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Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK, Porazinska DL. Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection. BMC Genomics 2024; 25:615. [PMID: 38890582 PMCID: PMC11184840 DOI: 10.1186/s12864-024-10500-1] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
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Affiliation(s)
- Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyin Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | | | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - W Kelly Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
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2
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Zeng JL, Chen HX, Ni XF, Kang JY, Li L. Molecular phylogeny of the family Rhabdiasidae (Nematoda: Rhabditida), with morphology, genetic characterization and mitochondrial genomes of Rhabdias kafunata and R. bufonis. Parasit Vectors 2024; 17:100. [PMID: 38429838 PMCID: PMC10908064 DOI: 10.1186/s13071-024-06201-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The family Rhabdiasidae (Nematoda: Rhabditida) is a globally distributed group of nematode parasites, with over 110 species parasitic mainly in amphibians and reptiles. However, the systematic position of the family Rhabdiasidae in the order Rhabditida remains unsolved, and the evolutionary relationships among its genera are still unclear. Moreover, the present knowledge of the mitochondrial genomes of rhabdiasids remains limited. METHODS Two rhabdiasid species: Rhabdias kafunata Sata, Takeuchi & Nakano, 2020 and R. bufonis (Schrank, 1788) collected from the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) in China, were identified based on morphology (light and scanning electron microscopy) and molecular characterization (sequencing of the nuclear 28S and ITS regions and mitochondrial cox1 and 12S genes). The complete mitochondrial genomes of R. kafunata and R. bufonis were also sequenced and annotated for the first time. Moreover, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes (PCGs) of the mitochondrial genomes were performed to clarify the systematic position of the family Rhabdiasidae in the order Rhabditida using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses based on the 28S + ITS sequences, were also inferred to assess the evolutionary relationships among the genera within Rhabdiasidae. RESULTS The detailed morphology of the cephalic structures, vulva and eggs in R. kafunata and R. bufonis was revealed using scanning electron microscopy (SEM) for the first time. The characterization of 28S and ITS regions of R. kafunata was reported for the first time. The mitogenomes of R. kafunata and R. bufonis are 15,437 bp and 15,128 bp long, respectively, and both contain 36 genes, including 12 PCGs (missing atp8). Comparative mitogenomics revealed that the gene arrangement of R. kafunata and R. bufonis is different from all of the currently available mitogenomes of nematodes. Phylogenetic analyses based on the ITS + 28S data showed Neoentomelas and Kurilonema as sister lineages, and supported the monophyly of Entomelas, Pneumonema, Serpentirhabdias and Rhabdias. Mitochondrial phylogenomic results supported Rhabdiasidae as a member of the superfamily Rhabditoidea in the suborder Rhabditina, and its occurrance as sister to the family Rhabditidae. CONCLUSIONS The complete mitochondrial genome of R. kafunata and R. bufonis were reported for the first time, and two new gene arrangements of mitogenomes in Nematoda were revealed. Mitogenomic phylogenetic results indicated that the family Rhabdiasidae is a member of Rhabditoidea in Rhabditina, and is closely related to Rhabditidae. Molecular phylogenies based on the ITS + 28S sequence data supported the validity of Kurilonema, and showed that Kurilonema is sister to Neoentomelas. The present phylogenetic results also indicated that the ancestors of rhabdiasids seem to have initially infected reptiles, then spreading to amphibians.
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Affiliation(s)
- Jia-Lu Zeng
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Hui-Xia Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Xue-Feng Ni
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Jia-Yi Kang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Liang Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei, People's Republic of China.
