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1.
G3 (Bethesda) ; 11(2)2021 02 09.
Artículo en Inglés | MEDLINE | ID: mdl-33604668

RESUMEN

Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of "supergenes," as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.


Asunto(s)
Genoma , Caracoles , Animales , Genómica , Anotación de Secuencia Molecular , Polimorfismo Genético , Selección Genética
2.
Zoology (Jena) ; 136: 125692, 2019 10.
Artículo en Inglés | MEDLINE | ID: mdl-31655447

RESUMEN

The genus Waminoa currently contains two described species, which each contains two types of endosymbiotic algae. Waminoa individuals are basically brown in body color, derived from these algal symbionts, and their body shape has been described as "discoid to obcordate". They have been found as associates of various anthozoans (Cnidaria) in the Indo-Pacific Ocean and the Red Sea. In order to reveal the diversity of the genus Waminoa and their hosts, we conducted phylogenetic and morphological analyses on acoelomate flatworms specimens collected from Japan, Palau and Indonesia. At least 18 Waminoa morphotypes were found on at least 20 anthozoan host species, and two specimens were found on species of two sea stars. Overall, there were two main body shapes of specimens; obcordate, as seen in W. litus and W. brickneri, and the other molar-like with an elongated body. These two body shapes each represented a separate clade in 18S rDNA and mitochondrial cytochrome c oxidase subunit 1 (COI) phylogenetic trees, with W. brickneri included in the obcordate subclade. Automatic Barcode Gap Discovery (ABGD) analyses on COI sequences of our specimens revealed the presence of at least five operational taxonomic units (OTUs). These five OTUs consisted of one large group of all obcordate animals, three OTUs consisting of one specimen each within the molar-like clade, and one large group of the remaining molar-like specimens. Both clades contain numerous morphotypes and were associated with a variety of hosts. Finally, based on genetic distances, the molar-like specimens are considered as an unnamed genus group separate from Waminoa, which needs to be clarified in future studies.


Asunto(s)
Filogenia , Platelmintos/anatomía & histología , Platelmintos/clasificación , Animales , Complejo IV de Transporte de Electrones/genética , Océano Pacífico , Platelmintos/genética , ARN Ribosómico 18S/genética , Especificidad de la Especie
3.
BMC Genomics ; 13: 114, 2012 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-22448618

RESUMEN

BACKGROUND: This study describes how the complete mitogenome of a terrestrial snail, Cylindrus obtusus (Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mitogenome was obtained with Illumina GAIIx shot gun sequencing. Although the used specimen was collected relatively recently and kept in a DNA-friendly preservative (not formalin as frequently used with old museum specimens), we believe that the exclusion of PCRs as facilitated by NGS (Next Generation Sequencing) removes a great obstacle in DNA sequencing of collection specimens. A brief comparison is made between our Illumina GAIIx approach and a similar study that made use of the Roche 454-FLX platform. RESULTS: The mtDNA sequence of C. obtusus is 14,610 bases in length (about 0.5 kb larger than other stylommatophoran mitogenomes reported hitherto) and contains the 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs) typical for metazoans. Except for a swap between the position of tRNA-Pro and tRNA-Ala, the gene arrangement of C. obtusus is identical to that reported for Cepaea nemoralis. The 'aberrant' rearrangement of tRNA-Thr and COIII compared to that of other Sigmurethra (and the majority of gastropods), is not unique for C. nemoralis (subfamily Helicinae), but is also shown to occur in C. obtusus (subfamily Ariantinae) and might be a synapomorphy for the family Helicidae. CONCLUSIONS: Natural history collections potentially harbor a wealth of information for the field of evolutionary genetics, but it can be difficult to amplify DNA from such specimens (due to DNA degradation for instance). Because NGS techniques do not rely on primer-directed amplification (PCR) and allow DNA to be fragmented (DNA gets sheared during library preparation), NGS could be a valuable tool for retrieving DNA sequence data from such specimens. A comparison between Illumina GAIIx and the Roche 454 platform suggests that the former might be more suited for de novo sequencing of mitogenomes.


