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82 results for “Cherax”
Dataset for "Nanopore-led long-read genome assembly of the Australian yabby, Cherax destructor"
<p>Intermediate_Assemblies.tar.gz: Intermediate genome assemblies e.g. raw wtdbg assembly (CD.raw.fa), polished wtdbg assembly (CD.cns.fa), 1st pilon polished assembly (CDF2_pilon1.fasta), 2nd pilon polished assembly (CDF2_pilon2.fasta) and RNA-scaffolded assembly (CDF2_pilon2_prna.fasta). Folders with run_"assembly name" are BUSCO output for each of the assembly.</p> <p>BRAKER2.tar.gz: BRAKER2 genome annotation output containing the initial set of predicted protein-coding genes as well as training intermediate files.</p> <p>BUSCOv3.tar.gz: BUSCO assessment of publicly available Decapod crustacean genome assemblies</p> <p>Cdes.filtered.codingseq: Filtered set of protein-coding sequences</p> <p>Cdes.filtered.faa: Translation of the filtered protein-coding sequences</p> <p>CDF2.NCBI.fasta.masked.gz: Repeat-masked (softmasked) Cherax destructor genome</p> <p>Cqua_transcriptome.tar.gz: rnaSPAdes output (combined fasta) of all Cherax quadricarinatus transcriptomes and its reduced dataset generated by EvidentialGene. </p> <p>Quast.tar.gz: Quast output of all Decapod crustacean genome assemblies assessed in this study</p> <p>Repeat_Annotation.tar.gz: Repeat annotation (.gff3) based on Cherax destructor-specific de novo repeat library and its summary (.tbl)</p> <p>RepeatLibrary.tar.gz: Cherax destructor-specific de novo repeat library generated by RepeatModeler</p> <p>Wtdbg2_assembly.log: Wtdbg2.5 log file showing exact command used, kmer distribution, memory usage and assembly duration.</p> <p>CAZY_Annotation.tar.gz: dbCAN2 Identification of CAZy in the selected crustacean proteomes as well as list of cellulase-associated GH groups (glycoside hydrolase). </p> <p>Orthofinder.tar.gz: Orthofinder2 output and proteomes of each crustacean used to infer orthologous clustering.</p> <p>GH9_Analysis.tar.gz: Selected GH9-associated protein sequences, amino acid alignment and IQTree output. </p> <p>Cdes_mito.gbf: GenBank file of the annotated complete mitogenome</p> <p>Cdes.filtered.codingseq: Cherax destructor protein-coding genes with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p> <p>Cdes.filtered.faa: Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p> <p>Cdes.ortholog.list: List of predicted Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. </p>
Data from: Phylogeography and species delimitation of Cherax destructor (Decapoda: Parastacidae) using genome-wide SNPs
Cherax is a genus of 58 species of decapod crustaceans that are widespread across Australia and New Guinea. We use single-nucleotide polymorphisms (SNPs) to examine phylogeographic patterns in the most widespread species of Cherax, namely, C. destructor, and test the distinctiveness of one undescribed species, two C. destructor subspecies, previously proposed evolutionarily significant units, and management units. Both the phylogenetic analyses and the analysis of fixed allelic differences between populations support the current species-level taxonomy of C. setosus, C. depressus, C. dispar and C. destructor, the distinctiveness of C. destructor albidus and C. d. destructor and the existence of one undescribed species. The two populations of C. d. albidus from the Glenelg and Wimmera rivers were significantly distinct, with eight diagnostic differences (<1% fixed differences, null expectation is four fixed differences), but this low level of divergence is interpreted as within the range that might be expected of management units, that is, among allopatric populations of a single species or subspecies. A southern clade of C. d. destructor comprising the Murray River and its tributaries upstream from its confluence with the Darling River is genetically distinct from a northern clade comprising populations from the Lake Eyre Basin, the northern half of the Murray–Darling Basin (Darling River catchment) and the Lower Murray River below the Darling confluence.
FIGURE 2. Cherax gherardii n in Cherax (Astaconephrops) gherardii, a new crayfish (Decapoda: Parastacidae) from West Papua, Indonesia
FIGURE 2. Cherax gherardii n. sp.: A. lateral view of carapace; B. lateral view of antennal peduncle; C. dorsal view of right chela; D. dorsal view of carapace; E. ventral view of right chela; F. epistome and coxicerite of antennal peduncle; G. dorsal view of right scaphocerite; A from allotype, B–G from holotype.