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3
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Balog LE, Ahmed M, Holovachov O. Redescription of three pinworms of the genus Cephalobellus Cobb, 1920 (Nematoda: Oxyuridomorpha: Thelastomatidae) from scarab beetle grubs from Hungary. Syst Parasitol 2024; 101:21. [PMID: 38369578 PMCID: PMC10874908 DOI: 10.1007/s11230-023-10124-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/02/2023] [Indexed: 02/20/2024]
Abstract
Larvae of European rose chafer Cetonia aurata (Linnaeus, 1758) and cockchafer Melolontha sp. beetles were collected in Hungary for parasitological study. Intestinal examination revealed the presence of three well-known thelastomatid nematodes belonging to the genus Cephalobellus Cobb, 1920. We report for the first-time Cephalobellus cuspidatum (Rudolphi, 1814) Leibersperger, 1960, C. osmodermae Leibersperger, 1960, and C. potosiae Leibersperger, 1960 in Hungary, all found in scarab beetle larvae. Due to incomplete original descriptions, a comprehensive redescription with detailed morphological data is presented. Additionally, an identification key for closely related Cephalobellus, Thelastoma and Severianoia species infesting scarab beetles worldwide is provided. Newly generated 18S and 28S rDNA gene sequences of C. osmodermae place it as one of the early branches within Thelastomatidae.
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Affiliation(s)
- Luca Eszter Balog
- Doctoral School of Biology, Institute of Biology and Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, 1117, Hungary
| | - Mohammed Ahmed
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 104 05, Stockholm, Sweden
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7AB, UK
| | - Oleksandr Holovachov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 104 05, Stockholm, Sweden.
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4
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Huo C, Bao F, Long H, Qin T, Zhang S. The complete mitochondrial genome of Wellcomia compar (Spirurina: Oxyuridae) and its genome characterization and phylogenetic analysis. Sci Rep 2023; 13:14426. [PMID: 37660220 PMCID: PMC10475117 DOI: 10.1038/s41598-023-41638-9] [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: 03/27/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023] Open
Abstract
Wellcomia compar (Spirurina: Oxyuridae) is a pinworm that infects wild and captive porcupines. Despite clear records of its morphological structure, its genetics, systematics, and biology are poorly understood. This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. We sequenced the complete mt genome of W. comparand conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. The complete mt genome is 14,373 bp in size and comprises 36 genes, including 12 protein-coding, two rRNA and 22 tRNA genes. Apart from 28 intergenic regions, one non-coding region and one overlapping region also occur. A comparison of the gene arrangements of Oxyuridomorpha revealed relatively similar features in W. compar and Wellcomia siamensis. Phylogenetic analysis also showed that W. compar and W. siamensis formed a sister group. In Oxyuridomorpha the genetic distance between W. compar and W. siamensis was 0.0805. This study reports, for the first time, the complete W. compar mt genome sequence obtained from Chinese porcupines. It provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals.
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Affiliation(s)
- Chunmao Huo
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Fengyun Bao
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Hong Long
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Tingyang Qin
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Shibin Zhang
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China.
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5
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Mladineo I, Rončević T, Gerdol M, Tossi A. Helminthic host defense peptides: using the parasite to defend the host. Trends Parasitol 2023; 39:345-357. [PMID: 36890022 DOI: 10.1016/j.pt.2023.02.004] [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: 12/12/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 03/08/2023]
Abstract
Parasitic helminths are destined to share niches with a variety of microbiota that inevitably influence their interaction with the host. To modulate the microbiome for their benefit and defend against pathogenic isolates, helminths have developed host defense peptides (HDPs) and proteins as integral elements of their immunity. These often exert a relatively nonspecific membranolytic activity toward bacteria, sometimes with limited or no toxicity toward host cells. With a few exceptions, such as nematode cecropin-like peptides and antibacterial factors (ABFs), helminthic HDPs are largely underexplored. This review scrutinizes current knowledge on the repertoire of such peptides in helminths and promotes their research as potential leads for an anti-infective solution to the burgeoning problem of antibiotic resistance.
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Affiliation(s)
- Ivona Mladineo
- Laboratory of Functional Helminthology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology BC CAS, Branišovska 31, Česke Budejovice 37005, Czech Republic.
