Genome and functional annotation of Nerium oleander reveal environmental stress-associated and metabolic pathways

Naira Ibrahim, Ananda Nanjundaswamy, Daniel P. Schmitt & Vinayak Kapatral

Abstract

We generated a high-quality draft genome assembly for Nerium oleander of approximately 447 Mb, comprising 269 contigs with a GC content of 33%. Genome annotation identified 33,243 protein-coding genes and 3,078 RNA features. Predicted functional annotation revealed identification of gene families associated with stress response and metal homeostasis, including pathways related to amino acid metabolism, glutathione metabolism, ABC transporters, and NRAMP transporter families. In addition, genes putatively involved in secondary metabolism and phytohormone biosynthesis were identified, including those associated with salicylic acid, gibberellic acid, brassinosteroids, auxins, cytokinin, abscisic acid, and jasmonic acid pathways, as well as metal-binding and detoxification-related compounds such as phytochelatins and metallothioneins. These results provide genomic evidence for a broad repertoire of stress-associated and metal-responsive pathways in N. oleander. The genome blueprint establishes a foundation for future transcriptomic and functional studies to validate gene expression and regulatory mechanisms under heavy metal and other abiotic stress conditions and supports its potential application in phytoremediation and stress tolerance research.

Whole-genome sequence and annotation of Penstemon davidsonii

Kate L Ostevik, Magdy Alabady, Mengrui Zhang, Mark D Rausher

Penstemon is the most speciose flowering plant genus endemic to North America. Penstemon species’ diverse morphology and adaptation to various environments have made them a valuable model system for studying evolution. Here, we report the first full reference genome assembly and annotation for Penstemon davidsonii. Using PacBio long-read sequencing and Hi-C scaffolding technology, we constructed a de novo reference genome of 437,568,744 bases, with a contig N50 of 40 Mb and L50 of 5. The annotation includes 18,199 gene models, and both the genome and transcriptome assembly contain over 95% complete eudicot BUSCOs. This genome assembly will serve as a valuable reference for studying the evolutionary history and genetic diversity of the Penstemon genus.

New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species

Lauren J. Frazee, Joanna Rifkin 2 Dinusha C. Maheepala, Alannie-Grace Grant, Stephen Wright , Susan Kalisz, Amy Litt, and Rachel Spigler

The evolutionary transition from outcross- to self-fertilization is one of the most common in angiosperms and is often associated with a parallel shift in floral morphological and developmental traits, such as reduced flower size and pollen to ovule ratios, known as the “selfing syndrome.” How these convergent phenotypes arise, the extent to which they are shaped by selection, and the nature of their underlying genetic basis are unsettled questions in evolutionary biology. The genus Collinsia (Plantaginaceae) includes seven independent transitions from outcrossing or mixed mating to high selfing rates accompanied by selfing syndrome traits. Accordingly, Collinsia represents an ideal system for investigating this parallelism, but requires genomic resource development. We present a high quality de novo genome assembly for the highly selfing species Collinsia rattanii. To begin addressing the basis of selfing syndrome developmental shifts, we evaluate and contrast patterns of gene expression from floral transcriptomes across three stages of bud development for C. rattanii and its outcrossing sister species Collinsia linearis. Relative to C. linearis, total gene expression is less variable among individuals and bud stages in C. rattanii. In addition, there is a common pattern among differentially expressed genes: lower expression levels that are more constant across bud development in C. rattanii relative to C. linearis. Transcriptional regulation of enzymes involved in pollen formation specifically in early bud development may influence floral traits that distinguish selfing and outcrossing Collinsia species through pleiotropic functions. Future work will include additional Collinsia outcrossing-selfing species pairs to identify genomic signatures of parallel evolution. Keywords: Collinsia; RNA-seq; selfing syndrome; pollen; floral development; differential gene expression; DESeq2; dichogamy; evolutionary genomics; Hi-C scaffolding; parallel evolution