1774 1243Agriculture, Fisheries and Conservation Department (AFCD), Hong Kong SAR Government, Hong Kong, China
| | - Wing Chi Tsui
- grid.484292.10000 0004 1774 1243Agriculture, Fisheries and Conservation Department (AFCD), Hong Kong SAR Government, Hong Kong, China
| | - Huabin Zhao
- grid.49470.3e0000 0001 2331 6153Department of Ecology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei China
| | - Benoit Guénard
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
| | - Simon Yung Wa Sin
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, China
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12
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Brabec J, Rochat EC, Knudsen R, Scholz T, Blasco-Costa I. Mining various genomic resources to resolve old alpha-taxonomy questions: A test of the species hypothesis of the Proteocephalus longicollis species complex (Cestoda: Platyhelminthes) from salmonid fishes. Int J Parasitol 2023; 53:197-205. [PMID: 36706803 DOI: 10.1016/j.ijpara.2022.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/27/2023]
Abstract
High-throughput sequencing strategies became commonly employed to study non-model parasites, but the corresponding genomes and transcriptomes were seldom mined following the original publication. Similar to the data generated with genome skimming techniques based on shallow-depth shotgun genomes, various genomic and transcriptomic resources can be screened for useful molecular phylogenetic markers traditionally characterised with Sanger sequencing. Here, we provide an example of a strategy using reduced-representation genomic as well as transcriptomic data to obtain broad insights into the molecular diversity of the cestode Proteocephalus longicollis, a common parasite of salmonids distributed throughout the Holarctic region. We extract popular mitochondrial and nuclear ribosomal markers from various genomic resources for hundreds of parasite specimens from multiple European whitefish populations and compare those with Proteocephalus representatives from other species of salmonids and various geographical regions. In contrast with the previous morphology-based assessments, molecular phylogeny reveals a high degree of genetic divergence between Proteocephalus isolates from different salmonids, contrastingly low genetic differentiation within the parasite's populations hosted by the European whitefish (Coregonus lavaretus species complex), and a sister species relationship of Proteocephalus from European whitefish and Proteocephalus percae, a parasite of European perch (Perca fluviatilis). Proteocephalus spp. from North American lake whitefish, brown trout and Arctic charr each formed clearly distinct lineages. These results advance our understanding of the interrelationships of the Proteocephalus-aggregate, a well-recognized clade of Holarctic freshwater fish proteocephalids, and support resurrection of some of the nominal species of Proteocephalus, including Proteocephalus exiguus La Rue, 1911 from North American coregonids and Proteocephalus fallax La Rue, 1911 from European C. lavaretus, reserving Proteocephalus longicollis (Zeder, 1800) exclusively for parasites of Salmo trutta.
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Affiliation(s)
- Jan Brabec
- Department of Invertebrates, Natural History Museum of Geneva, Geneva, Switzerland; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Eloïse C Rochat
- Department of Arctic Biology, The Arctic University of Norway, Tromsø, Norway
| | - Rune Knudsen
- Department of Arctic Biology, The Arctic University of Norway, Tromsø, Norway.
| | - Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Isabel Blasco-Costa
- Department of Invertebrates, Natural History Museum of Geneva, Geneva, Switzerland; Department of Arctic Biology, The Arctic University of Norway, Tromsø, Norway
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13
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Scholz T, Kuchta R. Fish tapeworms (Cestoda) in the molecular era: achievements, gaps and prospects. Parasitology 2022; 149:1876-1893. [PMID: 36004800 PMCID: PMC11010522 DOI: 10.1017/s0031182022001202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 12/29/2022]
Abstract
The tapeworms of fishes (Chondrichthyes and Actinopterygii) account one-third (1670 from around 5000) of the total tapeworm (Platyhelminthes: Cestoda) species diversity. In total 1186 species from 9 orders occur as adults in elasmobranchs (sharks, rays and chimaeras), and 484 species from 8 orders mature in ray-finned fishes (referred to here as teleosts). Teleost tapeworms are dominated by freshwater species (78%), but only 3% of elasmobranch tapeworms are known from freshwater rays of South America and Asia (Borneo). In the last 2 decades, vast progress has been made in understanding species diversity, host associations and interrelationships among fish tapeworms. In total, 172 new species have been described since 2017 (149 from elasmobranchs and 23 from teleosts; invalidly described taxa are not included, especially those from the Oriental region). Molecular data, however, largely limited to a few molecular markers (mainly 28S rDNA, but also 18S and cox1), are available for about 40% of fish tapeworm species. They allowed us to significantly improve our understanding of their interrelationships, including proposals of a new, more natural classification at the higher-taxonomy level (orders and families) as well as at the lower-taxonomy level (genera). In this review, we summarize the main advances and provide perspectives for future research.