Asunto(s)
Genoma Mitocondrial/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Caracoles/genética , Animales , ADN Mitocondrial/genética , ADN Mitocondrial/metabolismo , Sistemas de Lectura Abierta/genética , Reacción en Cadena de la Polimerasa , ARN Ribosómico/genética , ARN de Transferencia/genética
4.
Mol Phylogenet Evol ; 61(3): 914-23, 2011 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-21930220

RESUMEN

A paper on the 'Molecular phylogeny of Western Palaearctic Helicidae s.l.', published by Steinke et al. (2004) in this journal, is critically analysed. Several obvious errors are corrected and methodological weaknesses are revealed. BLAST searches on the sequences published in that paper and now in GenBank, showed high percentages of similarity of the alleged species with taxa that are considered only distantly related in the literature. Inspection of the so-called voucher specimens showed that some shells were misidentified, whereas others contained dirt or were bleached, indicating that these had been collected empty. Obviously the sequences published for those species could not have originated from those specimens, which cannot be considered vouchers therefore, even if they are from the same locality. In other instances, spurious sequences were published for correctly identified voucher specimens. For several species for which we collected specimens ourselves, the COI or the 16S sequence, or both, clearly differed from the results published by Steinke et al. The consequences of our results for the molecular data on helicid gastropods and their classification are listed.


Asunto(s)
Bases de Datos Genéticas , Evolución Molecular , Gastrópodos/genética , Filogenia , Exoesqueleto/anatomía & histología , Animales , Regiones Árticas , Teorema de Bayes , Complejo IV de Transporte de Electrones/genética , Homología de Secuencia de Ácido Nucleico
5.
Forensic Sci Int ; 210(1-3): 91-5, 2011 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-21376487

RESUMEN

The beetle family Cholevidae (Coleoptera: Staphylinoidea), sometimes viewed as the subfamily Cholevinae of the Leiodidae, consists of some 1700 species worldwide. With the exception of specialized cave-dwelling species and species living in bird and mammal nests and burrows, the species are generalized soil-dwellers that, at least in temperate regions, are mostly found on vertebrate cadavers. Although they have been regularly reported from human corpses, and offer potential because of many species' peak activity in the cold season, they have not been a focus of forensic entomologists so far. This is probably due to their small size and the difficulty in identifying the adults and their larvae. In this paper, we show that DNA-barcoding can help make this group of necrobiont beetles available as a tool for forensic research. We collected 86 specimens of 20 species of the genera Catops, Fissocatops, Apocatops, Choleva, Nargus, Ptomaphagus, and Sciodrepoides from the Netherlands and France and show that a broad "barcoding gap" allows almost all species to be easily and unambiguously identified by the sequence of the "barcoding gene" cytochrome c oxidase I (COI). This opens up the possibility of adding Cholevidae to the set of insect taxa routinely used in forensic entomology.


Asunto(s)
Escarabajos/genética , Código de Barras del ADN Taxonómico , Complejo IV de Transporte de Electrones/genética , Animales , Entomología , Conducta Alimentaria , Patologia Forense , Humanos , Masculino , Filogenia , Reacción en Cadena de la Polimerasa , Cambios Post Mortem
6.
PLoS One ; 3(3): e1835, 2008 Mar 19.
Artículo en Inglés | MEDLINE | ID: mdl-18350170

RESUMEN

A persistent controversy surrounds the flightless island hen of Tristan da Cunha, Gallinula nesiotis. Some believe that it became extinct by the end of the 19th century. Others suppose that it still inhabits Tristan. There is no consensus about Gallinula comeri, the name introduced for the flightless moorhen from the nearby island of Gough. On the basis of DNA sequencing of both recently collected and historical material, we conclude that G. nesiotis and G. comeri are different taxa, that G. nesiotis indeed became extinct, and that G. comeri now inhabits both islands. This study confirms that among gallinules seemingly radical adaptations (such as the loss of flight) can readily evolve in parallel on different islands, while conspicuous changes in other morphological characters fail to occur.


Asunto(s)
ADN/genética , Galliformes/genética , Animales , Secuencia de Bases , Cartilla de ADN , Galliformes/clasificación , Filogenia , Reacción en Cadena de la Polimerasa
7.
Nature ; 439(7075): 409, 2006 Jan 26.
Artículo en Inglés | MEDLINE | ID: mdl-16437103

RESUMEN

Darwin was fascinated by the transportation of land snails across great swathes of open ocean by birds--he even immersed snails in sea water to see how long they would survive. Here we follow a molecular phylogenetic trail that reveals the incredible transequatorial dispersal of the land snail Balea from Europe to the Azores and the Tristan da Cunha islands, and back again. This long-distance dispersal is unexpected for what are proverbially considered the most pedestrian of creatures.


Asunto(s)
Migración Animal , Aves/fisiología , Geografía , Modelos Biológicos , Caracoles/fisiología , Animales , ADN Mitocondrial/genética , Europa (Continente) , Islandia , Filogenia , Caracoles/clasificación , Caracoles/genética
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