De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda).
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ABSTRACT:
SUBMITTER: Chueca LJ
PROVIDER: S-EPMC8496239 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Prior to this study, few collections and records were made of the land snails in Cambodia and the historical taxa had never been reviewed. Herein a report on the land snail diversity based on specimens collected recently from karstic and non-karstic areas in southern Cambodia is provided. This checklist presents 36 species of land snails (two Neritimorpha, six Caenogastropoda, and 28 Heterobranchia). Illustrations and brief taxonomic notes/remarks are provided for every species. We also described Georrisa carinata Sutcharit & Jirapatrasilp, sp. nov. based on some distinct shell morphological characters. Since the first descriptions during the colonial period in the nineteenth century, some land snail species (e.g., Trichochloritis norodomiana, Durgella russeola, Anceyoconcha siamensis obesula comb. nov., Anceyoconcha chaudoensis comb. nov., and Succinea tenuis) have not been reported subsequently. This probably reflects a lack of knowledge concerning land snail biodiversity in this country. To our knowledge, this is the first comprehensive survey of land snails in southern Cambodia. A need for more field research and systematic revision of the land snails in this interesting region is also highlighted and demonstrated.
| S-EPMC7381483 | biostudies-literature
Project description:This paper presents the first land snail species checklist for Gunung Kuang (Kuang Hill), a limestone hill located next to Gunung Kanthan that is recognised as one of the most important limestone hills for its diverse land snail fauna in Kinta Valley. Samplings were carried out at five plots in Gunung Kuang. This survey documented 47 land snail species, in which six species were identified as unique to Gunung Kuang. Approximately half of the land snails from Gunung Kanthan were found in Gunung Kuang. In addition, one of six unique species from Gunung Kanthan was also found in Gunung Kuang. These rich land snail species in Gunung Kuang are similar to other hills in Kinta Valley, but it is relatively lesser than the adjacent Gunung Kanthan. In view of Gunung Kuang's unique land snail species, and its location closest to disturbed Gunung Kanthan, Gunung Kuang should be considered in the conservation management plan for Gunung Kanthan.
| S-EPMC6030181 | biostudies-literature
Project description:BackgroundHematophagy arose independently multiple times during metazoan evolution, with several lineages of vampire animals particularly diversified in invertebrates. However, the biochemistry of hematophagy has been studied in a few species of direct medical interest and is still underdeveloped in most invertebrates, as in general is the study of venom toxins. In cone snails, leeches, arthropods and snakes, the strong target specificity of venom toxins uniquely aligns them to industrial and academic pursuits (pharmacological applications, pest control etc.) and provides a biochemical tool for studying biological activities including cell signalling and immunological response. Neogastropod snails (cones, oyster drills etc.) are carnivorous and include active predators, scavengers, grazers on sessile invertebrates and hematophagous parasites; most of them use venoms to efficiently feed. It has been hypothesized that trophic innovations were the main drivers of rapid radiation of Neogastropoda in the late Cretaceous. We present here the first molecular characterization of the alimentary secretion of a non-conoidean neogastropod, Colubraria reticulata. Colubrariids successfully feed on the blood of fishes, throughout the secretion into the host of a complex mixture of anaesthetics and anticoagulants. We used a NGS RNA-Seq approach, integrated with differential expression analyses and custom searches for putative secreted feeding-related proteins, to describe in detail the salivary and mid-oesophageal transcriptomes of this Mediterranean vampire snail, with functional and evolutionary insights on major families of bioactive molecules.ResultsA remarkably low level of overlap was observed between the gene expression in the two target tissues, which also contained a high percentage of putatively secreted proteins when compared to the whole body. At least 12 families of feeding-related proteins were identified, including: 1) anaesthetics, such as ShK Toxin-containing proteins and turripeptides (ion-channel blockers), Cysteine-rich secretory proteins (CRISPs), Adenosine Deaminase (ADA); 2) inhibitors of primary haemostasis, such as novel vWFA domain-containing proteins, the Ectonucleotide pyrophosphatase/phosphodiesterase family member 5 (ENPP5) and the wasp Antigen-5; 3) anticoagulants, such as TFPI-like multiple Kunitz-type protease inhibitors, Peptidases S1 (PS1), CAP/ShKT domain-containing proteins, Astacin metalloproteases and Astacin/ShKT domain-containing proteins; 4) additional proteins, such the Angiotensin-Converting Enzyme (ACE: vasopressive) and the cytolytic Porins.ConclusionsColubraria feeding physiology seems to involve inhibitors of both primary and secondary haemostasis, anaesthetics, a vasoconstrictive enzyme to reduce feeding time and tissue-degrading proteins such as Porins and Astacins. The complexity of Colubraria venomous cocktail and the divergence from the arsenal of the few neogastropods studied to date (mostly conoideans) suggest that biochemical diversification of neogastropods might be largely underestimated and worth of extensive investigation.