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Affiliation(s)
- Tomáš Scholz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Roman Kuchta
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
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14
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Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 2022; 10:e13790. [PMID: 35959477 PMCID: PMC9359134 DOI: 10.7717/peerj.13790] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.
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Affiliation(s)
- Mykle L. Hoban
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, Hawai‘i, United States of America
| | - Jonathan Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, Hawai‘i, United States of America
| | - Allen G. Collins
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine R. Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Abigail J. Reft
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine E. Bemis
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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15
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Camacho MA, Cadar D, Horváth B, Merino-Viteri A, Murienne J. Revised phylogeny from complete mitochondrial genomes of phyllostomid bats resolves subfamilial classification. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Classically, molecular phylogenetic trees of Phyllostomidae have been inferred using a combination of a few mitochondrial and nuclear markers. However, there is still uncertainty in the relationships, especially among deep clades within the family. In this study, we provide newly sequenced complete mitochondrial genomes from 26 bat species, including genomes of 23 species reported here for the first time. By carefully analysing these genomes using maximum likelihood and Bayesian methods and different ingroup and outgroup samples, partition schemes and data types, we investigated the robustness and sensitivity of our phylogenetic results. The optimal topologies were those inferred from the complete data matrix of nucleotides, with complex and highly parameterized substitution models and partition schemes. Our results show a statistically robust picture of the evolutionary relationships between phyllostomid subfamilies and clarify hitherto uncertain relationships of Lonchorhininae and Macrotinae.
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Affiliation(s)
- M Alejandra Camacho
- Museo de Zoología (QCAZ), Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador , Quito, Pichincha , Ecuador
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier , Toulouse , France
| | - Dániel Cadar
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, BernhardNocht Institute for Tropical Medicine , Hamburg , Germany
| | - Balázs Horváth
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, BernhardNocht Institute for Tropical Medicine , Hamburg , Germany
| | - Andrés Merino-Viteri
- Museo de Zoología (QCAZ), Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador , Quito, Pichincha , Ecuador
- Laboratorio de Ecofisiología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católicadel Ecuador , Quito, Pichincha , Ecuador
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier , Toulouse , France
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High-throughput degraded DNA sequencing of subfossil shells of a critically endangered stenoendemic land snail in the Aegean. Mol Phylogenet Evol 2022; 175:107561. [PMID: 35779768 DOI: 10.1016/j.ympev.2022.107561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022]
Abstract
High-throughput sequencing has enabled the comprehensive genetic exploration of biological diversity, especially by using natural history collections to study hard-to-find, threatened or even extinct-in-the-wild taxa. Mollusk shells are under-exploited as a source for DNA-based approaches, despite their apparent advantages in the field of conservation genetics. More particularly, degraded DNA techniques combined with high-throughput sequencing have never been used to gain insights about the DNA preservation in land snail subfossil or historical shells. Here, we applied degraded DNA analysis on two historical shells of Levantina rechingeri, a stenoendemic Critically Endangered species that has never been found alive, in order to explore the patterns of DNA preservation on land snail shells originating from the eastern Mediterranean, as well as to infer its molecular phylogenetic placement. Our results showed that centuries to decades-old DNA from an empty shell collected in an Aegean island exhibits characteristic post-mortem damage patterns similar to those observed in ancient DNA from eastern Mediterranean terrestrial animals, setting a precedent for future museomics studies on taxa distributed in areas with similar climate. Finally, genome skimming of the empty shell allowed high coverage of multiple nuclear and mitochondrial loci, enabling the phylogenetic placement of the focal taxon, the re-evaluation of its taxonomic classification, and the revealing of a new Aegean land snail lineage, Aristina genus novum. This approach is a non-invasive way to sample DNA from threatened land snail species and suitable to study the evolutionary history of taxa with cryptic ecology, stenoendemics, or extinct-in-the-wild, as well as old museum specimens.
