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Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties and one wild pineapple relative. Their analysis supports the use of the pineapple as a reference genome for monocot comparative genomics and provides insight into the evolution of crassulacean acid metabolism photosynthesis. Pineapple ( Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C 3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis -regulatory elements associated with the regulation of circadian clock genes, providing the first cis -regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C 3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.

Background WRKY proteins comprise a large family of transcription factors that play important roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in pineapple ( Ananas comosus ), an important tropical fruits. The recent release of the whole-genome sequence of pineapple allowed us to perform a genome-wide investigation into the organization and expression profiling of pineapple WRKY genes. Results In the present study, 54 pineapple WRKY (AcWRKY) genes were identified and renamed on the basis of their respective chromosome distribution. According to their structural and phylogenetic features, the 54 AcWRKYs were further classified into three main groups with several subgroups. The segmental duplication events played a major role in the expansion of pineapple WRKY gene family. Synteny analysis and phylogenetic comparison of group III WRKY genes provided deep insight into the evolutionary characteristics of pineapple WRKY genes. Expression profiles derived from transcriptome data and real-time quantitative PCR analysis exhibited distinct expression patterns of AcWRKY genes in various tissues and in response to different abiotic stress and hormonal treatments. Conclusions Fifty four WRKY genes were identified in pineapple and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This systematic analysis provided a foundation for further functional characterization of WRKY genes with an aim of pineapple crop improvement.

Background The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple ( Ananas comosus ) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level. Results In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization. Conclusions In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple.

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

Background Pineapple ( Ananas comosus L.) is a major tropical fruit crop with considerable economic importance, and its growth and development are significantly impacted by low temperatures. The plant-specific GRAS gene family plays crucial roles in diverse processes, including flower and fruit development, as well as in stress responses. However, the role of the GRAS family in pineapple has not yet been systematically analyzed. Results In this study, 43 AcGRAS genes were identified in the pineapple genome; these genes were distributed unevenly across 19 chromosomes and 6 scaffolds and were designated as AcGRAS01 to AcGRAS43 based on their chromosomal locations. Phylogenetic analysis classified these genes into 14 subfamilies: OS19, HAM-1, HAM-2, SCL4/7, LISCL, SHR, PAT1, DLT, LAS, SCR, SCL3, OS43, OS4, and DELLA. Gene structure analysis revealed that 60.5% of the AcGRAS genes lacked introns. Expression profiling demonstrated tissue-specific expression, with most AcGRAS genes predominantly expressed in specific floral organs, fruit tissues, or during particular developmental stages, suggesting functional diversity in pineapple development. Furthermore, the majority of AcGRAS genes were induced by cold stress, but different members seemed to play distinct roles in short-term or long-term cold adaptation in pineapple. Notably, most members of the PAT1 subfamily were preferentially expressed during late petal development and were upregulated under cold stress, suggesting their special roles in petal development and the cold response. In contrast, no consistent expression patterns were observed among genes in other subfamilies, suggesting that various regulatory factors, such as miRNAs, transcription factors, and cis-regulatory elements, may contribute to the diverse functions of AcGRAS members, even within the same subfamily. Conclusions This study provides the first comprehensive analysis of GRAS genes in pineapple, offers valuable insights for further functional investigations of AcGRASs and provides clues for improving pineapple cold resistance breeding.

Pineapple (Ananas comosus (L.) Merr.) is an economically significant and delicious tropical fruit. Pineapple commercial production faces severe decline due to abiotic stresses, which affect the development and quality of pineapple fruit. Heat shock protein 70 (HSP70) plays an essential role in abiotic stress tolerance. However, the pineapple HSP70 family identification and expression analysis in response to abiotic stresses has not been studied. To explore the functional role of AcHSP70, different abiotic stress treatments were applied to pineapple cultivar “Bali” seedlings. A total of 21 AcHSP70 members were identified in the pineapple genome. The identified genes were classified into four subfamilies (I–IV) using phylogenetic analysis. The AcHSP70 family is expressed under different stress conditions. Quantitative real time polymerase chain reaction (qRT-PCR) revealed the expression pattern of the AcHSP70 family under cold, drought, salt, and heat stress. The expression level of genes such as AcHSP70-2 increased under heat, cold, and drought stress, while the expression level of genes such as AcHSP70-3 decreased under salt stress. Furthermore, the expression profile of AcHSP70s in different tissues and development stages was analyzed using transcriptome analysis. The HSP70 genes exhibited unique expression patterns in pineapple tissue at different developmental stages. The study therefore provides a list of HSP70 genes with substantial roles in abiotic stress response and valuable information for understanding AcHSP70 functional characteristics during abiotic stress tolerance in pineapple.