| S-EPMC4460706 | biostudies-literature
Project description:Complete mitochondrial (mt) genomes and the gene rearrangements are increasingly used as molecular markers for investigating phylogenetic relationships. Contributing to the complete mt genomes of Gastropoda, especially Pulmonata, we determined the mt genome of the freshwater snail Galba pervia, which is an important intermediate host for Fasciola spp. in China. The complete mt genome of G. pervia is 13,768 bp in length. Its genome is circular, and consists of 37 genes, including 13 genes for proteins, 2 genes for rRNA, 22 genes for tRNA. The mt gene order of G. pervia showed novel arrangement (tRNA-His, tRNA-Gly and tRNA-Tyr change positions and directions) when compared with mt genomes of Pulmonata species sequenced to date, indicating divergence among different species within the Pulmonata. A total of 3655 amino acids were deduced to encode 13 protein genes. The most frequently used amino acid is Leu (15.05%), followed by Phe (11.24%), Ser (10.76%) and IIe (8.346%). Phylogenetic analyses using the concatenated amino acid sequences of the 13 protein-coding genes, with three different computational algorithms (maximum parsimony, maximum likelihood and bayesian analysis), all revealed that the families Lymnaeidae and Planorbidae are closely related two snail families, consistent with previous classifications based on morphological and molecular studies. The complete mt genome sequence of G. pervia showed a novel gene arrangement and it represents the first sequenced high quality mt genome of the family Lymnaeidae. These novel mtDNA data provide additional genetic markers for studying the epidemiology, population genetics and phylogeographics of freshwater snails, as well as for understanding interplay between the intermediate snail hosts and the intra-mollusca stages of Fasciola spp..
| S-EPMC3406003 | biostudies-literature
Project description:The file ramshorn snail Planorbella pilsbryi Baker, 1926 (Gastropoda: Hygrophila: Planorbidae) is a widespread herbivorous North American freshwater snail found in diverse habitats, including standing and moving water bodies. Genome skimming by Illumina sequencing allowed the assembly of a complete nuclear rRNA repeat sequence and a complete circular mitogenome of 13,720 bp from P. pilsbryi consisting of 75.3% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the typical order found in panpulmonate snails. Planorbella pilsbryi COXI features a rare TTG start codon while COXII, CYTB, ND2, ND3, and ND5 exhibit incomplete stop codons completed by the addition of 3' A residues to the mRNA. Phylogenetic reconstruction of mitochondrial protein-coding gene and rRNA sequences places P. pilsbryi as sister taxon to Planorbella duryi (Planorbidae) within family Planorbidae, which is consistent with previous phylogenetic hypotheses.
| S-EPMC8567931 | biostudies-literature
Project description:The ability of invertebrates to discriminate quantities is poorly studied, and it is unknown whether other phyla possess the same richness and sophistication of quantification mechanisms observed in vertebrates. The dune snail, Theba pisana, occupies a harsh habitat characterised by sparse vegetation and diurnal soil temperatures well above the thermal tolerance of this species. To survive, a snail must locate and climb one of the rare tall herbs each dawn and spend the daytime hours in an elevated refuge position. Based on their ecology, we predicted that dune snails would prefer larger to smaller groups of refuges. We simulated shelter choice under controlled laboratory conditions. Snails' acuity in discriminating quantity of shelters was comparable to that of mammals and birds, reaching the 4 versus 5 item discrimination, suggesting that natural selection could drive the evolution of advanced cognitive abilities even in small-brained animals if these functions have a high survival value. In a subsequent series of experiments, we investigated whether snails used numerical information or based their decisions upon continuous quantities, such as cumulative surface, density or convex hull, which co-varies with number. Though our results tend to underplay the role of these continuous cues, behavioural data alone are insufficient to determine if dune snails were using numerical information, leaving open the question of whether gastropod molluscans possess elementary abilities for numerical processing.