FIGURE 5 in Cherax (Astaconephrops) gherardii, a new crayfish (Decapoda: Parastacidae) from West Papua, Indonesia
FIGURE 5. Bayesian analysis consensus phylogram of selected Cherax species based on combined COI and 16S dataset. ML bootstrap values and posterior probabilities are displayed next to each node.
FIGURE 4 in Cherax (Astaconephrops) gherardii, a new crayfish (Decapoda: Parastacidae) from West Papua, Indonesia
FIGURE 4. The Bird's Head Peninsula, West Papua, Indonesia, and the indicated locality of the Ajamaru Lakes.
FIGURE 2 in First record of a new epibionts suctorian ciliate Tokophrya huangmeiensis sp. n. (Ciliophora, Phyllopharyngea) from redclaw crayfish Cherax quadricarinatus von Martens 1868
FIGURE 2. Line drawings of T. huangmeiensis sp. n. (a) Body of T. huangmeiensis suspended on stalk. (b) Epistylis sp. as a substrate to Tokophrya sp. Scale bars: a=60 µm, b=1 mm.
FIGURE 1 in First record of a new epibionts suctorian ciliate Tokophrya huangmeiensis sp. n. (Ciliophora, Phyllopharyngea) from redclaw crayfish Cherax quadricarinatus von Martens 1868
FIGURE 1. Photomicrographs of T. huangmeiensis sp. n. found on redclaw crayfish (a) Cherax quadricarinatus collected from suspected fish farm. (b) Epistylis sp. as a substrate to T. huangmeiensis sp. n.; Abbreviations: Ep = Epistylis, Th = T. huangmeiensis sp. n. (c) Elongated pyramidal shaped and corrugated cell body of T. huangmeiensis sp. n., arrowhead showing macronucleus. (d) Apical part of the cell body showing single contractile vacuole. (e) Apical border of the cell body showing fascicle of finger-like tentacles. (f) Indicating basal plate which was concave up-word and gently dipped inside the cell body, under this basal plate transparent stalk is present with longitudinal striations. (g) Showing junction of Epistylis sp. as a substrate to Tokophrya sp., slightly protrude outward. Scale bars: b=100 µm, c=10 µm, d=5 µm, e=5 µm, f=5 µm, g=3 µm.
FIGURE 3 in First record of a new epibionts suctorian ciliate Tokophrya huangmeiensis sp. n. (Ciliophora, Phyllopharyngea) from redclaw crayfish Cherax quadricarinatus von Martens 1868
FIGURE 3. Phylogenetic tree generated by Bayesian analysis of SSU rDNA sequences of T. huangmeiensis sp. n. and related ciliates. Genbank accession numbers are listed adjacent to species names. Numbers given at nodes of branches are posterior probabilities (BI) and bootstrap values (ML), respectively. Asterisks are shown where values exceeded 95%. Dashes are shown for values under 50%.
FIGURE 6. A in Cherax acherontis (Decapoda: Parastacidae), the first cave crayfish from the Southern Hemisphere (Papua Province, Indonesia)
FIGURE 6. A, Hagepma entrance into the cave; B, wood debris in the river in the cave; C, dripstone decoration in the cave.
FIGURE 5 in Cherax acherontis (Decapoda: Parastacidae), the first cave crayfish from the Southern Hemisphere (Papua Province, Indonesia)
FIGURE 5. Map of Papua Province, Indonesia. The position of the cave near city of Wamena indicated by red triangle. The photo shows a typical terrain in the vicinity of the cave.
FIGURE 3. Cherax acherontis n in Cherax acherontis (Decapoda: Parastacidae), the first cave crayfish from the Southern Hemisphere (Papua Province, Indonesia)
FIGURE 3. Cherax acherontis n. sp., from holotype. A, lateral view of carapace; B, dorsal view of carapace; C, ventral view of right chela; D, dorsal view of right chela; E, epistome; F, dorsal view of right scaphocerite; G, third maxilliped.
