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Vacher JP, Kok PJR, Rodrigues MT, Lima A, Hrbek T, Werneck FP, Manzi S, Thébaud C, Fouquet A. Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy. Mol Phylogenet Evol 2024; 192:108008. [PMID: 38181828 DOI: 10.1016/j.ympev.2023.108008] [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: 09/25/2022] [Revised: 09/23/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.
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Affiliation(s)
- Jean-Pierre Vacher
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France.
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, Łódź 90-237, Poland; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, Caixa Postal 11.461, CEP 05508-090 São Paulo, Brazil
| | - Albertina Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, 69080-900 Manaus, AM, Brazil
| | - Fernanda P Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Antoine Fouquet
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
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Fanelli E, Gaffuri F, Troccoli A, Sacchi S, De Luca F. New occurrence of
Meloidogyne graminicola
(Nematoda: Meloidogyninae) from rice fields in Italy: Variability and phylogenetic relationships. Ecol Evol 2022; 12:e9326. [PMID: 36188499 PMCID: PMC9486484 DOI: 10.1002/ece3.9326] [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: 03/25/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Elena Fanelli
- Istituto per la Protezione Sostenibile delle Piante, Bari Consiglio Nazionale delle Ricerche Bari Italy
| | - Francesca Gaffuri
- Laboratorio Fitosanitario Regione Lombardia presso Fondazione Minoprio Vertemate con Minoprio Italy
| | - Alberto Troccoli
- Istituto per la Protezione Sostenibile delle Piante, Bari Consiglio Nazionale delle Ricerche Bari Italy
| | - Stefano Sacchi
- Laboratorio Fitosanitario Regione Lombardia presso Fondazione Minoprio Vertemate con Minoprio Italy
| | - Francesca De Luca
- Istituto per la Protezione Sostenibile delle Piante, Bari Consiglio Nazionale delle Ricerche Bari Italy
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Singh PR, van de Vossenberg BTLH, Rybarczyk-Mydłowska K, Kowalewska-Groszkowska M, Bert W, Karssen G. An Integrated Approach for Synonymization of Rotylenchus rhomboides with R. goodeyi (Nematoda: Hoplolaimidae) Reveals High Intraspecific Mitogenomic Variation. PHYTOPATHOLOGY 2022; 112:1152-1164. [PMID: 34818905 DOI: 10.1094/phyto-08-21-0363-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rotylenchus is a widely distributed, economically important plant-parasitic nematode group whose species-level identification relies largely on limited morphological characters, including character-based tabular keys and molecular data of ribosomal and mitochondrial genes. In this study, a combined morphological and molecular analysis of three populations of Rotylenchus goodeyi from Belgium, Poland, and the Netherlands revealed important character variations of this species, leading to synonymization of R. rhomboides with R. goodeyi and a high nucleotide variation within cox1 gene sequences in these populations. Additional Illumina sequencing of DNA from individuals of the Dutch population revealed two variants of mitogenomes, each approximately 23 Kb in size, differing by approximately 9% and containing 11 protein-coding genes, 2 ribosomal RNA genes, and as many as 29 transfer RNA genes. In addition to the first representative whole-genome shotgun sequence datasets of the genus Rotylenchus, this study also provides the full-length mitogenome and the ribosomal DNA sequences of R. goodeyi.
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Affiliation(s)
| | - Bart T L H van de Vossenberg
- National Plant Protection Organization, National Reference Centre for Plant Health, 6706 EA Wageningen, The Netherlands
| | | | | | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, Belgium
- National Plant Protection Organization, National Reference Centre for Plant Health, 6706 EA Wageningen, The Netherlands
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Meloidogyne graminicola-A Threat to Rice Production: Review Update on Distribution, Biology, Identification, and Management. BIOLOGY 2021; 10:biology10111163. [PMID: 34827156 PMCID: PMC8614973 DOI: 10.3390/biology10111163] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/05/2022]
Abstract
Simple Summary New risks to plant health are constantly emerging. Such is the case of the rice root knot nematode Meloidogyne graminicola, adapted to flooded conditions and representing a risk to all types of rice agro-systems. It has been recently detected in Italy and added to the European and Mediterranean Plant Protection Organization (EPPO) Alert List. The presence of this nematode in Europe poses a threat to rice production, as there is a high probability to spread, due to trade activities and climate changes. In view of its importance, an extensive updated review was carried out. Abstract Rice (Oryza sativa L.) is one of the main cultivated crops worldwide and represents a staple food for more than half of the world population. Root-knot nematodes (RKNs), Meloidogyne spp., and particularly M. graminicola, are serious pests of rice, being, probably, the most economically important plant-parasitic nematode in this crop. M. graminicola is an obligate sedentary endoparasite adapted to flooded conditions. Until recently, M. graminicola was present mainly in irrigated rice fields in Asia, parts of the Americas, and South Africa. However, in July 2016, it was found in northern Italy in the Piedmont region and in May 2018 in the Lombardy region in the province of Pavia. Following the first detection in the EPPO region, this pest was included in the EPPO Alert List as its wide host range and ability to survive during long periods in environments with low oxygen content, represent a threat for rice production in the European Union. Considering the impact of this nematode on agriculture, a literature review focusing on M. graminicola distribution, biology, identification, and management was conducted.
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Thi Phan N, Besnard G, Ouazahrou R, Sánchez WS, Gil L, Manzi S, Bellafiore S. Genome sequence of the coffee root-knot nematode Meloidogyne exigua. J Nematol 2021; 53:e2021-65. [PMID: 34296190 PMCID: PMC8290501 DOI: 10.21307/jofnem-2021-065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Root-knot nematodes (Meloidogyne spp.) cause serious damages on most crops. Here, we report a high-quality genome sequence of Meloidogyne exigua (population Mex1, Costa Rica), a major pathogen of coffee. Its mitogenome (20,974 bp) was first assembled and annotated. The nuclear genome was then constructed consisting of 206 contigs, with an N50 length of 1.89 Mb and a total assembly length of 42.1 Mb.