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17
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Cay SB, Cinar YU, Kuralay SC, Inal B, Zararsiz G, Ciftci A, Mollman R, Obut O, Eldem V, Bakir Y, Erol O. Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukšāns. PLoS One 2022; 17:e0269747. [PMID: 35704623 PMCID: PMC9200356 DOI: 10.1371/journal.pone.0269747] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Crocus istanbulensis (B.Mathew) Rukšāns is one of the most endangered Crocus species in the world and has an extremely limited distribution range in Istanbul. Our recent field work indicates that no more than one hundred individuals remain in the wild. In the present study, we used genome skimming to determine the complete chloroplast (cp) genome sequences of six C. istanbulensis individuals collected from the locus classicus. The cp genome of C. istanbulensis has 151,199 base pairs (bp), with a large single-copy (LSC) (81,197 bp), small single copy (SSC) (17,524 bp) and two inverted repeat (IR) regions of 26,236 bp each. The cp genome contains 132 genes, of which 86 are protein-coding (PCGs), 8 are rRNA and 38 are tRNA genes. Most of the repeats are found in intergenic spacers of Crocus species. Mononucleotide repeats were most abundant, accounting for over 80% of total repeats. The cp genome contained four palindrome repeats and one forward repeat. Comparative analyses among other Iridaceae species identified one inversion in the terminal positions of LSC region and three different gene (psbA, rps3 and rpl22) arrangements in C. istanbulensis that were not reported previously. To measure selective pressure in the exons of chloroplast coding sequences, we performed a sequence analysis of plastome-encoded genes. A total of seven genes (accD, rpoC2, psbK, rps12, ccsA, clpP and ycf2) were detected under positive selection in the cp genome. Alignment-free sequence comparison showed an extremely low sequence diversity across naturally occurring C. istanbulensis specimens. All six sequenced individuals shared the same cp haplotype. In summary, this study will aid further research on the molecular evolution and development of ex situ conservation strategies of C. istanbulensis.
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Affiliation(s)
- Selahattin Baris Cay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Yusuf Ulas Cinar
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Selim Can Kuralay
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Behcet Inal
- Department of Agricultural Biotechnology, Faculty of Agriculture, University of Siirt, Siirt, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Almila Ciftci
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Rachel Mollman
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Onur Obut
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - Vahap Eldem
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
- * E-mail:
| | - Yakup Bakir
- Department of Plant Bioactive Metabolites, ACTV Biotechnology, Inc., Istanbul, Turkey
| | - Osman Erol
- Department of Biology, Faculty of Sciences, Istanbul University, Istanbul, Turkey
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18
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De Vivo M, Lee HH, Huang YS, Dreyer N, Fong CL, de Mattos FMG, Jain D, Wen YHV, Mwihaki JK, Wang TY, Machida RJ, Wang J, Chan BKK, Tsai IJ. Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum. Sci Rep 2022; 12:9973. [PMID: 35705661 PMCID: PMC9200733 DOI: 10.1038/s41598-022-14121-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1-18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.
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Affiliation(s)
- Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yu-Sin Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Niklas Dreyer
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Natural History Museum of Denmark, University of Copenhagen, Faculty of Science, Copenhagen, Denmark
| | - Chia-Ling Fong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Felipe Monteiro Gomes de Mattos
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Dharmesh Jain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Yung-Hui Victoria Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
| | - John Karichu Mwihaki
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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19
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Li X, Wang L, Yang D. The complete mitochondrial genome of Ornithomya biloba (Diptera, Hippoboscidae). Mitochondrial DNA B Resour 2022; 7:856-858. [PMID: 35573599 PMCID: PMC9103512 DOI: 10.1080/23802359.2022.2075286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome (mitogenome) of Ornithomya biloba (Dufour 1827) was first sequenced and annotated in this study as the first representative of the genus Ornithomya. The complete mitogenome is 18,654 bp in length and contains 37 genes (13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and control region). The phylogenetic analysis based on 13 PCGs in IQ-TREE supports the monophyly of Hippoboscidae, which was a sister group of Streblidae. Families Hippoboscidae and Streblidae formed the monophyletic Hippoboscoidea clade.
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Affiliation(s)
- Xin Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Liang Wang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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20
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Trevisan B, Jacob Machado D, Lahr DJG, Marques FPL. Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms). Front Genet 2022; 12:788871. [PMID: 35003223 PMCID: PMC8727539 DOI: 10.3389/fgene.2021.788871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernando P L Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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21
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Pouchon C, Boyer F, Roquet C, Denoeud F, Chave J, Coissac E, Alsos IG, Lavergne S. ORTHOSKIM: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications. Mol Ecol Resour 2022; 22:2018-2037. [PMID: 35015377 DOI: 10.1111/1755-0998.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in non-model organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: 1) global sequence assembly, 2) mapping against reference sequences, and 3) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and non-coding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g. ultra-conserved elements) or collections of single-copy ortholog genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and 4 RNAseq libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 license and is available at: https://github.com/cpouchon/ORTHOSKIM.