| | - Tomislav Rončević
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, Split 21000, Croatia
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
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6
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Hellekes V, Claus D, Seiler J, Illner F, Schiffer PH, Kroiher M. CRISPR/Cas9 mediated gene editing in non-model nematode Panagrolaimus sp. PS1159. Front Genome Ed 2023; 5:1078359. [PMID: 36818277 PMCID: PMC9935820 DOI: 10.3389/fgeed.2023.1078359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The phylum Nematoda harbors a huge diversity of species in a broad range of ecosystems and habitats. Nematodes share a largely conserved Bauplan but major differences have been found in early developmental processes. The development of the nematode model organism Caenorhabditis elegans has been studied in great detail for decades. These efforts have provided the community with a large number of protocols and methods. Unfortunately, many of these tools are not easily applicable in non-Caenorhabditis nematodes. In recent years it has become clear that many crucial genes in the C. elegans developmental toolkit are absent in other nematode species. It is thus necessary to study the developmental program of other nematode species in detail to understand evolutionary conservation and novelty in the phylum. Panagrolaimus sp. PS1159 is a non-parasitic nematode exhibiting parthenogenetic reproduction and we are establishing the species to comparatively study evolution, biodiversity, and alternative reproduction and survival strategies. Here, we demonstrate the first successful application of the CRISPR/Cas9 system for genome editing in Panagrolaimus sp. PS1159 and the closely related hermaphroditic species Propanagrolaimus sp. JU765 applying the non-homologous end joining and the homology-directed repair (HDR) mechanisms. Using microinjections and modifying published protocols from C. elegans and P. pacificus we induced mutations in the orthologue of unc-22. This resulted in a visible uncoordinated twitching phenotype. We also compared the HDR efficiency following the delivery of different single-stranded oligodeoxynucleotides (ssODNs). Our work will expand the applicability for a wide range of non-model nematodes from across the tree and facilitate functional analysis into the evolution of parthenogenesis, changes in the developmental program of Nematoda, and cryptobiosis.
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Affiliation(s)
- Viktoria Hellekes
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany,Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany,*Correspondence: Viktoria Hellekes,
| | - Denise Claus
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Johanna Seiler
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Felix Illner
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Philipp H. Schiffer
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Michael Kroiher
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
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7
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Lai CK, Lee YC, Ke HM, Lu MR, Liu WA, Lee HH, Liu YC, Yoshiga T, Kikuchi T, Chen PJ, Tsai IJ. The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes. Mol Ecol Resour 2023; 23:905-919. [PMID: 36597348 DOI: 10.1111/1755-0998.13752] [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: 09/24/2022] [Revised: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023]
Abstract
Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.
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Affiliation(s)
- Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Yi-Chien Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Min R Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-An Liu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Peichen J Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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8
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Guo W, Wang M, Li H, Wang C. Description of a new nematode species, Chromadorinacommunis sp. nov. (Nematoda, Chromadoridae), from Changdao Island, China and phylogenetic analysis of Chromadorida based on small subunit rRNA gene sequences. Zookeys 2023; 1159:121-131. [PMID: 37213530 PMCID: PMC10193274 DOI: 10.3897/zookeys.1159.100908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
Chromadorinacommunissp. nov. is described from Changdao Island at the confluence of the Yellow and the Bohai seas. The new species is characterized by its medium-sized body; finely striated cuticle with homogeneous punctations; absence of ocelli; buccal cavity with three equal-sized, solid teeth; four cephalic setae; oval amphidial fovea which is positioned between cephalic setae; curved spicules with tapered distal ends; simple, boat-shaped gubernaculums; five or six cup-shaped precloacal supplements; and conical tail with a very short spinneret. A phylogenetic analysis of small subunit rRNA gene sequences using maximum-likelihood and Bayesin inference confirmed the taxonomic position of Chromadorinacommunissp. nov. within Chromadorinae. Tree topology in Chromadorida shows six morphological families clustered into a monophyletic clade and verifies the taxonomic position of the family Neotonchidae based on morphological and molecular analysis.
