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Dataset results
14 results for “Penaeus monodon”
Fig 1a in Efficacy of Doob grass, Cynodon dactylon against white spot syndrome virus in Penaeus monodon
Fig 1a: GCMS chromatogram of Cynodon dactylon extract showing fraction peaks at normal (300C) temperature. The peak in circle shows the original presence of ingredients in the C. dactylon before heating at higher temperature.
Fig 1b in Efficacy of Doob grass, Cynodon dactylon against white spot syndrome virus in Penaeus monodon
Fig 1b: GCMS chromatogram of Cynodon dactylon extract showing fraction peaks at higher (85 0C) temperature. The red arrows indicate the disappearance of active ingredient peak after heating at 85 0C which indicates the non-effectiveness of feed produced above 85 0C.
De novo whole genome assembly of the giant tiger prawn (Penaeus monodon) from Vietnam
<p>Basecalled Nanopore FastQ files for the Vietnamese giant tiger prawn and its genome assemblies.</p> <p>FastQ files (LSK109 sample prep sequenced on a MinION device for 48 hours). Read stats are in *_stat.txt:</p> <p>TP_A.fastq : gDNA was extracted using Zymo quick DNA minikit from ethanol-preserved muscle tissue</p> <p>TP_B.fastq : Same as TP_A.fastq</p> <p>TP_C.fastq : gDNA was extracted using conventional salting out method (longer read length but reduced yield)</p> <p>Assemblies:</p> <p>v1_MaSuRCA.fasta: Assembly using poly-G trimmed Illumina reads</p> <p>v2_NanoporeScaf.fasta : Scaffolding with Nanopore long reads</p> <p>v3_RNA_NanoporeScaf.fasta: Scaffolding of v2 with RNA reads</p> <p>v4_NCBI_Filt.fasta: post NCBI contaminant and carry-over adapter removal (final version)</p> <p>Annotation:</p> <p>Braker2_annotation.gff3.gz: Inititial Braker2 gff3 output</p> <p>Braker2_CDS.fna.gz: Initial Braker2 predicted genes</p> <p>Braker2_prot.faa.gz: Protein translation of Braker2_CDS.fna</p> <p>CAZy.tar.gz: CAZy annotation for four crustacean species</p> <p>Filtered_Gene.tar.gz: List of genes with functional annotation and/or orthologs</p> <p>Interproscan_result.tsv: Raw InterProScan output</p> <p>OrthoFinder2.tar.gz: OrthoFinder2 output. Proteins used to infer orthologs are included as ".faa".</p>
Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
<p><i><span>Background</span></i></p> <p><span>The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in <i>de-novo</i> genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (<i>Penaeus monodon</i>) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).</span></p> <p><i><span>Results</span></i></p> <p><span>Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 </span>± 14.7 to 93.0% ± 3.5%<span>), </span>increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7<span>), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.</span></p> <p><i><span>Conclusion</span></i></p> <p><span>Importantly, this assay equips the <em>P. monodon</em> industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as <em>P. monodon</em> breeding programs transition to undertaking genomic selection.</span></p>
Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
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Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence
<p>Abstract Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.</p>
Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence
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Identification of differentially expressed genes against WSSV infection in Penaeus monodon by microarray
GEO Series GSE52895. Penaeus monodon. 16 samples. Type: Expression profiling by array.
Effects of eyestalk ablation on the gene expression levels in female black tiger shrimp broodstock (Penaeus monodon)
GEO Series GSE29025. Penaeus monodon. 8 samples. Type: Expression profiling by array.
Stress induced gene expression profiling in Penaeus monodon
GEO Series GSE7456. Penaeus monodon. 48 samples. Type: Expression profiling by array.
Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)
GEO Series GSE22090. Penaeus monodon. 9 samples. Type: Expression profiling by array.
Identification of fatty acid regulatory genes using in silico analysis from Ovary and Hepatopancreas ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)
GEO Series GSE111471. Penaeus monodon. 16 samples. Type: Expression profiling by array.
Transcriptomic analysis of polychaete-enhanced testicular maturation in male broodstock of the black tiger shrimp (Penaeus monodon)
GEO Series GSE87738. Penaeus monodon. 16 samples. Type: Expression profiling by array.
A cDNA Microarray, UniShrimpChip, for Identification of Genes Relevant to Testicular Development in the Black Tiger Shrimp (Penaeus monodon)
GEO Series GSE21890. Penaeus monodon. 18 samples. Type: Expression profiling by array.
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Allen Brain Atlas
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