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Affiliation(s)
- Charles Pouchon
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Cristina Roquet
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057, Evry, France
| | - Jérome Chave
- Laboratoire Évolution et Diversité Biologique (EDB), UMR CNRS-IRD-UPS 5174, 31062, Toulouse Cedex, France
| | - Eric Coissac
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | | | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
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22
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Emser SV, Schaschl H, Millesi E, Steinborn R. Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet 2021; 12:685806. [PMID: 35027919 PMCID: PMC8749263 DOI: 10.3389/fgene.2021.685806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Enriching mitochondrial DNA (mtDNA) for sequencing entire mitochondrial genomes (mitogenomes) can be achieved by single long-range PCR. This avoids interference from the omnipresent nuclear mtDNA sequences (NUMTs). The approach is currently restricted to the use of samples collected from humans and ray-finned fishes. Here, we extended the use of single long-range PCR by introducing back-to-back oligonucleotides that target a sequence of extraordinary homology across vertebrates. The assay was applied to five hibernating rodents, namely alpine marmot, Arctic and European ground squirrels, and common and garden dormice, four of which have not been fully sequenced before. Analysis of the novel mitogenomes focussed on the prediction of mitochondrial-derived peptides (MDPs) providing another level of information encoded by mtDNA. The comparison of MOTS-c, SHLP4 and SHLP6 sequences across vertebrate species identified segments of high homology that argue for future experimentation. In addition, we evaluated four candidate polymorphisms replacing an amino acid in mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) system that were reported in relation to cold-adaptation. No obvious pattern was found for the diverse sets of mammalian species that either apply daily or multiday torpor or otherwise cope with cold. In summary, our single long-range PCR assay applying a pair of back-to-back primers that target a consensus sequence motif of Vertebrata has potential to amplify (intact) mitochondrial rings present in templates from a taxonomically diverse range of vertebrates. It could be promising for studying novel mitogenomes, mitotypes of a population and mitochondrial heteroplasmy in a sensitive, straightforward and flexible manner.
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Affiliation(s)
- Sarah V. Emser
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
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23
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Mining museums for historical DNA: advances and challenges in museomics. Trends Ecol Evol 2021; 36:1049-1060. [PMID: 34456066 DOI: 10.1016/j.tree.2021.07.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/22/2023]
Abstract
Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.
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24
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Malukiewicz J, Cartwright RA, Dergam JA, Igayara CS, Nicola PA, Pereira LMC, Ruiz-Miranda CR, Stone AC, Silva DL, Silva FDFRD, Varsani A, Walter L, Wilson MA, Zinner D, Roos C. Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world's most threatened primates. Sci Rep 2021; 11:17279. [PMID: 34446741 PMCID: PMC8390465 DOI: 10.1038/s41598-021-96404-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/10/2021] [Indexed: 12/28/2022] Open
Abstract
The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world's most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.
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Affiliation(s)
- Joanna Malukiewicz
- German Primate Center, Leibniz Institute for Primate Research, Primate Genetics Laboratory, Göttingen, 37077, Germany.
- Universidade de São Paulo, Faculdade de Medicina, São Paulo, São Paulo, 05403-000, Brazil.
