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3 results for “Cherax destructor”
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.
Data from: Phylogeography and species delimitation of Cherax destructor (Decapoda: Parastacidae) using genome-wide SNPs
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