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Nitta M. Capsalid monogeneans of fishes from the Seto Inland Sea, Japan: Description of Benedenia kobudai n. sp. parasitic on Semicossyphus reticulatus (Perciformes: Labridae). Parasitol Int 2023; 92:102677. [DOI: 10.1016/j.parint.2022.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/24/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022]
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Gastineau R, Bouguerche C, Tazerouti F, Justine JL. Morphological and molecular characterisation of Tristoma integrum Diesing, 1850 (Monogenea, Capsalidae), including its complete mitogenome. Parasite 2023; 30:16. [PMID: 37191588 DOI: 10.1051/parasite/2023016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Capsalids are monopisthocotylean monogenean parasites found on the skin and gills of fish. Capsalines (subfamily Capsalinae) are large-sized capsalids, parasitic on highly prized gamefish, and species of Tristoma parasitise only the gills of swordfish (Xiphias gladius). We obtained specimens of Tristoma integrum Diesing, 1850 from swordfish collected off Algeria in the Mediterranean Sea. Here, we describe the specimens, including the key systematics characters of dorsolateral body sclerites. One specimen was used for a next generation sequencing analysis but a part of it, including the sclerites, was mounted on a permanent slide, drawn, and deposited in a curated collection. We characterised the complete mitogenome, the ribosomal cluster (including 18S and 28S) and additional genes such as Elongation factor 1 alpha (EF1α) and Histone 3. We also retrieved molecular information from the host tissue present in the gut of the monogenean and provide the sequence of the complete rRNA cluster of the host, X. gladius. The mitogenome of T. integrum is 13 968 bp in length and codes for 12 protein, 2 rRNA and 22 tRNA. Phylogenies of capsalids were generated from 28S sequences and concatenated mitochondrial protein-coding genes, respectively. In the 28S phylogeny, most subfamilies based on morphology were not found to be monophyletic, but the Capsalinae were monophyletic. In both phylogenies, the closest member to Tristoma spp. was a member of the Capsaloides. In an Appendix, we report the complex nomenclatural history of Tristoma Cuvier, 1817 and its species.
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Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, 70-383 Szczecin, Poland
| | - Chahinez Bouguerche
- Department of Zoology, Swedish Museum of Natural History Naturhistoriska riksmuseet, Stockholm, Sweden
| | - Fadila Tazerouti
- Université des Sciences et de la Technologie Houari Boumédiène, Faculté des Sciences Biologiques, Laboratoire de Biodiversité et Environnement: Interactions - Génomes, BP 32, El Alia Bab Ezzouar, Alger, Algérie
| | - Jean-Lou Justine
- Institut Systématique Évolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005 Paris, France
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Yang C, Shan B, Liu Y, Wang L, Wu Q, Luo Z, Sun D. Complete Mitochondrial Genome of Two Ectoparasitic Capsalids (Platyhelminthes: Monogenea: Monopisthocotylea): Gene Content, Composition, and Rearrangement. Genes (Basel) 2022; 13:genes13081376. [PMID: 36011287 PMCID: PMC9407395 DOI: 10.3390/genes13081376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 12/10/2022] Open
Abstract
The capsalid monogeneans are important pathogens that generally infect marine fishes and have a substantial impact on fish welfare in aquaculture systems worldwide. However, the current mitogenome information on capsalids has received little attention, limiting the understanding of their evolution and phylogenetic relationships with other monogeneans. This paper reports the complete mitochondrial genomes of Capsala katsuwoni and Capsala martinieri for the first time, which we obtained using a next-generation sequencing method. The mitogenomes of C. katsuwoni and C. martinieri are 13,265 and 13,984 bp in length, respectively. Both species contain the typical 12 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The genome compositions show a moderate A+T bias (66.5% and 63.9% for C. katsuwoni and C. martinieri, respectively) and exhibit a negative AT skew but a positive GC skew in both species. One gene block rearrangement was found in C. katsuwoni in comparison with other capsalid species. Instead of being basal to the Gyrodactylidea and Dactylogyridea or being clustered with Dactylogyridea, all species of Capsalidea are grouped into a monophyletic clade. Our results clarify the gene rearrangement process and evolutionary status of Capsalidae and lay a foundation for further phylogenetic studies of monogeneans.
