Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties

Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears

Unbiased subgenome evolution following a recent whole-genome duplication in pear (Pyrus bretschneideri Rehd.)

Following a trail of duplicated pear DNA Genomic sleuthing reveals insights into an ancestral chromosomal duplication event from the early evolution of the pear tree. Such ‘whole-genome duplication’ is common among plants, and can arise from the combination of genetic material of plants from either the same (autopolyploid) or different (allopolyploid) species. The pear is known to have undergone a duplication event 30 million years ago, and Shaoling Zhang and colleagues at Nanjing Agricultural University in China set out to assess the nature of this genome expansion. After analysis of pear genome data and comparison against other fruit plant species, the researchers determined that the pear is an autopolyploid, and that genes found in just one ‘subgenome’ have subsequently evolved expression profiles that differ noticeably from those genes that are present as multiple homologues amongst the duplicated chromosomes

Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants

Abstract Background The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. Results We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. Conclusions We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes

Comprehensive Genomic Analysis of <i>SnRK</i> in Rosaceae and Expression Analysis of <i>RoSnRK2</i> in Response to Abiotic Stress in <i>Rubus occidentalis</i>

The sucrose nonfermenting 1-related protein kinase (SnRK) plays an important role in responding to abiotic stresses by phosphorylating the target protein to regulate various signaling pathways. However, little is known about the characteristics, evolutionary history, and expression patterns of the SnRK family in black raspberry (Rubus occidentalis L.) or other Rosaceae family species. In this study, a total of 209 SnRK genes were identified in 7 Rosaceae species and divided into 3 subfamilies (SnRK1, SnRK2, and SnRK3) based on phylogenetic analysis and specific motifs. Whole-genome duplication (WGD) and dispersed duplication (DSD) were considered to be major contributions to the SnRK family expansion. Purifying selection was the primary driving force in the SnRK family evolution. The spatial expression indicated that the RoSnRK genes may play important roles in different tissues. In addition, the expression models of 5 RoSnRK2 genes in response to abiotic stresses were detected by qRT-PCR. The proteins encoded by RoSnRK2 genes localize to the cytoplasm and nucleus in order to perform their respective functions. Taken together, this study provided an analysis of the SnRK gene family expansion and evolution, and contributed to the current knowledge of the function of 5 RoSnRK2 genes, which in turn expanded understanding of the molecular mechanisms of black raspberry responses to abiotic stress

Aroma volatile characterisation and gene expression analysis during fruit development and ripening of five pear (<i>Pyrus L.</i>) species

Bartlett, Hongnanguo, Korla Xiangli, Dangshansuli and Housui are representative cultivars from the five cultivated pear species that were chosen to identify aromatic compounds in fruit during developmental, mature and storage periods. We explored the expression levels of aroma formation-related genes during developmental and storage periods. The concentrations of the aromatic compounds first decreased, then increased in all five cultivars. For the climacteric pears, Bartlett and Hongnanguo, the increase continued to optimal sensory quality (OSQ), whereas those for the non-climacteric pears, Korla Xiangli, Dangshansuli and Housui decreased. Aldehydes contributing the 'green' odour and 1,4-benzoquinone were the primary components during early and middle developmental periods. Esters contributing the 'fruity' and 'sweet' odour, were the primary components in Bartlett, Hongnanguo and Korla Xiangli fruits during storage and at OSQ. Methyl- and ethyl-(E, Z)-2,4-decadienoate (pear-like odour), ethyl caproate (liquor odour), and hexyl acetate (fruity odour) were the key characteristic odorants in mature pear fruits of Bartlett, Hongnanguo and Korla Xiangli, respectively. Alcohol dehydrogenase (PbrADH-1 and PbrADH-2) and lipoxygenase (PbrLOX3) might participate in the formation of C6 and C9 volatile aldehydes and alcohols. The aroma content and volatiles of pear fruits during development and storage probably revealed a common pattern.</p

The genomic basis of the plant island syndrome in Darwin’s giant daisies

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies