Data from: Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anticancer and antimalarial cardenolides

Calotropis gigantea produces specialized secondary metabolites known as cardenolides which have anti-cancer and anti-malarial 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 in 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 engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications

CAL_genome_asm_v2.2_1000_rmscaff_soft_masked.fasta

Final soft masked genome assembly for C. gigante

Data from: Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anticancer and antimalarial cardenolides

Calotropis gigantea produces specialized secondary metabolites known as cardenolides which have anti-cancer and anti-malarial 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 in 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 engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications

Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides

Calotropis 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

Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue‐specific circadian clocks

Abstract The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue‐specific clocks connected by mobile signals have previously been found to run at different speeds in Arabidopsis thaliana tissues. However, tissue variation in circadian clocks in crop species is unknown. In this study, leaf and tuber global gene expression in cultivated potato under cycling and constant environmental conditions was profiled. In addition, we used a circadian‐regulated luciferase reporter construct to study tuber gene expression rhythms. Diel and circadian expression patterns were present among 17.9% and 5.6% of the expressed genes in the tuber. Over 500 genes displayed differential tissue specific diel phases. Intriguingly, few core circadian clock genes had circadian expression patterns, while all such genes were circadian rhythmic in cultivated tomato leaves. Furthermore, robust diel and circadian transcriptional rhythms were observed among detached tubers. Our results suggest alternative regulatory mechanisms and/or clock composition is present in potato, as well as the presence of tissue‐specific independent circadian clocks. We have provided the first evidence of a functional circadian clock in below‐ground storage organs, holding important implications for other storage root and tuberous crops

Zea_mays.OrthoFinder.by.Zm.txt

Orthologous and paralogous groups identified by OrthoFinder listed by AGPv4 maize gen

Zea_mays.MSU.FKPM.matrix.txt

FPKM matrix for AGPv4 gene

Zea_mays.PAV.by.Inbred.txt

PAV matrix where an AGPv4 gene considered a PAV is listed by inbred; data comes from Brohammer et al. (2018) (https://doi.org/10.1111/tpj.13765

Zea_mays.MSU.GO.terms.gene.txt

Gene Ontology term assignments for AGPv4 genes identified from InterPro hit

README.txt

README.tx