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Affiliation(s)
- Changping Yang
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Binbin Shan
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Yan Liu
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Liangming Wang
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Qiaer Wu
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Zhengli Luo
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
- School of Fisheries of Zhejiang Ocean University, Zhoushan 316022, China
| | - Dianrong Sun
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
- Correspondence:
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Liu H, Fu Z, Zhou S, Hu J, Yang R, Yu G, Ma Z. The Complete Mitochondrial Genome of Pennella sp. Parasitizing Thunnus albacares. Front Cell Infect Microbiol 2022; 12:945152. [PMID: 35846765 PMCID: PMC9280153 DOI: 10.3389/fcimb.2022.945152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
In the study, the parasite from the yellowfin tuna (Thunnus albacares) was separated, and morphological observation and molecular identification were carried out. Our results showed that the parasite was similar to Pennella sp. Its cephalothorax was covered by spherical to spherical non-branched nipples of almost the same size, which were very similar in shape and arrangement. A pair of slightly larger, the unbranched antenna was present on the outer margin of the small papillae-covered area. The gene sequence of COX1 with a length of 1,558 bp in the mitochondria of the parasite was 100% similar to Pennella sp. (MZ934363). The mitochondrial genome had a total length of 14,620 bp. It consisted of 36 genes (12 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs) and a dummy control region, but the mitochondrial genome had no ATP8 gene. Morphological observation showed that Pennella sp. was dark red, with a convex cephalothorax, with a total length of 8.42 cm, parasitic on the dorsal side of yellowfin tuna. Pennella sp. included the cephalothorax, neck, trunk, abdomen and egg belt. This study was the first report on the mitochondrial genome of Pennella sp. The results provide basic data for further identifying the parasites of Pennella genus.
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Affiliation(s)
- Hongyan Liu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Zhengyi Fu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Shengjie Zhou
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Jing Hu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Rui Yang
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Gang Yu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Zhenhua Ma
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, China
- Sanya Tropical Fisheries Research Institute, Sanya, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- *Correspondence: Zhenhua Ma,
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Cháves-González LE, Morales-Calvo F, Mora J, Solano-Barquero A, Verocai GG, Rojas A. What lies behind the curtain: Cryptic diversity in helminth parasites of human and veterinary importance. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2022; 2:100094. [PMID: 35800064 PMCID: PMC9253710 DOI: 10.1016/j.crpvbd.2022.100094] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Parasite cryptic species are morphologically indistinguishable but genetically distinct organisms, leading to taxa with unclear species boundaries. Speciation mechanisms such as cospeciation, host colonization, taxon pulse, and oscillation may lead to the emergence of cryptic species, influencing host-parasite interactions, parasite ecology, distribution, and biodiversity. The study of cryptic species diversity in helminth parasites of human and veterinary importance has gained relevance, since their distribution may affect clinical and epidemiological features such as pathogenicity, virulence, drug resistance and susceptibility, mortality, and morbidity, ultimately affecting patient management, course, and outcome of treatment. At the same time, the need for recognition of cryptic species diversity has implied a transition from morphological to molecular diagnostic methods, which are becoming more available and accessible in parasitology. Here, we discuss the general approaches for cryptic species delineation and summarize some examples found in nematodes, trematodes and cestodes of medical and veterinary importance, along with the clinical implications of their taxonomic status. Lastly, we highlight the need for the correct interpretation of molecular information, and the correct use of definitions when reporting or describing new cryptic species in parasitology, since molecular and morphological data should be integrated whenever possible.