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Affiliation(s)
- Ngan Thi Phan
- PHIM Plant Health Institute, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, EDB, 118 route de Narbonne, Université Paul Sabatier, 31062 Toulouse, France
| | | | | | - Lisa Gil
- US 1426, GeT-PlaGe, Genotoul, INRAE, Castanet-Tolosan, France
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, EDB, 118 route de Narbonne, Université Paul Sabatier, 31062 Toulouse, France
| | - Stéphane Bellafiore
- PHIM Plant Health Institute, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Chapuis E, Ali N, Noûs C, Besnard G. Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractCultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) from natural and agricultural environments. Seventeen populations of M. javanica were sampled on cultivated and wild olives in Morocco, then maintained in controlled conditions for a ‘common garden’ experiment. We estimated the genetic variation based on three traits (stylet size, neck width and body width) by a quantitative genetic design (ten families per population and nine individuals per family were measured), and molecular variation was investigated with a mitochondrial marker to identify the genetic lineages of nematode isolates sampled from wild and cultivated olives. Significant morphological differences were detected between individuals from wild vs. cultivated hosts for the three traits, whereas no phylogenetic clustering was observed among isolates collected on those two hosts. Our results thus suggest an adaptive response of the asexual parasite, possibly related to the deep modification of soil nematode communities between natural olive stands and orchards.
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Affiliation(s)
- Elodie Chapuis
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nadeen Ali
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Guillaume Besnard
- CNRS, UPS, IRD, UMR5174, EDB, Université Toulouse III Paul Sabatier, Toulouse Cedex, France
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Vacher JP, Manzi S, Rodrigues MT, Fouquet A. The complete mitochondrial genome of Iphisa elegans (Reptilia: Squamata: Gymnophthalmidae). Mitochondrial DNA B Resour 2020; 5:3088-3090. [PMID: 33458069 PMCID: PMC7782234 DOI: 10.1080/23802359.2020.1797549] [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: 05/21/2020] [Accepted: 07/11/2020] [Indexed: 11/03/2022] Open
Abstract
The complete mitogenome of the lizard Iphisa elegans Gray, 1851 was sequenced using a shotgun approach on an Illumina HiSeq 3000 platform, providing the first mitogenome for Gymnophthalmidae. The genome was 18,622 bp long, with 13 protein-coding genes, two rRNA (12S and 16S), and 22 tRNA, as well as the control region. A maximum likelihood phylogenetic analysis including I. elegans and all other available mitogenomes of Squamata provided a tree in accordance with previous phylogenetic relationships inferred for Squamata.
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Affiliation(s)
- Jean-Pierre Vacher
- Laboratoire Évolution et diversité biologique (EDB), UMR5174, CNRS-UPS-IRD, Bât. 4R1, Université Paul Sabatier, Toulouse, France
| | - Sophie Manzi
- Laboratoire Évolution et diversité biologique (EDB), UMR5174, CNRS-UPS-IRD, Bât. 4R1, Université Paul Sabatier, Toulouse, France
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Antoine Fouquet
- Laboratoire Évolution et diversité biologique (EDB), UMR5174, CNRS-UPS-IRD, Bât. 4R1, Université Paul Sabatier, Toulouse, France
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8
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Kim T, Lee Y, Kil HJ, Park JK. The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda). PeerJ 2020; 8:e9108. [PMID: 32440374 PMCID: PMC7229770 DOI: 10.7717/peerj.9108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.
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Affiliation(s)
- Taeho Kim
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Yucheol Lee
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Hyun-Jong Kil
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
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On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia. Genes (Basel) 2019; 10:genes10020175. [PMID: 30823612 PMCID: PMC6410229 DOI: 10.3390/genes10020175] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 12/20/2022] Open
Abstract
Meloidogyne graminicola is a facultative meiotic parthenogenetic root-knot nematode (RKN) that seriously threatens agriculture worldwide. We have little understanding of its origin, genomic structure, and intraspecific diversity. Such information would offer better knowledge of how this nematode successfully damages rice in many different environments. Previous studies on nuclear ribosomal DNA (nrDNA) suggested a close phylogenetic relationship between M. graminicola and Meloidogyne oryzae, despite their different modes of reproduction and geographical distribution. In order to clarify the evolutionary history of these two species and explore their molecular intraspecific diversity, we sequenced the genome of 12 M. graminicola isolates, representing populations of worldwide origins, and two South American isolates of M. oryzae. k-mer analysis of their nuclear genome and the detection of divergent homologous genomic sequences indicate that both species show a high proportion of heterozygous sites (ca. 1–2%), which had never been previously reported in facultative meiotic parthenogenetic RKNs. These analyses also point to a distinct ploidy level in each species, compatible with a diploid M. graminicola and a triploid M. oryzae. Phylogenetic analyses of mitochondrial genomes and three nuclear genomic sequences confirm close relationships between these two species, with M. graminicola being a putative parent of M. oryzae. In addition, comparative mitogenomics of those 12 M. graminicola isolates with a Chinese published isolate reveal only 15 polymorphisms that are phylogenetically non-informative. Eight mitotypes are distinguished, the most common one being shared by distant populations from Asia and America. This low intraspecific diversity, coupled with a lack of phylogeographic signal, suggests a recent worldwide expansion of M. graminicola.
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Somvanshi VS, Tathode M, Shukla RN, Rao U. Nematode Genome Announcement: A Draft Genome for Rice Root-Knot Nematode, Meloidogyne graminicola. J Nematol 2018; 50:111-116. [PMID: 30451432 DOI: 10.21307/jofnem-2018-018] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The rice root-knot nematode Meloidogyne graminicola has emerged as a devastating pest of rice in South-East Asian countries. Here we present a draft genome sequence for M. graminicola , assembled using data from short and long insert libraries sequenced on Illumina GAIIx sequencing platform.
