First description of a new cryptic species, Simulium vanluni from Peninsular Malaysia: An integrated morpho-taxonomical and genetic approach for naming cryptic species in the family Simuliidae

Ya’cob, Zubaidah; Takaoka, Hiroyuki; Low, Van Lun; Sofian‐Azirun, Mohd

doi:10.1016/j.actatropica.2016.12.009

Cited by 18 publications

(6 citation statements)

References 23 publications

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“…Indeed, mitochondrial genes, such as cox1, cox2 and rns, are being increasingly used in taxonomy, both for phylogenetic analysis 85 , and for discriminating among species with similar morphological features. For example, mtDNA genes have been employed to reveal several cryptic species in Ciliophora 86,87 and metazoan such as annelids 88 and insects 89 , or to discriminate between subspecies of the bee Apis mellifera 90 . The limited number of available mitochondrial genome sequences of ciliates currently does not permit phylogenomic analyses based either on sequences or on colinearity.…”

Section: : E Alatus E Antarcticus E Balteatus E Charon E Crementioning

confidence: 99%

Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov.

Serra

Gammuto

Nitla

et al. 2020

Sci Rep

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Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as “holobionts”. We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont “Candidatus Pinguicoccus supinus” gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.

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Section: : E Alatus E Antarcticus E Balteatus E Charon E Crementioning

confidence: 99%

Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov.

Serra

Gammuto

Nitla

et al. 2020

Sci Rep

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“…Indeed, mitochondrial genes, such as cox1, cox2 and rns, are being increasingly used in taxonomy, both for phylogenetic analysis (Dumilag et al 2018), and for discriminating between species with similar morphological features. For example, mtDNA genes have been employed to reveal several cryptic species in Ciliophora (Barth et al 2006;Doerder 2019) and metazoan such as annelids (Nygren et al 2018) and insects (Ya'cob et al 2017), or to discriminate between subspecies of the bee Apis mellifera (Ilyasov et al 2016). The limited number of available mitochondrial genome sequences of ciliates currently does not allow to perform phylogenetic analyses based neither on sequences nor on colinearity.…”

Section: Mitochondrial Genomementioning

confidence: 99%

Next generation taxonomy: integrating traditional species description with the holobiont concept and genomic approaches - The in-depth characterization of a novelEuplotesspecies as a case study

Serra

Gammuto

Nitla

et al. 2019

Preprint

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In 1991 Margulis defined holobionts as the assemblage of "two or more organisms, members of different species" which remain associate "throughout a significant portion of the life history". In recent times, holobionts have been described among many and far-related groups of living beings, such as plants, algae, insects, corals, and even humans. These studies have arisen an increasing interest in different contexts but, to our knowledge, the holobiont concept has not been applied in taxonomy. Here we propose a new approach to modern taxonomy, aimed to integrate the holobiont concept and genomic and bioinformatic analyses with the classical/morphological tools traditionally used in taxonomy. The inclusion of symbiont morphology, and of mitochondrial and symbiont genomes will allow the discipline to move toward what could become the "next generation taxonomy". As an example of this new paradigm in the characterization of holobionts, we herein provide the taxonomic description of the ciliate protist Euplotes vanleeuwenhoeki sp. nov. (Euplotia, Ciliophora) and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. (Opitutae, Verrucomicrobia). Interestingly, we found that this endosymbiont has an extremely reduced genome (~163 Kbp), which is suggestive of a high integration with the host and represents the first case of such an extreme reduction in Verrucomicrobia, and the first case in a protist host.University of Pisa PRA_2018_63 project (to GP); the Italian Ministry of Education, University and Research (MIUR): Dipartimenti di Eccellenza Program (2018-2022) -

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“…Coupled with other taxonomic approaches, DNA barcoding also complements the description of cryptic species. Some notable examples include the description of S. ( N. ) pairoti from S. ( N. ) feuerborni [ 26 ] and the naming of S. ( S. ) nobile cryptic species in Peninsular Malaysia as S. ( S. ) vanluni [ 27 ]. Additionally, S. ( S. ) rufibasis Brunetti in Japan and Korea was revised as S. ( S. ) yamatoense Takaoka, Adler & Fukuda after the morphological, chromosomal and molecular re-examinations of the species [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia

Hew,

Ya’cob,

Adler

et al. 2023

Parasites Vectors

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Background DNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Methods Genomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested. Results The DNA barcodes successfully distinguished most morphologically distinct species (> 80% of sampled taxa). Nonetheless, high maximum intraspecific distances (3.32–13.94%) in 11 species suggested cryptic diversity. Notably, populations of the common taxa Simulium (Gomphostilbia) cheongi, S. (Gomphostilbia) sheilae, S. (Nevermannia) feuerborni and S. (Simulium) tani in the islands of Indonesia were genetically distinct from those on the Southeast Asian mainland (Malaysia and Thailand). Integrated morphological, cytogenetic and nuclear DNA studies are warranted to clarify the taxonomic status of these more complex taxa. Conclusions The findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species. Graphical abstract

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First description of a new cryptic species, Simulium vanluni from Peninsular Malaysia: An integrated morpho-taxonomical and genetic approach for naming cryptic species in the family Simuliidae

Cited by 18 publications

References 23 publications

Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov.

Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov.

Next generation taxonomy: integrating traditional species description with the holobiont concept and genomic approaches - The in-depth characterization of a novelEuplotesspecies as a case study

DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia

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