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Affiliation(s)
- Luis Enrique Cháves-González
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Fernando Morales-Calvo
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Javier Mora
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Alberto Solano-Barquero
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Guilherme G. Verocai
- Department of Veterinary Pathobiology, Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
| | - Alicia Rojas
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
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Baeza JA, García-De León FJ. Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis. BMC Genomics 2022; 23:320. [PMID: 35459089 PMCID: PMC9027416 DOI: 10.1186/s12864-022-08482-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Background Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within-species genealogical and among-species phylogenetic relationships. Most often, ‘primer walking’ or ‘long PCR’ strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we first confirmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a ‘gold’ standard reference mitochondrial chromosome assembled using Illumina short-reads sequencing. Results Using a specialized bioinformatics tool, we first produced a short-reads mitochondrial genome assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705 bp in length and 934 bp shorter than a previously assembled genome (17,639 bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based workflows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the flanks of homopolymer regions explained most of the dissimilarities observed between the ‘gold’ standard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochondrial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitochondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species. Conclusions This study confirms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fin fishing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fishery. This study will also assist with the transferring of high-throughput sequencing technology to middle- and low-income countries so that international scientists can explore population genomics in sharks using inclusive research strategies. Lastly, we recommend assembling mitochondrial genomes using specialized assemblers instead of other assemblers developed for bacterial and/or nuclear genomes.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile.
| | - F J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur, Mexico
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Benovics M, Gettová L, Šimková A. De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea): Revealing the phylogeographic pattern of population structure in the generalist parasite Dactylogyrus vistulae. Ecol Evol 2021; 11:16585-16599. [PMID: 34938459 PMCID: PMC8668815 DOI: 10.1002/ece3.8230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022] Open
Abstract
Approaches using microsatellite markers are considered the gold standard for modern population genetic studies. However, although they have found application in research into various platyhelminth taxa, they remained substantially underutilized in the study of monogeneans. In the present study, a newly developed set of 24 microsatellite markers was used to investigate the genetic diversity of the generalist monogenean species Dactylogyrus vistulae. The analyzed parasite specimens were collected from 13 cyprinoid species from 11 sites in the Apennine and Balkan peninsulas. A total of 159 specimens were genotyped at each of the loci and the number of alleles per locus ranged from 2 to 16, with a mean number of 6.958 alleles per locus. Exceptionally high genetic diversity was observed among D. vistulae individuals in the southern Balkans (mean N A per locus = 3.917), suggesting that generalist D. vistulae expanded from the south to the north in the Balkans and later into central Europe. The initial clustering analysis divided all investigated specimens into three major clusters; however, the results of the subsequent analyses revealed the existence of various subpopulations, suggesting that the population structure of D. vistulae is associated with the diversification of their cyprinoid hosts. In addition, the partition of the parasite population was observed in regions of the sympatric occurrence of two host species, indicating that these hosts may represent a barrier for gene flow, even for generalist parasite species.
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Affiliation(s)
- Michal Benovics
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Lenka Gettová
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
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Nitta M. Capsalids (Platyhelminthes: Monogenea) from marine fishes off Okinawa in Japan with the proposal of two new genera. Parasitol Int 2021; 85:102448. [PMID: 34481081 DOI: 10.1016/j.parint.2021.102448] [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] [Received: 06/18/2021] [Revised: 08/29/2021] [Accepted: 08/29/2021] [Indexed: 11/26/2022]
Abstract
Molecular studies of the Capsalidae suggested that the genus Benedenia is polyphyletic, but a taxonomic organization of the genus that reflects molecular data has not yet been proposed. As a result of molecular analysis (28S rDNA, ITS1-5.8S-ITS2, and cox1 data) including specimens of Benedeniinae newly obtained from Okinawa-jima Island in Japan, two new genera and the revival of Tareenia independent to the genus Benedenia are proposed. Gracilobenedenia n. gen. is distinguished from the other genera of Benedeniinae based on morphological characteristics. This new genus comprises 6 species: G. lutjani n. comb. (type species), G. anticavaginata n. comb., G. rohdei n. comb., G. beverleyburtonae n. comb., G. kuremibai n. gen., n. sp., and G. hichi n. gen., n. sp. Armatobenedenia n. gen. is a monotypic genus for A. armata n. comb. The present molecular phylogenetic analysis showed the independence of Tareenia, and it can be morphologically separated from the other benedeniines. Four species including two new species obtained from Okinawa-jima Island are reported: G. kuremibai n. sp., G. hichi n. sp., G. lutjani n. comb., and Metabenedeniella parva. Furthermore, in the species identification and phylogenetic analysis of capsalids, the usefulness of not only the 28S rDNA but also ITS and the cox1 regions was suggested. These genes were evaluated the efficacy of those regions in DNA barcoding, and the ITS and cox1 regions shown to be useful for DNA barcoding in capsalids compared to the 28S rDNA sequence.