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Affiliation(s)
- Vishal Singh Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, LBS Center, PUSA Campus, New Delhi 110012, India
| | - Madhura Tathode
- Bionivid Technology Private Limited, 209, 4th Cross, Kasturi Nagar, Bangalore 560043, India
| | - Rohit Nandan Shukla
- Bionivid Technology Private Limited, 209, 4th Cross, Kasturi Nagar, Bangalore 560043, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, LBS Center, PUSA Campus, New Delhi 110012, India
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The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites. Sci Rep 2018; 8:7558. [PMID: 29765106 PMCID: PMC5954100 DOI: 10.1038/s41598-018-25981-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/02/2018] [Indexed: 01/06/2023] Open
Abstract
Bilaterian mitochondrial (mt) genomes are circular molecules that typically contain 37 genes. To date, only a single complete mitogenome sequence is available for the species-rich sarcoptiform mite order Oribatida. We sequenced the mitogenome of Paraleius leontonychus, another species of this suborder. It is 14,186 bp long and contains 35 genes, including only 20 tRNAs, lacking tRNAGly and tRNATyr. Re-annotation of the mitogenome of Steganacarus magnus increased the number of mt tRNAs for this species to 12. As typical for acariform mites, many tRNAs are highly truncated in both oribatid species. The total number of tRNAs and the number of tRNAs with a complete cloverleaf-like structure in P. leontonychus, however, clearly exceeds the numbers previously reported for Sarcoptiformes. This indicates, contrary to what has been previously assumed, that reduction of tRNAs is not a general characteristic for sarcoptiform mites. Compared to other Sarcoptiformes, the two oribatid species have the least rearranged mt genome with respect to the pattern observed in Limulus polyphemus, a basal arachnid species. Phylogenetic analysis of the newly sequenced mt genome and previously published data on other acariform mites confirms paraphyly of the Oribatida and an origin of the Astigmata within the Oribatida.
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12
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Phan NT, De Waele D, Lorieux M, Xiong L, Bellafiore S. A Hypersensitivity-Like Response to Meloidogyne graminicola in Rice (Oryza sativa). PHYTOPATHOLOGY 2018; 108:521-528. [PMID: 29161206 DOI: 10.1094/phyto-07-17-0235-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Meloidogyne graminicola is a major plant-parasitic nematode affecting rice cultivation in Asia. Resistance to this nematode was found in the African rice genotypes Oryza glaberrima and O. longistaminata; however, due to interspecific hybrid sterility, the introgression of resistance genes in the widely consumed O. sativa varieties remains challenging. Recently, resistance was found in O. sativa and, here, we report for the first time the histological and genetic characterization of the resistance to M. graminicola in Zhonghua 11, an O. sativa variety. Bright-light microscopy and fluorescence observations of the root tissue of this variety revealed that the root cells surrounding the nematode displayed a hypersensitivity-like reaction with necrotic cells at early stages of infection when nematodes are migrating in the root's mesoderm. An accumulation of presumably phenolic compounds in the nematodes' neighboring root cells was also observed. In addition, at a later stage of infection, not only were few feeding sites observed but also the giant cells were underdeveloped, underlining an incompatible interaction. Furthermore, we generated a hybrid O. sativa population by crossing Zhonghua 11 with the susceptible O. sativa variety IR64 in order to describe the genetic background of this resistance. Our data suggested that the resistance to M. graminicola infection was qualitative rather than quantitative and, therefore, major resistance genes must be involved in this infection process. The full characterization of the defense mechanism and the preliminary study of the genetic inheritance of novel sources of resistance to Meloidogyne spp. in rice constitute a major step toward their use in crop breeding.
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Affiliation(s)
- Ngan Thi Phan
- First author: Laboratoire Mixte International (LMI) RICE2, Agriculture Genetics Institute (AGI), Hanoi, Vietnam, and IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; second author: Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem De Croylaan 42, B-3001 Heverlee, Belgium; and Unit for Environmental Sciences and Management, North-West University, 56405, Private Bag X6001, 2520 Potchefstroom, South Africa; third author: Institut de recherche pour le développement (IRD), CIRAD, University of Montpellier, DIADE, Montpellier, France; fourth author: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 47895, Wuhan, Hubei, 430070, China; and fifth author: IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; and LMI RICE2, AGI, Hanoi
| | - Dirk De Waele
- First author: Laboratoire Mixte International (LMI) RICE2, Agriculture Genetics Institute (AGI), Hanoi, Vietnam, and IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; second author: Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem De Croylaan 42, B-3001 Heverlee, Belgium; and Unit for Environmental Sciences and Management, North-West University, 56405, Private Bag X6001, 2520 Potchefstroom, South Africa; third author: Institut de recherche pour le développement (IRD), CIRAD, University of Montpellier, DIADE, Montpellier, France; fourth author: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 47895, Wuhan, Hubei, 430070, China; and fifth author: IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; and LMI RICE2, AGI, Hanoi
| | - Mathias Lorieux
- First author: Laboratoire Mixte International (LMI) RICE2, Agriculture Genetics Institute (AGI), Hanoi, Vietnam, and IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; second author: Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem De Croylaan 42, B-3001 Heverlee, Belgium; and Unit for Environmental Sciences and Management, North-West University, 56405, Private Bag X6001, 2520 Potchefstroom, South Africa; third author: Institut de recherche pour le développement (IRD), CIRAD, University of Montpellier, DIADE, Montpellier, France; fourth author: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 47895, Wuhan, Hubei, 430070, China; and fifth author: IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; and LMI RICE2, AGI, Hanoi
| | - Lizhong Xiong
- First author: Laboratoire Mixte International (LMI) RICE2, Agriculture Genetics Institute (AGI), Hanoi, Vietnam, and IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; second author: Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem De Croylaan 42, B-3001 Heverlee, Belgium; and Unit for Environmental Sciences and Management, North-West University, 56405, Private Bag X6001, 2520 Potchefstroom, South Africa; third author: Institut de recherche pour le développement (IRD), CIRAD, University of Montpellier, DIADE, Montpellier, France; fourth author: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 47895, Wuhan, Hubei, 430070, China; and fifth author: IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; and LMI RICE2, AGI, Hanoi