| S-EPMC7881015 | biostudies-literature
Project description:The land snails collected by the 'Comisión Científica del Pacifíco' (CCP), a Spanish expedition to South and Central America from 1862-1866, are restudied and revised. The historical context of the expedition and the study of its collected material are described. Biographical data is given for the main persons involved. The land snails were previously studied by Joaquin Hidalgo between 1867 and 1893. A total of 3,470 specimens belonging to 211 species are treated in this paper. Of 34 species mentioned by Hidalgo is his catalogue, the corresponding material could not be located. Bulimus visendus Hidalgo, 1869 is now placed in the genus Synapterpes Pilsbry, 1896, a new combination.
| S-EPMC5354113 | biostudies-literature
Project description:The radula is the anatomical structure used for feeding in most species of Mollusca. Previous studies have revealed that radulae can be adapted to the food or the substrate the food lies on, but the real, in vivo forces exerted by this organ on substrates and the stresses that are transmitted by the teeth are unknown. Here, we relate physical properties of the radular teeth of Cornu aspersum (Müller. 1774 Vermium terrestrium et fluviatilium, seu animalium infusoriorum, helminthicorum, et testaceorum, non marinorum, succincta historia. Volumen alterum. Heineck & Faber, Havniæ & Lipsiæ.), a large land snail, with experiments revealing their radula scratching force. The radula motion was recorded with high-speed video, and the contact area between tooth cusps and the substrate was calculated. Forces were measured in all directions; highest forces (106.91 mN) were exerted while scratching, second highest forces while pulling the radula upwards and pressing the food against its counter bearing, the jaw, because the main ingesta disaggregation takes place during those two processes. Nanoindentation revealed that the tooth hardness and elasticity in this species are comparable to wood. The teeth are softer than some of their ingesta, but since the small contact area of the tooth cusps (227 µm2) transmits high local pressure (4698.7 bar) on the ingesta surface, harder material can still be cut or pierced with abrasion. This method measuring the forces produced by the radula during feeding could be used in further experiments on gastropods for better understanding functions and adaptations of radulae to ingesta or substrate, and hence, gastropods speciation and evolution.
| S-EPMC6689628 | biostudies-literature
Project description:BACKGROUND: The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. METHODS: In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. RESULTS: We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.
| S-EPMC3369186 | biostudies-literature
Project description:MotivationThere are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage. It is not uncommon that assembly methods involving the overlap graph model are not able to successfully compute greater datasets, mainly due to memory limitation of a computer. This was the reason for developing in last decades mainly de Bruijn-based assembly methods, fast and fairly accurate. However, the latter methods can fail for longer or more repetitive genomes, as they decompose reads to shorter fragments and lose a part of information. An efficient assembler for processing big datasets and using the overlap graph model is still looked out.ResultsWe propose a new genome-scale de novo assembler based on the overlap graph approach, designed for short-read sequencing data. The method, ALGA, incorporates several new ideas resulting in more exact contigs produced in short time. Among these ideas, we have creation of a sparse but quite informative graph, reduction of the graph including a procedure referring to the problem of minimum spanning tree of a local subgraph, and graph traversal connected with simultaneous analysis of contigs stored so far. What is rare in genome assembly, the algorithm is almost parameter-free, with only one optional parameter to be set by a user. ALGA was compared with nine state-of-the-art assemblers in tests on genome-scale sequencing data obtained from real experiments on six organisms, differing in size, coverage, GC content and repetition rate. ALGA produced best results in the sense of overall quality of genome reconstruction, understood as a good balance between genome coverage, accuracy and length of resulting sequences. The algorithm is one of tools involved in processing data in currently realized national project Genomic Map of Poland.Availability and implementationALGA is available at http://alga.put.poznan.pl.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC8289375 | biostudies-literature