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Affiliation(s)
- Masato Nitta
- Setouchi Parasite Biodiversity Laboratory, 3-2-20-103, Ushita-Honmachi, Higashi-ku, Hiroshima 732-0066, Japan; Laboratory of Bioresources, National Institute for Basic Biology, 38, Nishigonaka, Myodaiji, Okazaki, Aichi 444-8787, Japan.
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First Report of Blood Fluke Pathogens with Potential Risk for Emerging Yellowtail Kingfish ( Seriola lalandi) Aquaculture on the Chilean Coast, with Descriptions of Two New Species of Paradeontacylix (Aporocotylidae). Pathogens 2021; 10:pathogens10070849. [PMID: 34357999 PMCID: PMC8308527 DOI: 10.3390/pathogens10070849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022] Open
Abstract
Blood flukes are digeneans that infect wild and farmed fish that can cause a severe and potentially lethal disease in farmed fish. These parasites are undetectable in the larval stage based on macroscopic observations in the definitive host with the infection becoming evident when eggs accumulate in the branchial vessels. There are nine known species of the genus Paradeontacylix and seven exclusively parasitize Seriola spp. from several geographical areas. Seriola lalandi aquaculture farms are emerging at various localities in northern Chile. Here, we report, for the first time, two blood fluke species parasitizing S. lalandi in the Southeastern Pacific (Chile). In the laboratory, the gills and heart of fish were removed. The retained blood flukes were separated according to the infection site, fixed in 70% or 95% ethanol for taxonomic and molecular analysis, respectively. Morphometrical differences among the fluke species were evaluated with a principal component analysis (PCA) using proportional body measurements. Phylogenetic trees were constructed based on 28S rDNA, cox1 mDNA using Bayesian inference (BI), and maximum likelihood (ML). Based on morphology, morphometry, and molecular analyses, two new species are proposed: P. humboldti n. sp. from the gills and P. olivai n. sp. from the heart of S. lalandi. Both were clearly distinguished from other species of Paradeontacylix by a combination of morphologic features (posterior tegumental spines, testes arrangement, body size). The genetic distance (based on cox1) among species was >10%. P. humboldti n. sp. and P. olivai n. sp. are sister species (with a common ancestor) independent of P. godfreyi from S. lalandi in Australia. The newly identified parasites may pose a risk to farmed S. lalandi as aporocotylids have been the cause of diseases in farmed fish from other geographical areas. In addition, some cages of S. lalandi are currently maintained in an open circulating system, which could favor the transmission of these parasites (if involved hosts are present in the environment).
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Park JC, Kim DH, Kim MS, Hagiwara A, Lee JS. The genome of the euryhaline rotifer Brachionus paranguensis: Potential use in molecular ecotoxicology. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100836. [PMID: 33940320 DOI: 10.1016/j.cbd.2021.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Brachionus spp. rotifers have been proposed as model organisms for ecotoxicological studies. We analyzed the whole-genome sequence of B. paranguensis through NextDenovo, resulting in a total length of 106.2 Mb and 71 contigs. The N50 and the GC content were 4.13 Mb and 28%, respectively. A total of 18,501 genes were predicted within the genome of B. paranguensis. Prominent detoxification-related gene families of phase I and II detoxifications have been investigated. In parallel with other Brachionus rotifers, high gene expansion was observed in CYP clan 3 and GST sigma class in B. paranguensis. Moreover, species-specific expansion of sulfotransferase (SULTs) and gain of UDP-glucuronosyltransferases (UGTs) through horizontal gene transfer has been specifically found within B. plicatilis complex. This whole-genome analysis of B. paranguensis provides a basis for molecular ecotoxicological studies and provides useful information for comparative studies of the evolution of detoxification mechanisms in Brachionus spp.