Fig. 3 in First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase
Fig. 3 Expression of 65 transcripts categorized into 16 GH families measured in log2 of (TPM + 1) values. The descriptions of GH families were assigned based on InterPro annotations of transcripts in each family (Online Resource 3), providing higher confidence of its putative function. In contrast, GH30, GH31, and GH39 do not have descriptions as their corre- sponding transcripts do not pos- sess detectable domains or signatures that point to any enzymatic functions
Fig. 2 in First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase
Fig. 2 Annotation and information on the Cherax quadricarinatus transcriptome. a Distribution of transcript lengths with blue bars representing the lengths of all transcripts and red bars showing the length distribution only for transcripts with at least one annotation. b Venn diagram showing the number of shared and unique transcripts in different tissue types expressed at a TPM threshold of 100. c Transcript
Fig. 1 in First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase
Fig. 1 Workflow diagram for the analysis of the Cherax quadricarinatus transcriptome. Analyses included the de novo assembly of the transcriptome, annotation of transcripts, expression analysis in multiple tissues, and the identification of putative cellulases
Data from: Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda : Parastacidae) in the wild
Hybridization and genetic introgression following the introduction of exotic species can pose a significant threat to the survival of geographically restricted species. A remnant population of the critically endangered freshwater crayfish Cherax tenuimanus in the upper reaches of the Margaret River in southwestern Australia is under threat following the introduction and spread of its congener Cherax cainii. Here, we examine the extent of hybridization and introgression between the two species using twelve polymorphic microsatellite loci. Our study reveals there are three times more C. cainii than C. tenuimanus at our study site in the upper reaches of the Margaret River. There is also evidence of hybridization and introgression between C. tenuimanus and C. cainii at this site, with F1, F2 and backcrossed individuals identified. While interbreeding was confirmed in this study, our simulations suggest that the levels of introgression are much lower than would be expected under random mating, indicating partial reproductive barriers exist. Nevertheless, it is apparent that hybridization and introgression with C. cainii pose a serious threat to C. tenuimanus and their survival in the wild will require active adaptive management and continued genetic monitoring to evaluate management effectiveness.
FIGURE 11 in Cherax latimanus sp. nov., a new burrow-dwelling freshwater crayfish (Decapoda Parastacidae) from the mid-Murray River catchment, Australia
FIGURE 11. Soil-capped burrow with (upper), and without (lower), embedded sticks, northern Millewa Forest, NSW, 12 January 2017 (Image: Dale McNeil).
FIGURE 10 in Cherax latimanus sp. nov., a new burrow-dwelling freshwater crayfish (Decapoda Parastacidae) from the mid-Murray River catchment, Australia
FIGURE 10. An almost completed burrow cap of moist soil, just north of Euroa and east of Hume Freeway (area now under freeway fuel station), 24/11/2005—note, small foggy patch is moisture on the camera lens (Image: Richard Francis).
FIGURE 9 in Cherax latimanus sp. nov., a new burrow-dwelling freshwater crayfish (Decapoda Parastacidae) from the mid-Murray River catchment, Australia
FIGURE 9. Open entrance to burrow of Cherax latimanus sp. nov., though blocked with a soil plug deeper down, Reedy Lake, Victoria (Image: Robert McCormack).
FIGURE 6 in Cherax latimanus sp. nov., a new burrow-dwelling freshwater crayfish (Decapoda Parastacidae) from the mid-Murray River catchment, Australia
FIGURE 6. Cherax latimanus sp. nov., adult, from Thornton, displaying a) a thin, sparse, band of dorsal mesial propodal marginal setae (white arrow), and distinctive blue colour on side of cephalon (yellow arrow), and b) dense ventral propodal setae (white arrow), and with distinctive blue colour on side of cephalon (yellow arrow) (Images: Robert McCormack).
FIGURE 8 in Cherax latimanus sp. nov., a new burrow-dwelling freshwater crayfish (Decapoda Parastacidae) from the mid-Murray River catchment, Australia
FIGURE 8. Multiple soil-capped burrows (light coloured patches on the ground) of Cherax latimanus sp. nov. surrounding Lake Moira, NSW, 13 August 2009 (Image: Robert McCormack).
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