| | - Stephane Bellafiore
- First author: Laboratoire Mixte International (LMI) RICE2, Agriculture Genetics Institute (AGI), Hanoi, Vietnam, and IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; second author: Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem De Croylaan 42, B-3001 Heverlee, Belgium; and Unit for Environmental Sciences and Management, North-West University, 56405, Private Bag X6001, 2520 Potchefstroom, South Africa; third author: Institut de recherche pour le développement (IRD), CIRAD, University of Montpellier, DIADE, Montpellier, France; fourth author: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 47895, Wuhan, Hubei, 430070, China; and fifth author: IRD, CIRAD, University of Montpellier, IPME, Montpellier, France; and LMI RICE2, AGI, Hanoi
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Cabasan MTN, Kumar A, Bellafiore S, De Waele D. Reproductive, pathogenic and genotypic characterisation of five Meloidogyne graminicola populations from the Philippines on susceptible and resistant rice varieties. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Five populations of Meloidogyne graminicola isolated from different rice-growing areas in the Philippines were characterised. The populations showed little phenotypic variability of second-stage juveniles and female perineal pattern. Differences in reproduction among M. graminicola populations were not observed on mature resistant Oryza glaberrima varieties ‘TOG5674’, ‘TOG5675’, ‘RAM131’ and ‘CG14’, or on susceptible O. sativa varieties ‘IR64’ and ‘UPLRi-5’. In all infected rice varieties, plant growth and yield-contributing traits showed no differences among the populations. A search on M. graminicola populations from the Philippines for single-nucleotide polymorphism on the sequences of Internal Transcribed Spacer (ITS) of rDNA genes and mtDNA indicated only few points of heteroplasmy. Nematode reproduction and disease induction of the five M. graminicola populations in the Philippines exerted the same level of aggressiveness and virulence. The absence of resistance-breaking populations of M. graminicola is important for the maintenance of durability of resistance to this important rice pathogen.
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Affiliation(s)
- Ma. Teodora Nadong Cabasan
- 1Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem de Croylaan 42, 3001 Heverlee, Belgium
- 2International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- 3Department of Biological Sciences, College of Arts and Sciences, University of Southern Mindanao, Kabacan 9407, Cotabato, Philippines
| | - Arvind Kumar
- 2International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Stéphane Bellafiore
- 4Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ Montpellier, Montpellier, France
- 5Laboratoire Mixte International RICE2, Agriculture Genetics Institute (AGI), Hanoi, Vietnam
| | - Dirk De Waele
- 1Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem de Croylaan 42, 3001 Heverlee, Belgium
- 2International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- 6Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, 2520 Potchefstroom, South Africa
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Mitochondrial genome diversity in dagger and needle nematodes (Nematoda: Longidoridae). Sci Rep 2017; 7:41813. [PMID: 28150734 PMCID: PMC5288807 DOI: 10.1038/srep41813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/30/2016] [Indexed: 11/23/2022] Open
Abstract
Dagger and needle nematodes included in the family Longidoridae (viz. Longidorus, Paralongidorus, and Xiphinema) are highly polyphagous plant-parasitic nematodes in wild and cultivated plants and some of them are plant-virus vectors (nepovirus). The mitochondrial (mt) genomes of the dagger and needle nematodes, Xiphinema rivesi, Xiphinema pachtaicum, Longidorus vineacola and Paralongidorus litoralis were sequenced in this study. The four circular mt genomes have an estimated size of 12.6, 12.5, 13.5 and 12.7 kb, respectively. Up to date, the mt genome of X. pachtaicum is the smallest genome found in Nematoda. The four mt genomes contain 12 protein-coding genes (viz. cox1-3, nad1-6, nad4L, atp6 and cob) and two ribosomal RNA genes (rrnL and rrnS), but the atp8 gene was not detected. These mt genomes showed a gene arrangement very different within the Longidoridae species sequenced, with the exception of very closely related species (X. americanum and X. rivesi). The sizes of non-coding regions in the Longidoridae nematodes were very small and were present in a few places in the mt genome. Phylogenetic analysis of all coding genes showed a closer relationship between Longidorus and Paralongidorus and different phylogenetic possibilities for the three Xiphinema species.
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Mantelin S, Bellafiore S, Kyndt T. Meloidogyne graminicola: a major threat to rice agriculture. MOLECULAR PLANT PATHOLOGY 2017; 18:3-15. [PMID: 26950515 PMCID: PMC6638252 DOI: 10.1111/mpp.12394] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
TAXONOMY Superkingdom Eukaryota; Kingdom Metazoa; Phylum Nematoda; Class Chromadorea; Order Tylenchida; Suborder Tylenchina; Infraorder Tylenchomorpha; Superfamily Tylenchoidea; Family Meloidogynidae; Subfamily Meloidogyninae; Genus Meloidogyne. BIOLOGY Microscopic non-segmented roundworm. Plant pathogen; obligate sedentary endoparasitic root-knot nematode. Reproduction: facultative meiotic parthenogenetic species in which amphimixis can occur at a low frequency (c. 0.5%); relatively fast life cycle completed in 19-27 days on rice depending on the temperature range. HOST RANGE Reported to infect over 100 plant species, including cereals and grass plants, as well as dicotyledonous plants. Main host: rice (Oryza sativa). SYMPTOMS Characteristic hook-shaped galls (root swellings), mainly formed at the root tips of infected plants. Alteration of the root vascular system causes disruption of water and nutrient transport, stunting, chlorosis and loss of vigour, resulting in poor growth and reproduction of the plants with substantial yield losses in crops. DISEASE CONTROL Nematicides, chemical priming, constant immersion of rice in irrigated fields, crop rotation with resistant or non-host plants, use of nematode-free planting material. Some sources of resistance to Meloidogyne graminicola have been identified in African rice species (O. glaberrima and O. longistaminata), as well as in a few Asian rice cultivars. AGRONOMIC IMPORTANCE Major threat to rice agriculture, particularly in Asia. Adapted to flooded conditions, Meloidogyne graminicola causes problems in all types of rice agrosystems.