| | - Reed A Cartwright
- School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Jorge A Dergam
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | | | - Patricia A Nicola
- Centro de Conservação e Manejo de Fauna da Caatinga, Universidade Federal do Vale do São Francisco, Petrolina, PE, 56300-000, Brazil
| | - Luiz M C Pereira
- Centro de Conservação e Manejo de Fauna da Caatinga, Universidade Federal do Vale do São Francisco, Petrolina, PE, 56300-000, Brazil
| | - Carlos R Ruiz-Miranda
- Laboratório das Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Arizona State University, Institute of Human Origins, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Daniel L Silva
- Núcleo de Pesquisas em Ciências Biológicas - NUPEB, Federal University of Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Lutz Walter
- German Primate Center, Leibniz Institute for Primate Research, Primate Genetics Laboratory, Göttingen, 37077, Germany
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Dietmar Zinner
- German Primate Center, Leibniz Institute for Primate Research, Cognitive Ethology Laboratory, Göttingen, 37077, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, 37077, Germany
- Department of Primate Cognition, Georg-August-University, Göttingen, 37077, Germany
| | - Christian Roos
- German Primate Center, Leibniz Institute for Primate Research, Primate Genetics Laboratory, Göttingen, 37077, Germany
- German Primate Center, Leibniz Institute for Primate Research, Gene Bank of Primates, Göttingen, 37077, Germany
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25
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Rachtman E, Bafna V, Mirarab S. CONSULT: accurate contamination removal using locality-sensitive hashing. NAR Genom Bioinform 2021; 3:lqab071. [PMID: 34377979 PMCID: PMC8340999 DOI: 10.1093/nargab/lqab071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
A fundamental question appears in many bioinformatics applications: Does a sequencing read belong to a large dataset of genomes from some broad taxonomic group, even when the closest match in the set is evolutionarily divergent from the query? For example, low-coverage genome sequencing (skimming) projects either assemble the organelle genome or compute genomic distances directly from unassembled reads. Using unassembled reads needs contamination detection because samples often include reads from unintended groups of species. Similarly, assembling the organelle genome needs distinguishing organelle and nuclear reads. While k-mer-based methods have shown promise in read-matching, prior studies have shown that existing methods are insufficiently sensitive for contamination detection. Here, we introduce a new read-matching tool called CONSULT that tests whether k-mers from a query fall within a user-specified distance of the reference dataset using locality-sensitive hashing. Taking advantage of large memory machines available nowadays, CONSULT libraries accommodate tens of thousands of microbial species. Our results show that CONSULT has higher true-positive and lower false-positive rates of contamination detection than leading methods such as Kraken-II and improves distance calculation from genome skims. We also demonstrate that CONSULT can distinguish organelle reads from nuclear reads, leading to dramatic improvements in skim-based mitochondrial assemblies.
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Affiliation(s)
- Eleonora Rachtman
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, UC San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, UC San Diego, CA 92093, USA
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26
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Trevisan B, Caira JN. Three New Species of Rhinebothrium (Cestoda: Rhinebothriidea) from the Leopard Whipray, Himantura Leoparda, in Australia. J Parasitol 2021; 106:789-801. [PMID: 33351949 DOI: 10.1645/19-192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Examination of 4 specimens of the leopard whipray Himantura leoparda, a dasyatid stingray from northern Australia, led to the discovery of 3 new species of Rhinebothrium. Rhinebothrium leopardensis n. sp., Rhinebothrium nandoi n. sp., and Rhinebothrium ruhnkei n. sp. are described, increasing the diversity of the genus to 51 species globally. All 3 new species differ from their congeners in terms of testis number, proglottid number, loculus number, and size. With respect to one another, R. leopardensis n. sp. has bothridia that are weakly constricted at their centers and has a greater number of proglottids than the other 2 species (93-108 vs. 11-15, and 48-78, respectively). Rhinebothrium nandoi n. sp. is the smallest of the 3 species found in H. leoparda (3.6-5 vs. 10-15 mm and 10.1-15.8 mm in total length [TL], respectively) and bears bothridia that are constricted at their centers. Rhinebothrium ruhnkei n. sp. bears bothridia that are conspicuously constricted at their centers and has more testes than R. leopardensis and fewer than R. nandoi (7-10 vs. fewer than 7 and 21-33, respectively). Before this study, 56% (27 of 48) of Rhinebothrium species had been described from the freshwater river systems of South America and the marine waters surrounding South and North America. In contrast, despite the remarkably diverse nature of its batoid fauna, only 19 species were known from the Indo-Pacific region. Our work increases this number to 22, emphasizing the highly underestimated nature of Rhinebothrium diversity in this region of the globe. The discovery of these 3 new species was not unexpected, given the relatively poor status of our current knowledge of the cestode faunas of dasyatid stingrays in the Indo-Pacific region, and given the fact that it is common for a single batoid species to host 2 or more species of Rhinebothrium. Our results suggest that additional work on the cestode faunas of the batoids, especially dasyatids, from the Indo-Pacific region is likely to be highly productive in terms of contributing to the knowledge of Rhinebothrium diversity.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, 101 Matão Street, Tv. 14, University of São Paulo, SP 05508-090, Brazil
