Congratulations to Ashley Yow, PhD. Ashley defended her dissertation on October 19 and graduated on December 16, 2022 from the Department of Horticultural Science. During her time at PHHI, Ashley was a graduate mentor in the Plant Pathways Elucidation Program, where she guided undergraduate interns through a summer research project. Ashley’s research focus was on Developing a Genomic Framework for Studying Agronomic and Nutritional Traits in Pineapple. Read the abstract of her work below or find the full text here.
Pineapple (Ananas comosus(L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. High-quality genomic resources, including genome assemblies and annotations are necessary for studying important traits in fruit crops like pineapple. Two of these important traits include bromelain enzyme content and cold stress tolerance. Bromelain enzymes are papain-family proteases with high medicinal value due to their proteolytic activity and anti-inflammatory effects and cold stress-induced flowering is one of the major bottlenecks for pineapple production.For these reasons, we aimed to develop an improved pineapple genome assembly and annotation, and to identify bromelain enzyme genes and elucidate mechanisms for cold stress tolerance in pineapple.
In this work, we utilized PacBio and Hi-C data to develop a new, high-quality genome assembly and gene prediction for MD2. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50length, phased chromosomes, and >6000 new genes.The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome.The new assembly also facilitated the comparison of the two individual haplotypes of theMD2 genome and provided a strong foundation for studying FAR1-RELATED SEQUENCE (FRS) genes, bromelain enzyme genes, and the relationship between cold stress and precocious flowering in pineapple.
The haplotype diversity of the MD2 genome indicated that a high level of heterozygosity in this pineapple contributes to maintaining functional alleles. A total of 82FRS genes were identified in the new MD2 genome and it appeared that this gene family was expanded in pineapple and rice, and that their expansion contributed to evolving specialized functions in reproductive tissues.
Bromelain enzymes are economically important proteases extracted from pineapple waste tissues. Papain-family proteases in the predicted protein set for the MD2v2 genome were used as the basis for identifying the bromelain subfamily. Orthologous and phylogenetic analyses indicated that bromelain subfamily genes are belong to one orthogroup (189) and one phylogenetic clade (VI). Duplication mechanism and synteny results indicated that the bromelain subfamily diverged from the larger papain family of proteases in the pineapple lineage and that transposed duplication played a large role in the divergence of the papain family and bromelain subfamily of proteases.Four of the bromelain subfamily enzymes identified in this work were expressed at the mRNA and protein levels, as observed by transcriptomic and proteomic analyses. The genes encoding these four bromelains can be used for future applied scientific research, such as targeted transgenic efforts to increase bromelain content and studies that evaluate therapeutic potential of individual bromelain enzymes.
Two pineapple genotypes, one susceptible (MD2) and one tolerant (Dole-17) to precocious flowering, were used to identify genes and gene networks that are likely associated with cold stress response and stress-mediated regulation of flowering time in pineapple. Through differential expression and weighted gene co-expression network analyses, a number of genes were identified that were likely responsible for differences in cold response between genotypes and were primarily involved in ethylene signaling, carbohydrate accumulation, and physiological adaptation to cold.Given the results of this study, we determined that MD2 likely has a higher susceptibility to cold stress and ethylene production, leading to earlier induction of flowering.
The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple. In addition, the genes and gene families identified here can serve as a foundation for determining medicinal or therapeutic potential of specific bromelains and for developing new pineapple varieties with higher bromelain content, increased cold tolerance, and later flowering time.