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Affiliation(s)
- Sophie Mantelin
- The James Hutton Institute, Dundee Effector ConsortiumInvergowrieDundeeDD2 5DAUK
| | - Stéphane Bellafiore
- IRD‐CIRAD‐Université Montpellier II, UMR Interactions Plantes Microorganismes Environnement (IPME)34394MontpellierFrance
- LMI‐RICEHanoiVietnam
| | - Tina Kyndt
- Department of Molecular BiotechnologyGhent University9000GhentBelgium
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SALALIA RAJAN, WALIA RK, SOMVANSHI VISHALSINGH, KUMAR PUNEET, KUMAR ANIL. Morphological, Morphometric, and Molecular Characterization of Intraspecific Variations within Indian Populations of Meloidogyne graminicola. J Nematol 2017. [DOI: 10.21307/jofnem-2017-071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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17
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Yilmaz E, Fritzenwanker M, Pantchev N, Lendner M, Wongkamchai S, Otranto D, Kroidl I, Dennebaum M, Le TH, Anh Le T, Ramünke S, Schaper R, von Samson-Himmelstjerna G, Poppert S, Krücken J. The Mitochondrial Genomes of the Zoonotic Canine Filarial Parasites Dirofilaria (Nochtiella) repens and Candidatus Dirofilaria (Nochtiella) hongkongensis Provide Evidence for Presence of Cryptic Species. PLoS Negl Trop Dis 2016; 10:e0005028. [PMID: 27727270 PMCID: PMC5058507 DOI: 10.1371/journal.pntd.0005028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/09/2016] [Indexed: 11/18/2022] Open
Abstract
Background Cutaneous dirofilariosis is a canine mosquito-borne zoonosis that can cause larva migrans disease in humans. Dirofilaria repens is considered an emerging pathogen occurring with high prevalence in Mediterranean areas and many parts of tropical Asia. In Hong Kong, a second species, Candidatus Dirofilaria hongkongensis, has been reported. The present study aimed to compare mitochondrial genomes from these parasites and to obtain population genetic information. Methods and Findings Complete mitochondrial genomes were obtained by PCR and Sanger sequencing or ILLUMINA sequencing for four worms. Cytochrome oxidase subunit 1 sequences identified three as D. repens (all from Europe) and one as C. D. hongkongensis (from India). Mitochondrial genomes have the same organization as in other spirurid nematodes but a higher preference for thymine in the coding strand. Phylogenetic analysis was in contradiction to current taxonomy of the Onchocercidae but in agreement with a recent multi-locus phylogenetic analysis using both mitochondrial and nuclear markers. D. repens and C. D. hongkongensis sequences clustered together and were the common sister group to Dirofilaria immitis. Analysis of a 2.5 kb mitochondrial genome fragment from macrofilaria or canine blood samples from Europe (42), Thailand (2), India (1) and Vietnam (1) revealed only small genetic differences in the D. repens samples including all European and the Vietnam sample. The Indian C. D. hongkongensis and the two Thai samples formed separate clusters and differences were comparatively large. Conclusion Genetic differences between Dirofilaria spp. causing cutaneous disease can be considerable whereas D. repens itself was genetically quite homogenous. C. D. hongkongensis was identified for the first time from the Indian subcontinent. The full mitochondrial genome sequence strengthens the hypothesis that it represents an independent species and the Thai samples might represent another cryptic species, Candidatus Dirofilaria sp. ‘Thailand II’, or a quite divergent population of C. D. hongkongensis. The mitochondrial genomes of the zoonotic parasite species Dirofilaria repens and Candidatus Dirofilaria hongkongensis were characterized and compared to the genomes of other filariae. The resulting phylogeny is largely in agreement with recent molecular data. C. D. hongkongensis was placed as a sister group to D. repens and both as a common sister to D. immitis. The large genetic difference between D. repens and C. D. hongkongensis further supports the hypothesis that both are distinct valid species. Two canine samples from Thailand that were diagnosed as D. repens are either from a C. D. hongkongensis population that is quite divergent from the Indian population or might represent another currently unrecognized species in the genus.
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Affiliation(s)
- Esra Yilmaz
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Moritz Fritzenwanker
- Institute of Medical Microbiology, Justus-Liebig-University, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | | | - Mathias Lendner
- Institut für Parasitologie, Universität Leipzig, Leipzig, Germany
| | - Sirichit Wongkamchai
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Bari, Italy
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich (LMU); German Center for Infection Research (DZIF), Partner site Munich, Germany
| | - Martin Dennebaum
- Section Clinical Tropical Medicine, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Thanh Hoa Le
- Immunology Department, Institute of Biotechnology, Ha Noi, Viet Nam
| | - Tran Anh Le
- Department of Parasitology, Viet Nam Veterinary Medical University, Ha Noi, Viet Nam
| | - Sabrina Ramünke
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | | | - Sven Poppert
- University Medical Center, Hamburg-Eppendorf, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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Besnard G, Thèves C, Mata X, Holota H, Rakotozafy LMA, Pedrono M. Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4543-4544. [PMID: 27159683 DOI: 10.3109/19401736.2015.1101554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.