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Affiliation(s)
- Wen Guo
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, ChinaLiaocheng UniversityLiaochengChina
| | - Mengna Wang
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, ChinaLiaocheng UniversityLiaochengChina
| | - Haotian Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, ChinaLiaocheng UniversityLiaochengChina
| | - Chunming Wang
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, ChinaLiaocheng UniversityLiaochengChina
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9
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Deng YP, Suleman, Zhang XL, Li R, Li LY, Fu YT, Liu GH, Yao C. Aonchotheca (Nematoda: Capillariidae) is validated as a separated genus from Capillaria by both mitochondrial and nuclear ribosomal DNA. Parasit Vectors 2022; 15:493. [PMID: 36585724 PMCID: PMC9805247 DOI: 10.1186/s13071-022-05609-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The family Capillariidae is a group of thread-like nematodes of 27 genera and over 300 species that infect a great variety of hosts including humans. Among these, some taxa such as the genus Aonchotheca have remained controversial regarding their systematic status for decades. The aim of the current study was to verify Aonchotheca's systemic status and to further determine whether it is a distinct genus from Capillaria using molecular and phylogenetic analyses. RESULTS We sequenced the mitochondrial (mt) genome and nuclear small subunit (18S) rRNA gene of Aonchotheca putorii, a representative species of the genus, and investigated its systematic status in Trichinellida using maximum likelihood and Bayesian inference. The differences in amino acid sequences of 13 protein-coding genes were 12.69-67.35% among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillaria with cox1 (12.69%) and atp8 (67.35%) as the most and the least conserved gene, respectively, and the difference of two mt rRNAs was 18.61-34.15%. Phylogenetic analyses of the complete mt genome and 18S rRNAs unequivocally showed that Aonchotheca was a distinct genus from Capillaria. CONCLUSIONS Large difference exists among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillarias. Aonchotheca putorii is the first species in the genus Aonchotheca for which a complete mitogenome has been sequenced. These data are useful for phylogenetics, systematics and the evolution of Capillariidae.
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Affiliation(s)
- Yuan-Ping Deng
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Suleman
- grid.502337.00000 0004 4657 4747Department of Zoology, University of Swabi, Swabi, 23561 Khyber Pakhtunkhwa Pakistan
| | - Xue-Ling Zhang
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Rong Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Le-Yan Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Yi-Tian Fu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Guo-Hua Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Chaoqun Yao
- grid.412247.60000 0004 1776 0209Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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10
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Pereira FB, González-Solís D. Review of the parasitic nematodes of marine fishes from off the American continent. Parasitology 2022; 149:1928-1941. [PMID: 36076284 PMCID: PMC11010509 DOI: 10.1017/s0031182022001287] [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: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 12/29/2022]
Abstract
The ichthyofauna of the Atlantic and Pacific coasts off the American continent is very rich. Consequently, a high biodiversity of nematodes parasitizing these vertebrates is also expected. Currently, data on nematode parasites of marine fish off the Americas are fragmented. A review of all adult nematode species reported parasitizing marine fish from off the American continent is herein presented, as well as comments on their patterns of diversity, life cycles and advances in the taxonomic and phylogenetic knowledge. A total of 209 valid species, 19 species inquirendae and 6 dubious records have been recorded, the majority from the fish taxa Eupercaria and Perciformes. The families Sciaenidae, Serranidae and Lutjanidae, as well as the tropical and temperate Atlantic waters, exhibited the highest records of parasitic nematodes. The Cucullanidae, Philometridae and Cystidicolidae were the most speciose families of nematodes, which may be related to technological advances and relatively recent efforts of taxonomists, resulting in description of new taxa and the resolution of taxonomic problems. Numerous taxonomic questions still need resolution and, even though genetic data have been important for this process, the database is very scarce. This is the first review on all currently known nematode species parasitizing marine fish off the Americas and may serve as an important basis of reference for future approaches on these organisms.
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Affiliation(s)
- Felipe B. Pereira
- Department of Parasitology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - David González-Solís
- El Colegio de la Frontera Sur, Unidad Chetumal, Av. Centenario km 5.5, C.P. 77014, Chetumal, Quintana Roo, Mexico
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Tihelka E, Howard RJ, Cai C, Lozano-Fernandez J. Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization. BIOLOGY 2022; 11:biology11101516. [PMID: 36290419 PMCID: PMC9598930 DOI: 10.3390/biology11101516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 01/24/2023]
Abstract
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian-Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian-Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental "Cambrian explosion" a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian-Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land.