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Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Baeza JA, González MT. A first look at the 'repeatome' of Benedenia humboldti, a major pathogen in yellowtail aquaculture: Repetitive element characterization, nuclear rRNA operon assembly, and microsatellite discovery. Mar Genomics 2021; 58:100848. [PMID: 34217484 DOI: 10.1016/j.margen.2021.100848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 11/19/2022]
Abstract
The monogenean Benedenia humboldti is a pathogen of the yellowtail Seriola lalandi in the South-Eastern Pacific ocean. Using low-coverage short Illumina 150bp pair-end reads sequencing, this study examines, for the first time, the 'repeatome' (= repetitive genomic elements), including the 45S ribosomal RNA DNA operon and microsatellites, in B. humboldti. Repetitive elements comprised a large fraction of the nuclear genome and a considerable proportion of them could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to the 45S ribosomal RNA operon or were classified as satellite DNA and Class I - Long Interspersed Nuclear Elements (LINEs) which were considerably more abundant than Class I - LTR elements. The ribosomal RNA gene operon in B. humboldti is comprised of, in the following order, a 5' ETS (length = 233 bp), ssrDNA (2082 bp), ITS1 (346 bp), 5.8S rDNA (150 bp), ITS2 (572 bp), lsrDNA (3887 bp), and a 3' ETS (1097 bp). A total of 15 SSRs were identified. These newly developed genomic resources will contribute to the better understanding of meta-population connectivity in this species, cryptic species in the genus, and will advance pest management strategies.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949, USA; Departamento de Biología Marina, Universidad Católica del Norte, Larrondo 1281, Coquimbo, IV Region, Chile.
| | - Maria Teresa González
- Laboratorio Eco-parasitologia y Epidemiologia Marina (LEPyEM), Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile.
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Caña-Bozada V, Llera-Herrera R, Fajer-Ávila EJ, Morales-Serna FN. Mitochondrial genome of Scutogyrus longicornis (Monogenea: Dactylogyridea), a parasite of Nile tilapia Oreochromis niloticus. Parasitol Int 2021; 81:102281. [PMID: 33401015 DOI: 10.1016/j.parint.2020.102281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Víctor Caña-Bozada
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán 82112, Sinaloa, Mexico.
| | - Raúl Llera-Herrera
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán 82040, Sinaloa, Mexico.
| | - Emma J Fajer-Ávila
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán 82112, Sinaloa, Mexico.
| | - F Neptalí Morales-Serna
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán 82112, Sinaloa, Mexico; Consejo Nacional de Ciencia y Tecnología (CONACYT), Ciudad de México, Mexico.
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Baeza JA. Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus. BMC Genomics 2020; 21:882. [PMID: 33297960 PMCID: PMC7726883 DOI: 10.1186/s12864-020-07292-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022] Open
Abstract
Background Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ‘primer walking’ or ‘long PCR’ followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a ‘gold’ standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region. Results LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not ‘perfect’, phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder. Conclusions This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Tang Y, Zheng X, Liu H, Sunxie F. Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (Cephalopoda: Octopodidae). Genomics 2020; 112:3893-3902. [PMID: 32603760 DOI: 10.1016/j.ygeno.2020.06.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 12/28/2022]
Abstract
This study presented 96 cox1 and 76 cox3 genes of Amphioctopus neglectus populations. Three distinct lineages were formed from phylogenetic trees and networks constructed using haplotypes. Mitogenomes of A. neglectus-a and A. neglectus-b as the representatives of two lineages separated from population genetics were sequenced to compare with A. neglectus at the genome-level. Amphioctopus neglectus-a showed significant differences with A. neglectus, mainly reflected in gene length, intergenic regions and the secondary structure of tandem repeat motifs. Notably, two sequence deletions in mitogenomes of the two representative species were detected in different positions of major non-coding regions, which were the most distinct differences with A. neglectus. Pairwise genetic distances and the phylogenetic analysis supported the relationship of (A. neglectus-a + (A. neglectus + A. neglectus-b)). This study suggested that A. neglectus-a should be considered as a potential cryptic species of this complex, while A. neglectus-b needed further verification to be defined.