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Affiliation(s)
| | - Catherine Thèves
- b Laboratoire AMIS , UMR 5288, Université de Toulouse/CNRS , Toulouse , France
| | - Xavier Mata
- b Laboratoire AMIS , UMR 5288, Université de Toulouse/CNRS , Toulouse , France
| | - Hélène Holota
- a Laboratoire EDB , UMR5174, CNRS-UPS-ENFA , Toulouse , France
| | - Lucien M A Rakotozafy
- c Laboratoire de Zooarchéologie , Institut des Civilisations, Musée d'Art et d'Archéologie de l'Université d'Antananarivo , Antananarivo , Madagascar
| | - Miguel Pedrono
- d CIRAD, UPR AGIRs , Antananarivo , Madagascar.,e CIRAD, UPR AGIRs, Campus International de Baillarguet , Montpellier , France
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19
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Vacher JP, Fouquet A, Holota H, Thébaud C. The complete mitochondrial genome of Anomaloglossus baeobatrachus (Amphibia: Anura: Aromobatidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:338-340. [PMID: 33644376 PMCID: PMC7871838 DOI: 10.1080/23802359.2016.1172053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The complete mitogenome of the rocket frog Anomaloglossus baeobatrachus was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA), providing the first mitogenome for this genus. The genome was 17,572 bp long and presents the typical organization found in other neobatrachian anurans. A phylogenetic analysis including A. baeobatrachus and all other available mitogenomes of Hyloidea provided relationships in accordance with previous phylogenetic studies.
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Affiliation(s)
| | - Antoine Fouquet
- Laboratoire Écologie, Évolution, Interactions Des Systèmes Amazoniens (LEEISA), Université De Guyane, CNRS Guyane, Cayenne, French Guiana
| | - Hélène Holota
- Laboratoire EDB, UMR5174, CNRS-UPS-ENFA, Toulouse, France
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20
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Coissac E, Hollingsworth PM, Lavergne S, Taberlet P. From barcodes to genomes: extending the concept of DNA barcoding. Mol Ecol 2016; 25:1423-8. [DOI: 10.1111/mec.13549] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/28/2015] [Accepted: 01/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Coissac
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
| | | | - Sébastien Lavergne
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
| | - Pierre Taberlet
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
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21
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Moreira DA, Furtado C, Parente TE. The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae). Gene 2015; 573:171-5. [DOI: 10.1016/j.gene.2015.08.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/20/2015] [Accepted: 08/28/2015] [Indexed: 11/27/2022]
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Gnathostoma spinigerum Mitochondrial Genome Sequence: a Novel Gene Arrangement and its Phylogenetic Position within the Class Chromadorea. Sci Rep 2015; 5:12691. [PMID: 26228511 PMCID: PMC4521153 DOI: 10.1038/srep12691] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/06/2015] [Indexed: 01/21/2023] Open
Abstract
Human gnathostomiasis is an emerging food-borne parasitic disease caused by nematodes in the genus Gnathostoma. In spite of their significance as pathogens, these parasites remain poorly understood at the molecular level. In the present study, we sequenced the mitochondrial (mt) genome of G. spinigerum, which infects a range of definitive hosts including dogs, cats, tigers, leopards and humans. The mt genome of G. spinigerum is 14,079 bp in size and shows substantial changes in gene order compared to other nematodes studied to date. Phylogenetic analyses of mt genome sequences by Bayesian inference (BI) revealed that the infraorder Gnathostomatomorpha (represented by G. spinigerum) is closely related to the infraorder Ascaridomorpha. G. spinigerum is the first species from the infraorder Gnathostomatomorpha for which a complete mt genome has been sequenced. The new data will help understand the evolution, population genetics and systematics of this medically important group of parasites.
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Bellafiore S, Jougla C, Chapuis É, Besnard G, Suong M, Vu PN, De Waele D, Gantet P, Thi XN. Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam. C R Biol 2015; 338:471-83. [PMID: 26026576 DOI: 10.1016/j.crvi.2015.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/05/2015] [Accepted: 04/06/2015] [Indexed: 11/15/2022]
Abstract
Twenty years ago, the facultative meiotic parthenogenetic root-knot nematode (RKN), Meloidogyne graminicola, was recognised as an important rice pathogen in South Vietnam. Although this country is one of the most important rice exporters worldwide, a comprehensive picture of the occurrence of M. graminicola in Vietnamese rice fields is still not available. Therefore a nematode survey was carried out with the aim of better understanding the geographical distribution, and the pathogenic and genetic variability of the RKN in Vietnam. From the fields surveyed in a range of ecosystems, 21 RKN populations were recovered from infected rice roots. A diagnostic SCAR marker was developed showing that all Vietnamese populations belong to M. graminicola. Furthermore, sequencing of the Internal Transcribed Spacer (ITS) of the rDNA genes confirmed this identification. These populations were then characterised using morphometrics and pathogenicity tests (host plant range diversity, reproduction and virulence diversity) revealing intraspecific variability. We showed that morphometric traits are mainly genetically heritable characters with significant differences among the studied populations. Finally, a distinctive trait signature was found for the populations isolated from the upland rice cultures. All together, our study reveals the prevalence of M. graminicola populations in Vietnamese rice. Further investigations need to be developed to explore the population dynamics and evolutionary history of this species in South East Asia.