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Affiliation(s)
- Erik Tihelka
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Richard J. Howard
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Chenyang Cai
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jesus Lozano-Fernandez
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- Department of Genetics, Microbiology and Statistics & Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Spain
- Correspondence:
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12
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Tchesunov AV, Nikolaeva OV, Rusin LY, Sanamyan NP, Panina EG, Miljutin DM, Gorelysheva DI, Pegova AN, Khromova MR, Mardashova MV, Mikhailov KV, Yushin VV, Petrov NB, Lyubetsky VA, Nikitin MA, Aleoshin VV. Paraphyly of Marimermithida refines primary routes of transition to parasitism in roundworms. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Parasitic life-strategies in the phylum Nematoda (roundworms) are remarkably diverse and intricate in terms of evolution and taxonomy. By analysing novel rDNA data obtained on rare host-associated groups with unusual biology, we reveal paraphyly of the last major taxon with uncertain higher-rank classification that united solely parasitic nematodes (Marimermithida) to show that primarily marine parasitism only emerged independently and repeatedly in a few free-living lineages. We report secondary seaward ingression of land-based parasites (Mermithida) via invading hosts in the subtidal zone to illustrate the host-borne scenario of oceanic fish and mammal colonization by primarily terrestrial parasites (Spiruria). We also present the first molecular data on marine nematodes from unicellular hosts (foraminiferan protozoans) to demonstrate the independent origins of exploitative nematode associations at a microscopic scale. We argue that, in contrast with primarily intestinal associations arising from saprotrophy and commensalism, non-intestinal host capture (colonization of host body cavity or internal organs) is likely to be a primary route of transition to truly exploitative parasitism in roundworms. Predispositions to host capture in nematode morphology, ecology and life cycles imply its evolution as part of innate pre-adaptations to crossing environmental boundaries to enable multiple successful transitions to parasitism in the phylum history.
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Affiliation(s)
- Alexei V Tchesunov
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Olga V Nikolaeva
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Leonid Yu Rusin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Nadezda P Sanamyan
- Kamchatka Branch of Pacific Geographical Institute, Far Eastern Branch of the Russian Academy of Sciences , Petropavlovsk-Kamchatsky , Russia
| | - Elena G Panina
- Kamchatka Branch of Pacific Geographical Institute, Far Eastern Branch of the Russian Academy of Sciences , Petropavlovsk-Kamchatsky , Russia
| | | | - Daria I Gorelysheva
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences , Moscow , Russia
| | - Anna N Pegova
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Maria R Khromova
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Maria V Mardashova
- Marine Research Center, Lomonosov Moscow State University , Moscow , Russia
| | - Kirill V Mikhailov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Vladimir V Yushin
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences , Vladivostok , Russia
| | - Nikolai B Petrov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Vassily A Lyubetsky
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Mikhail A Nikitin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Vladimir V Aleoshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
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13
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Okamura B, Gruhl A, De Baets K. Evolutionary transitions of parasites between freshwater and marine environments. Integr Comp Biol 2022; 62:345-356. [PMID: 35604852 DOI: 10.1093/icb/icac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Evolutionary transitions of organisms between environments have long fascinated biologists but attention has focused almost exclusively on free-living organisms and challenges to achieve such transitions. This bias requires addressing because parasites are a major component of biodiversity. We address this imbalance by focusing on transitions of parasitic animals between marine and freshwater environments. We highlight parasite traits and processes that may influence transition likelihood (e.g. transmission mode, life cycle, host use), and consider mechanisms and directions of transitions. Evidence for transitions in deep time and at present are described, and transitions in our changing world are considered. We propose that environmental transitions may be facilitated for endoparasites because hosts reduce exposure to physiologically challenging environments and argue that adoption of an endoparasitic lifestyle entails an equivalent transitioning process as organisms switch from living in one environment (e.g. freshwater, seawater, or air) to living symbiotically within hosts. Environmental transitions of parasites have repeatedly resulted in novel forms and diversification, contributing to the tree of life. Recognising the potential processes underlying present-day and future environmental transitions is crucial in view of our changing world and the current biodiversity crisis.
