223 research outputs found
Length-at-age and Size-Selective Mortality of the Western Basin Lake Erie Walleye (Sander vitreus) Population, 2000-2008
No full textSize-selective mortality is common in systems where selective harvesting targets a specific size- or age-class. In general, commercial and recreational fisheries selectively remove the largest and fastest growing individuals, which may have evolutionary consequences. My goals were to examine length-at-age patterns, age at first and full recruitment to the fishery, and to determine if size-selective mortality existed in a commercially and recreationally fished population of walleye in Lake Erie of the Laurentian Great Lakes between 2000 and 2008. Mean fork length-at-age was found to increase from west to east within Lake Erie for age 2 and 3 walleye. However, mean fork-length at age 1 was not statistically different among sampling areas. Walleye first recruited to the fishery at age 1 and were not fully recruited by age 3. Smaller (slower growing) individuals were found to disproportionately survive to older ages than faster-growing fish, indicating that size-selective mortality of larger (faster growing) fish occurred. Size-selective mortality will likely have a negative effect on morphological (i.e., body size) and life history traits
Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides
No full textCalotropis gigantea produces specialized secondary metabolites known as cardenolides, which have anticancer and antimalarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high-quality de novo assembly was generated for C. gigantea, representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome data in the form of RNA-sequencing libraries from a developmental tissue series was generated to aid the annotation and construction of a gene expression atlas. Using an ab initio and evidence-driven gene annotation pipeline, 18,197 high-confidence genes were annotated. Homologous and syntenic relationships between C. gigantea and other species within the Apocynaceae family confirmed previously identified evolutionary relationships, and suggest the emergence or loss of the specialized cardenolide metabolites after the divergence of the Apocynaceae subfamilies. The C. gigantea genome assembly, annotation, and RNA-sequencing data provide a novel resource to study the cardenolide biosynthesis pathway, especially for understanding the evolutionary origin of cardenolides and the engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications
Data from: De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin
No full textCamptotheca acuminata is 1 of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. While transcriptome studies have been performed previously with various camptothecin-producing species, no genome sequence for a camptothecin-producing species is available to date. We generated a high-quality de novo genome assembly for C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50 scaffold size of 1752 kbp. Quality assessments of the assembly revealed robust representation of the genome sequence including genic regions. Using a novel genome annotation method, we annotated 31 825 genes encoding 40 332 gene models. Based on sequence identity and orthology with validated genes from Catharanthus roseus as well as Pfam searches, we identified candidate orthologs for genes potentially involved in camptothecin biosynthesis. Extensive gene duplication including tandem duplication was widespread in the C. acuminata genome, with 2571 genes belonging to 997 tandem duplicated gene clusters. To our knowledge, this is the first genome sequence for a camptothecin-producing species, and access to the C. acuminata genome will permit not only discovery of genes encoding the camptothecin biosynthetic pathway but also reagents that can be used for heterologous expression of camptothecin and camptothecin analogs with novel pharmaceutical applications
Genome Assembly and Annotation of the Medicinal Plant<i>Calotropis gigantea</i>, a Producer of Anticancer and Antimalarial Cardenolides
No full textAbstractCalotropis gigantea produces specialized secondary metabolites known as cardenolides, which have anticancer and antimalarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high-quality de novo assembly was generated for C. gigantea, representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome data in the form of RNA-sequencing libraries from a developmental tissue series was generated to aid the annotation and construction of a gene expression atlas. Using an ab initio and evidence-driven gene annotation pipeline, 18,197 high-confidence genes were annotated. Homologous and syntenic relationships between C. gigantea and other species within the Apocynaceae family confirmed previously identified evolutionary relationships, and suggest the emergence or loss of the specialized cardenolide metabolites after the divergence of the Apocynaceae subfamilies. The C. gigantea genome assembly, annotation, and RNA-sequencing data provide a novel resource to study the cardenolide biosynthesis pathway, especially for understanding the evolutionary origin of cardenolides and the engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications.</jats:p
De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin
No full textTranscriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance
No full textmissing_busco_list_asm_v2.2_1000.tsv
No full textList of missing Embryophyta orthologs from the genome assembl
Spud DB: A Resource for Mining Sequences, Genotypes, and Phenotypes to Accelerate Potato Breeding
No full textPotato is the world’s third most important crop, and is becoming increasingly important in developing countries. Cultivated potato is a highly heterozygous tetraploid (2 = 4 = 48) and suffers from significant inbreeding depression when selfed. As potato can be vegetatively propagated, breeding has been based primarily on phenotypic selection in F1 populations. However, recent advances in genome sequencing and genotyping methods have resulted in the development of large genomic, genetic, and phenotypic datasets that will enable more efficient and rapid breeding approaches. We have developed Spud DB () for the community to access the potato genome sequence and associated annotation datasets, along with phenotypic and genotypic data from a diversity panel of 250 potato clones. The Breeder’s Assistant is a web tool to retrieve pertinent phenotypic and genotypic data in a user-guided manner, and query polymorphic markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) to identify custom sets of markers for a gene or region of interest. To browse and query the potato genome, a genome browser with 94 tracks of genome annotation, sequence variants, and expression abundance has been deployed. Spud DB also provides a comprehensive search page to data mine the potato genome through tools that query sequence identifiers, functional annotation, gene ontology (GO), InterPro domains, and basic local alignment search tool (BLAST) databases. Collectively, this resource links potato genomic data with phenotypic and genotypic data from a large collection of potato lines for use by the potato community, especially breeders and geneticists
cac_genome_assembly_v2.4.fa
No full textGenome assembly of C. acuminata, containing 1,394 scaffold sequence
cal_FPKM_matrix.txt
No full textTable with FPKM expression values for high-confidence genes in C. gigante
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