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Affiliation(s)
- Stéphane Bellafiore
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France; IRD, LMI RICE, University of Science and Technology of Hanoi, Agricultural Genetics Institute, Hanoi, Viet Nam.
| | - Claire Jougla
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Élodie Chapuis
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire « Évolution & diversité biologique »), 118, route de Narbonne, 31062 Toulouse, France
| | - Malyna Suong
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France; IRD, LMI RICE, University of Science and Technology of Hanoi, Agricultural Genetics Institute, Hanoi, Viet Nam
| | - Phong Nguyen Vu
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France; Department of Biotechnology, Nong Lam University, Ho Chi Minh City, Viet Nam
| | - Dirk De Waele
- Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem de Croylaan 42, 3001 Heverlee, Belgium; International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines; Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, 2520 Potchefstroom, South Africa
| | - Pascal Gantet
- IRD, LMI RICE, University of Science and Technology of Hanoi, Agricultural Genetics Institute, Hanoi, Viet Nam; University of Montpellier-2, UMR DIADE, Montpellier, France
| | - Xuyen Ngo Thi
- Department of Plant Pathology, Faculty of Agronomy, Hanoi University of Agriculture Trau Qui, Gia Lam, Hanoi, Viet Nam
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Murienne J, Jeziorski C, Holota H, Coissac E, Blanchet S, Grenouillet G. PCR-free shotgun sequencing of the stone loach mitochondrial genome (Barbatula barbatula). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4211-4212. [PMID: 26000945 DOI: 10.3109/19401736.2015.1022744] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The complete mitochondrial genome of the stone loach Barbatula barbatula (Linnaeus, 1758) (Actinopterygii: Cypriniformes: Nemacheilidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2500 platform. The mitochondrial genome of B. barbatula was determined to be 16,630 bp long and presents an organization typical of vertebrate mitogenomes. The mean coverage was 82× with a minimum coverage of 33× for the control region and 52× for the remaining part of the genome. A phylogenetic analysis of the Nemacheilidae family shows the monophyly of the Barbatula genus with strong support.
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Affiliation(s)
- Jérôme Murienne
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Céline Jeziorski
- b INRA, UAR1209, Département de Génétique Animale , INRA Auzeville , Castanet-Tolosan , France.,c GeT-PlaGe, Genotoul, INRA Auzeville , Castanet-Tolosan , France
| | - Hélène Holota
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Eric Coissac
- d Laboratoire d'Ecologie Alpine , CNRS UMR , Grenoble , France , and
| | - Simon Blanchet
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France.,e Station Expérimentale du CNRS à Moulis, U.S.R , Moulis , France
| | - Gaël Grenouillet
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
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Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample. Mol Biol Evol 2015; 32:2302-16. [PMID: 25957318 PMCID: PMC4540967 DOI: 10.1093/molbev/msv111] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, Faculty of Life Sciences, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Matthew L Gimmel
- Department of Biology, Faculty of Education, Palacký University, Olomouc, Czech Republic
| | | | - Timothy D Cockerill
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chey Vun Khen
- Entomology Section, Forest Research Centre, Forestry Department, Sandakan, Sabah, Malaysia
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
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Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thébaud C. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12494] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Joris A. M. Bertrand
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Institute of Oceanography; National Taiwan University; n°1, sec. 4, Roosevelt Road, Daan District Taipei 10617 Taiwan
| | - Boris Delahaie
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Yann X. C. Bourgeois
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Zoological Institute; Department of Evolutionary Biology; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Emeline Lhuillier
- INRA; GeT-PlaGe; UAR 1209 Département de Génétique Animale; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Christophe Thébaud
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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García LE, Sánchez-Puerta MV. Comparative and evolutionary analyses of Meloidogyne spp. Based on mitochondrial genome sequences. PLoS One 2015; 10:e0121142. [PMID: 25799071 PMCID: PMC4370701 DOI: 10.1371/journal.pone.0121142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/12/2015] [Indexed: 01/11/2023] Open
Abstract
Molecular taxonomy and evolution of nematodes have been recently the focus of several studies. Mitochondrial sequences were proposed as an alternative for precise identification of Meloidogyne species, to study intraspecific variability and to follow maternal lineages. We characterized the mitochondrial genomes (mtDNAs) of the root knot nematodes M. floridensis, M. hapla and M. incognita. These were AT rich (81–83%) and highly compact, encoding 12 proteins, 2 rRNAs, and 22 tRNAs. Comparisons with published mtDNAs of M. chitwoodi, M. incognita (another strain) and M. graminicola revealed that they share protein and rRNA gene order but differ in the order of tRNAs. The mtDNAs of M. floridensis and M. incognita were strikingly similar (97–100% identity for all coding regions). In contrast, M. floridensis, M. chitwoodi, M. hapla and M. graminicola showed 65–84% nucleotide identity for coding regions. Variable mitochondrial sequences are potentially useful for evolutionary and taxonomic studies. We developed a molecular taxonomic marker by sequencing a highly-variable ~2 kb mitochondrial region, nad5-cox1, from 36 populations of root-knot nematodes to elucidate relationships within the genus Meloidogyne. Isolates of five species formed monophyletic groups and showed little intraspecific variability. We also present a thorough analysis of the mitochondrial region cox2-rrnS. Phylogenies based on either mitochondrial region had good discrimination power but could not discriminate between M. arenaria, M. incognita and M. floridensis.
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Affiliation(s)
- Laura Evangelina García
- IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
| | - M. Virginia Sánchez-Puerta
- IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Mendoza, Argentina
- * E-mail:
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Humphreys-Pereira DA, Elling AA. Mitochondrial genome plasticity among species of the nematode genus Meloidogyne (Nematoda: Tylenchina). Gene 2015; 560:173-83. [PMID: 25655462 DOI: 10.1016/j.gene.2015.01.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 11/30/2022]
Abstract
The mitochondrial (mt) genomes of the plant-parasitic root-knot nematodes Meloidogyne arenaria, Meloidogyne enterolobii and Meloidogyne javanica were sequenced and compared with those of three other root-knot nematode species in order to explore the mt genome plasticity within Meloidogyne. The mt genomes of M. arenaria, M. enterolobii and M. javanica are circular, with an estimated size of 18.8, 18.9 and 19.6 kb, respectively. Compared to other nematodes these mt genomes are larger, due to the presence of large non-coding regions. The mt genome architecture within the genus Meloidogyne varied in the position of trn genes and in the position, length and nucleotide composition of non-coding regions. These variations were observed independent of the species' natural environments or reproductive modes. M. enterolobii showed three main non-coding regions whereas Meloidogyne chitwoodi, Meloidogyne incognita, M. javanica and M. arenaria had two non-coding regions, and Meloidogyne graminicola had a unique large non-coding region interrupted by two trn genes. trn genes were positioned in different regions of the mt genomes in M. chitwoodi, M. enterolobii and M. graminicola, whereas the trn gene order was identical between M. arenaria, M. incognita and M. javanica. Importantly, M. graminicola had extra copies of trnV and trnS2. High divergence levels between the two copies of each trn might indicate duplication events followed by random loss and mutations in the anticodon. Tree-based methods based on amino acid sequences of 12 mt protein-coding genes support the monophyly for the tropical and mitotic parthenogenetic species, M. arenaria, M. enterolobii, M. incognita and M. javanica and for a clade that includes the meiotic parthenogenetic species, M. chitwoodi and M. graminicola. A comparison of the mt genome architecture in plant-parasitic nematodes and phylogenetic analyses support that Pratylenchus is the most recent ancestor of root-knot nematodes.