| | - Janine N Caira
- Department of Ecology & Evolutionary Biology, 75 North Eagleville Road, Unit 3043, University of Connecticut, Storrs, Connecticut 06269-3043
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27
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Psonis N, de Carvalho CN, Figueiredo S, Tabakaki E, Vassou D, Poulakakis N, Kafetzopoulos D. Molecular identification and geographic origin of a post-Medieval elephant finding from southwestern Portugal using high-throughput sequencing. Sci Rep 2020; 10:19252. [PMID: 33159124 PMCID: PMC7648095 DOI: 10.1038/s41598-020-75323-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/06/2020] [Indexed: 02/02/2023] Open
Abstract
Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable. Molecular markers have been used in forensic science to trace the geographic origin of wildlife products, such as ivory. So far, only a few studies have applied genetic methods to both identify the species and circumscribe the provenance of historic wildlife trade material. Here, by combining ancient DNA methods and genome skimming on a historical elephantid tooth found in southwestern Portugal, we aimed to identify its species, infer its placement in the elephantid phylogenetic tree, and triangulate its geographic origin. According to our results the specimen dates back to the eighteenth century CE and belongs to a female African forest elephant (non-hybrid Loxodonta cyclotis individual) geographically originated from west—west-central Africa, from areas where one of the four major mitochondrial clades of L. cyclotis is distributed. Historical evidence supports our inference, pointing out that the tooth should be considered as post-Medieval raw ivory trade material between West Africa and Portugal. Our study provides a comprehensive approach to study historical products and artefacts using archaeogenetics and contributes towards enlightening cultural and biological historical aspects of ivory trade in western Europe.
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Affiliation(s)
- Nikolaos Psonis
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece.
| | - Carlos Neto de Carvalho
- Naturtejo UNESCO Global Geopark-Geology Office of the Municipality of Idanha-a-Nova, Centro Cultural Raiano, Av. Joaquim Morão, 6060-101, Idanha-a-Nova, Portugal.,Instituto D. Luiz-IDL Ciências da Terra, Faculty of Sciences of the University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
| | - Silvério Figueiredo
- Polytechnic Institute of Tomar, Quinta do Contador, Estrada da Serra, 2300-313, Tomar, Portugal.,Portuguese Center of Geo-History and Prehistory, Largo de São Caetano, 2150-265, Golegã, Portugal.,Geosciences Center-University of Coimbra, Rua Sílvio Lima, University of Coimbra, 3030-790, Coimbra, Portugal
| | - Eugenia Tabakaki
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece
| | - Despoina Vassou
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409, Irakleio, Greece.,Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013, Irakleio, Greece
| | - Dimitris Kafetzopoulos
- Foundation for Research and Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology, Ancient DNA Lab, N. Plastira 100, Vassilika Vouton, 70013, Irakleio, Greece
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28
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Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics. Sci Rep 2020; 10:18823. [PMID: 33139764 PMCID: PMC7606482 DOI: 10.1038/s41598-020-74883-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/21/2020] [Indexed: 01/27/2023] Open
Abstract
Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquito species. Here we characterized the mitogenomes of mosquito species through low-coverage whole genome sequencing and data mining. A total of 37 draft mitogenomes of different species were assembled from which 16 are newly-sequenced species. We datamined additional 49 mosquito mitogenomes, and together with our 37 mitogenomes, we reconstructed the evolutionary history of 86 species including representatives from 15 genera and 7 tribes. Our results showed that most of the species clustered in clades with other members of their own genus with exception of Aedes genus which was paraphyletic. We confirmed the monophyletic status of the Mansoniini tribe including both Coquillettidia and Mansonia genus. The Aedeomyiini and Uranotaeniini were consistently recovered as basal to other tribes in the subfamily Culicinae, although the exact relationships among these tribes differed between analyses. These results demonstrate that low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge and hence generate basic fundamental information that will help in the understanding of the role of these species as pathogen vectors.
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29
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Peng F, Zhao Z, Xu B, Han J, Yang Q, Lei Y, Tian B, Liu ZL. Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus Dipelta and Their Phylogenomic Implications. Front Genet 2020; 11:573226. [PMID: 33101393 PMCID: PMC7545908 DOI: 10.3389/fgene.2020.573226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fangfang Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Bei Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Jie Han
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Qian Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yunjing Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Zhan-Lin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
- *Correspondence: Zhan-Lin Liu,
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30
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Abstract
Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.
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Affiliation(s)
- Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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