Background Pineapple ( Ananas comosus L.), an economically significant tropical fruit crop, is highly susceptible to low-temperature during cultivation. The abscisic acid (ABA) and stress-inducible HVA22 gene family is known to play important roles in growth regulation and abiotic stress response, but its functions in pineapple remain unclear. Results We identified 11 HVA22 genes ( AcHVA22A - AcHVA22K ) in the pineapple genome and grouped them into four phylogenetic clades. Expression analysis showed that most AcHVA22 genes displayed tissue- or developmental stage-specific expression patterns, suggesting their diverse functions in pineapple growth and development. Subcellular localization analyses revealed diverse localizations of AcHVA22 proteins, including plasma membrane, cytoplasm, and nucleus. And regulatory predictions indicated control by multiple cis -elements, transcription factors, and miRNAs, which may contribute to their functional diversification. Most AcHVA22 genes responded consistently to ABA, GA, and drought treatments, but their responses to high and low-temperatures varied. Notably, AcHVA22C/D/E/G/I/K were up-regulated under both short- and long-term cold treatments in two different pineapple varieties, highlighting their potential key roles in cold stress tolerance. Conclusions This study provided the first genome-wide characterization of the HVA22 gene family in pineapple. The identification of candidate genes involved in cold stress response offers new insights into HVA22 functions in tropical fruits and provides valuable resources for improving cold resistance in pineapple breeding.

Pineapple cultivation worldwide depends on a limited number of cultivars. In Brazil, the cultivar ‘‘Pérola’’ accounts for 85% of the commercial planted area but is susceptible to fusariosis, the most significant disease affecting pineapple crops. This study introduces the cultivar ‘Unemat Rubi’, emphasizing its superior fruit quality and resistance to fusariosis through multivariate analyses, correlation networks, and genetic parameters. Eighteen genotypes were evaluated for qualitative and quantitative traits and resistance to fusariosis, using a randomized block design with five replications and 20 plants per plot. The genotypes were grouped into two main clusters based on their resistance or susceptibility to fusariosis. ‘Unemat Rubi’ was classified in Cluster I, along with its female parent (‘BRS Imperial’), sharing resistance to fusariosis, cylindrical fruits with yellow pulp, and no leaf spines. However, ‘Unemat Rubi’ was superior to ‘BRS Imperial’ in terms of fruit weight and diameter, presenting a mass above 1.5 kg and an average diameter above 10 cm. No correlations were observed between the groups of chemical and physical traits of fruit and resistance to fusariosis, only between the groups of physical and chemical traits. There was a high and positive correlation for FMWOC and FMWC (0.99) and a strong and significant correlation between DLL with FMWOC and FMWC, both with 0.74. Heritability estimates exceeded 90% for most traits, except for fruit diameter. The cultivar ‘Unemat Rubi’, registered at the Brazilian Ministry of Agriculture and Livestock under number 56,622, represents a significant advancement in pineapple breeding by integrating superior fruit quality with fusariosis resistance, making it a promising candidate for commercial expansion.

A physiological disease of the pineapple fruit called pineapple translucency causes the pulp to become water-soaked, which affects the fruit’s taste, flavor, shelf life, and integrity. In the present study, we analyzed seven pineapple varieties, of which three were watery and four were non-watery. There were no apparent macronutritional (K, P, or N) differences in their pulp, but the non-watery pineapple varieties had higher dry matter and soluble sugar content. The metabolomic analysis found 641 metabolites and revealed differential expression of alkaloids, phenolic acids, nucleotide derivatives, lipids, and other metabolites among the seven species. Transcriptome analysis and further KEGG enrichment showed downregulation of ‘flavonoid biosynthesis’ pathways, differential expression of metabolic pathways, secondary metabolites biosynthesis, plant–pathogen interaction, and plant hormone signal transduction. We believe this study will provide critical molecular data supporting a deeper understanding of pineapple translucency formation and greatly benefit future research on this commercially important crop.

The fruit physico-chemical properties, antioxidant activity and mineral contents of 26 pineapple [Ananas comosus (L.) Merr.] genotypes grown in China were measured. The results showed great quantitative differences in the composition of these pineapple genotypes. Sucrose was the dominant sugar in all 26 genotypes, while citric acid was the principal organic acid. Potassium, calcium and magnesium were the major mineral constituents. The ascorbic acid (AsA) content ranged from 5.08 to 33.57 mg/100 g fresh weight (FW), while the total phenolic (TP) content varied from 31.48 to 77.55 mg gallic acid equivalents (GAE)/100 g FW. The two parameters in the predominant cultivars Comte de Paris and Smooth Cayenne were relative low. However, MD-2 indicated the highest AsA and TP contents (33.57 mg/100 g and 77.55 mg GAE/100 g FM, respectively), and it also showed the strongest antioxidant capacity 22.85 and 17.30 μmol TE/g FW using DPPH and TEAC methods, respectively. The antioxidant capacity of pineapple was correlated with the contents of phenolics, flavonoids and AsA. The present study provided important information for the further application of those pineapple genotypes.