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Affiliation(s)
| | - Axel A Elling
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA.
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Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach. C R Biol 2015; 338:149-60. [PMID: 25636225 DOI: 10.1016/j.crvi.2014.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 11/23/2022]
Abstract
Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases.
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Cally S, Lhuillier E, Iribar A, Garzón-Orduña I, Coissac E, Murienne J. Shotgun assembly of the complete mitochondrial genome of the neotropical cracker butterflyHamadryas epinome. ACTA ACUST UNITED AC 2014; 27:1864-6. [DOI: 10.3109/19401736.2014.971262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae). Gene 2014; 552:184-94. [PMID: 25240790 DOI: 10.1016/j.gene.2014.09.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/27/2014] [Accepted: 09/15/2014] [Indexed: 12/26/2022]
Abstract
The complete mitochondrial genome of the assassin bug Brontostoma colossus (Distant, 1902) (Heteroptera: Reduviidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including five assassin bug species, were retrieved to allow for comparisons and phylogenetic analyses. The mitochondrial genome of B. colossus was determined to be 16,625 bp long, and consists of 13 protein-coding genes (PCGs), 23 transfer-RNA genes (tRNAs), two ribosomal-RNA genes (rRNAs), and one control region. The nucleotide composition is biased toward adenine and thymine (A+T=73.4%). Overall, architecture, nucleotide composition and genome asymmetry are similar among all available assassin bug mitogenomes. All PCGs have usual start-codons (Met and Ile). Three T and two TA incomplete termination codons were identified adjacent to tRNAs, which was consistent with the punctuation model for primary transcripts processing followed by 3' polyadenylation of mature mRNA. All tRNAs exhibit the classic clover-leaf secondary structure except for tRNASer(AGN) in which the DHU arm forms a simple loop. Two notable features are present in the B. colossus mitogenome: (i) a 131 bp duplicated unit including the complete tRNAArg gene, resulting in 23 potentially functional tRNAs in total, and (ii) a 857 bp duplicated region comprising 277 bp of the srRNA gene and 580 bp of the control region. A phylogenetic analysis based on 55 true bug mitogenomes confirmed that B. colossus belongs to Reduviidae, but contradicted a widely accepted hypothesis. This highlights the limits of phylogenetic analyses based on mitochondrial data only.
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Sun L, Zhuo K, Lin B, Wang H, Liao J. The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina): a unique gene arrangement and its phylogenetic implications. PLoS One 2014; 9:e98558. [PMID: 24892428 PMCID: PMC4043755 DOI: 10.1371/journal.pone.0098558] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/05/2014] [Indexed: 12/05/2022] Open
Abstract
Meloidogyne graminicola is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of Pratylenchus vulnus (21,656 bp). The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of M. graminicola contains 36 genes (lacking atp8) that are transcribed in the same direction. The gene arrangement of the mt genome of M. graminicola is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while tRNASer(AGN) lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by tRNASer(UCN). Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea. In the clade of Tylenchoidea, M. graminicola is sister to P. vulnus, and H. glycines is sister to R. similis, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.
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Affiliation(s)
- Longhua Sun
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Kan Zhuo
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Borong Lin
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Honghong Wang
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Jinling Liao
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
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Sun L, Zhuo K, Wang H, Song H, Chi W, Zhang LH, Liao J. The complete mitochondrial genome of Aphelenchoides besseyi (Nematoda: Aphelenchoididae), the first sequenced representative of the subfamily Aphelenchoidinae. NEMATOLOGY 2014. [DOI: 10.1163/15685411-00002844] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The complete mitochondrial genome (mitogenome) ofAphelenchoides besseyiis 16 216 bp in size and has the typical organisation of nematode mitogenomes of Chromadorea, including 12 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and the AT-rich non-coding region. The nucleotide composition of the mitogenome ofA. besseyiis AT-biased (80.0%) and the AT skew is −0.289. The most common start codon forA. besseyiis ATT. Thenad3andnad4Lgenes have an incomplete stop codon consisting of just a T and the other PCGs stop with the full stop codons. All the tRNA genes display a non-typical cloverleaf structure of mitochondrial tRNA. The AT-rich non-coding region contains ten tandem repeat units with four different regions. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes showed that three Tylenchomorpha species, includingA. besseyi,Bursaphelenchus mucronatusandB. xylophilusfrom the superfamily Aphelenchoidea, are placed within a well-supported monophyletic clade, but far from the other six Tylenchomorpha speciesMeloidogyne chitwoodi,M. graminicola,M. incognita,Pratylenchus vulnus,Heterodera glycinesandRadopholus similisof Tylenchoidea. This phylogeny suggests thatAphelenchoideshas a close relative relationship withBursaphelenchusand that the Tylenchomorpha is not monophyletic.
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Affiliation(s)
- Longhua Sun
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Kan Zhuo
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Honghong Wang
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Handa Song
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Wenwei Chi
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Jinling Liao
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, P.R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, P.R. China
- Guangdong Vocational College of Ecological Engineering, Guangzhou 510520, P.R. China
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