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Affiliation(s)
- Beth Okamura
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | | | - Kenneth De Baets
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
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14
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Ahmed M, Roberts NG, Adediran F, Smythe AB, Kocot KM, Holovachov O. Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.769565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina, Rhabditina, and Tylenchina separately, and by analyzing a selection of species from the whole phylum Nematoda. The phylogeny of Trichinellida supported the division of Trichinella into encapsulated and non-encapsulated species and placed them as sister to Trichuris. The Spirurina subtree supported the clades formed by species from Ascaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea. The analysis of Tylenchina supported a clade that included all sampled species from Tylenchomorpha and placed it as sister to clades that included sampled species from Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis that postulates the single origin of the stomatostylet. The Rhabditina subtree placed a clade composed of all sampled species from Diplogastridae as sister to a lineage consisting of paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a clade composed of sampled species belonging to Strongylida. It also strongly supported all suborders within Strongylida. In the phylum-wide analysis, a clade composed of all sampled species belonging to Enoplia were consistently placed as sister to Dorylaimia + Chromadoria. The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida.
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Ahmed M, Holovachov O. Twenty Years after De Ley and Blaxter-How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda? Animals (Basel) 2021; 11:3479. [PMID: 34944255 PMCID: PMC8697950 DOI: 10.3390/ani11123479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/21/2022] Open
Abstract
Molecular phylogenetics brought radical changes to our understanding of nematode evolution, resulting in substantial modifications to nematode classification implemented by De Ley and Blaxter and widely accepted now. Numerous phylogenetic studies were subsequently published that both improved and challenged this classification. Here we present a summary of these changes. We created cladograms that summarise phylogenetic relationships within Nematoda using phylum-wide to superfamily-wide molecular phylogenies published in since 2005, and supplemented with the phylogenetic analyses for Enoplia and Chromadoria with the aim of clarifying the position of several taxa. The results show which parts of the Nematode tree are well resolved and understood, and which parts require more research, either by adding taxa that have not been included yet (increasing taxon coverage), or by changing the phylogenetic approach (improving data quality, using different types of data or different methods of analysis). The currently used classification of the phylum Nematoda in many cases does not reflect the phylogeny and in itself requires numerous improvements and rearrangements.
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Affiliation(s)
| | - Oleksandr Holovachov
- Department of Zoology, Swedish Museum of Natural History, 114 18 Stockholm, Sweden;
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17
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Kolicka M, Dabert M, Olszanowski Z, Dabert J. Sweet or salty? The origin of freshwater gastrotrichs (Gastrotricha, Chaetonotida) revealed by molecular phylogenetic analysis. Cladistics 2021; 36:458-480. [PMID: 34618974 DOI: 10.1111/cla.12424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2020] [Indexed: 11/29/2022] Open
Abstract
Chaetonotidae is the most diverse and widely distributed family of the order Chaetonotida (Gastrotricha) and includes both marine and freshwater species. Although the family is regarded as a sister taxon to the exclusively marine Xenotrichulidae, the type of environment, marine or freshwater, where Chaetonotidae originated is still not known. Here, we reconstructed the phylogeny of the family based on molecular sequence data and mapped both morphological and ecological characters to determine the ancestral environment of the first members of the family. Our results revealed that the freshwater genus Bifidochaetus is the earliest branching lineage in the paraphyletic Chaetonotidae (encompassing Dasydytidae and Neogosseidae). Moreover, we reconstructed Lepidochaetus-Cephalionotus clade as a monophyletic sister group to the remaining chaetonotids, which supports Kisielewski's morphological based hypothesis concerning undifferentiated type of body scales as a most primary character in Chaetonotidae. We also found that reversals to marine habitats occurred independently in different Chaetonotidae lineages, thus marine species in the genera Heterolepidoderma, Halichaetonotus, Aspidiophorus and subgenera Chaetonotus (Schizochaetonotus) or Chaetonotus (Marinochaetus) should be assumed as having secondarily invaded the marine environment. Character mapping revealed a series of synapomorphies that define the clade that includes Chaetonotidae (with Dasydytidae and Neogosseidae), the most important of which may be those linked to reproduction.
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Affiliation(s)
- Małgorzata Kolicka
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Ziemowit Olszanowski
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Jacek Dabert
- Department of Animal Morphology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
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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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