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Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China.
| | - Haijuan Liu
- Guangxi Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai 536000, China
| | - Feige Sunxie
- Dongshan Boguangtianxing Foods Co., Ltd., Zhangzhou 363000, China
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Ma X, Agudelo P, Richards VP, Baeza JA. The complete mitochondrial genome of the Columbia lance nematode, Hoplolaimus columbus, a major agricultural pathogen in North America. Parasit Vectors 2020; 13:321. [PMID: 32571423 PMCID: PMC7310197 DOI: 10.1186/s13071-020-04187-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/13/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America. This study describes, for the first time, the complete mitochondrial genome of H. columbus from South Carolina, USA. METHODS The mitogenome of H. columbus was assembled from Illumina 300 bp pair-end reads. It was annotated and compared to other published mitogenomes of plant-parasitic nematodes in the superfamily Tylenchoidea. The phylogenetic relationships between H. columbus and other 6 genera of plant-parasitic nematodes were examined using protein-coding genes (PCGs). RESULTS The mitogenome of H. columbus is a circular AT-rich DNA molecule 25,228 bp in length. The annotation result comprises 12 PCGs, 2 ribosomal RNA genes, and 19 transfer RNA genes. No atp8 gene was found in the mitogenome of H. columbus but long non-coding regions were observed in agreement to that reported for other plant-parasitic nematodes. The mitogenomic phylogeny of plant-parasitic nematodes in the superfamily Tylenchoidea agreed with previous molecular phylogenies. Mitochondrial gene synteny in H. columbus was unique but similar to that reported for other closely related species. CONCLUSIONS The mitogenome of H. columbus is unique within the superfamily Tylenchoidea but exhibits similarities in both gene content and synteny to other closely related nematodes. Among others, this new resource will facilitate population genomic studies in lance nematodes from North America and beyond.
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Affiliation(s)
- Xinyuan Ma
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634 USA
| | - Paula Agudelo
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634 USA
| | - Vincent P. Richards
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634 USA
| | - J. Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634 USA
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949 USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
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Roudnický P, Potěšil D, Zdráhal Z, Gelnar M, Kašný M. Laser capture microdissection in combination with mass spectrometry: Approach to characterization of tissue-specific proteomes of Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea). PLoS One 2020; 15:e0231681. [PMID: 32555742 PMCID: PMC7299319 DOI: 10.1371/journal.pone.0231681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Eudiplozoon nipponicum (Goto, 1891) is a hematophagous monogenean ectoparasite which inhabits the gills of the common carp (Cyprinus carpio). Heavy infestation can lead to anemia and in conjunction with secondary bacterial infections cause poor health and eventual death of the host. This study is based on an innovative approach to protein localization which has never been used in parasitology before. Using laser capture microdissection, we dissected particular areas of the parasite body without contaminating the samples by surrounding tissue and in combination with analysis by mass spectrometry obtained tissue-specific proteomes of tegument, intestine, and parenchyma of our model organism, E. nipponicum. We successfully verified the presence of certain functional proteins (e.g. cathepsin L) in tissues where their presence was expected (intestine) and confirmed that there were no traces of these proteins in other tissues (tegument and parenchyma). Additionally, we identified a total of 2,059 proteins, including 72 peptidases and 33 peptidase inhibitors. As expected, the greatest variety was found in the intestine and the lowest variety in the parenchyma. Our results are significant on two levels. Firstly, we demonstrated that one can localize all proteins in one analysis and without using laboratory animals (antibodies for immunolocalization of single proteins). Secondly, this study offers the first complex proteomic data on not only the E. nipponicum but within the whole class of Monogenea, which was from this point of view until recently neglected.
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Affiliation(s)
- Pavel Roudnický
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail:
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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