Rose without prickle: genomic insights linked to moisture adaptation.
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ABSTRACT:
SUBMITTER: Zhong MC
PROVIDER: S-EPMC8694671 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Rose is an economically important flowering plant that holds an essential place in cut flower, medicinal, and aromatic industries. The presence of prickles, epidermal outgrowths resembling trichomes, on rose is highly undesirable as these make harvesting and transportation difficult. Attempts were made for generating rose varieties lacking prickles via breeding and natural selections; however, these approaches obtained only chimeric and genetically unstable prickle-less mutants. The alternative way to get rid of prickles is via genetic manipulations, but the molecular mechanisms of prickle initiation and development in rose are almost unexplored. Therefore, the present study was carried out to understand the morphological, molecular, and correlated metabolic changes underlining prickle morphogenesis in a prickle-bearing Rosa hybrida L. cv. "First Red (FR)". The histological and metabolomic analyses at three distinct stages of the prickle morphogenesis, namely, emerging tiny initiating prickles, partially greenish soft prickles, and brownish hard prickles, demonstrated a gradually increasing deposition of phenolic compounds and lignification with development. Corresponding RNAseq analysis revealed an upregulation of the genes involved in secondary metabolism, especially in the phenylpropanoid biosynthetic pathway. A set of genes encoding a transcriptional network similar to the one regulating epidermal cell differentiation leading to phenylpropanoid accumulation and trichome development, was also upregulated. Differential expression of this transcriptional network in prickle-less R. hybrida L. cv. "Himalayan Wonder" compared to prickly FR plants substantiated its involvement in prickle morphogenesis. The results collectively supported the proposition that prickles are evolved from trichomes and provided molecular clues towards engineering prickle-less roses.Significance statementPrickles, the vasculature less epidermal outgrowths resembling trichomes, are defense organs protecting plants against herbivory. Despite biological significance, the mechanism of prickle morphogenesis remains obscure. Here, we show that like trichomes, prickles accumulate secondary metabolites, especially lignin and flavonoids, during morphogenesis. Cognate transcriptome analysis demonstrated that upregulation of a hormone-regulated transcriptional activation-inhibition network, known to govern trichome morphogenesis, likely triggers the differentiation of epidermal cells to outgrow into prickle.
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Project description:BackgroundPenicillium chrysogenum is a filamentous fungal species with diverse habitats, yet little is known about its genetics in adapting to extreme subseafloor sedimental environments.ResultsHere, we report the discovery of P. chrysogenum strain 28R-6-F01, isolated from deep coal-bearing sediments 2306 m beneath the seafloor. This strain possesses exceptional characteristics, including the ability to thrive in extreme conditions such as high temperature (45 °C), high pressure (35 Mpa), and anaerobic environments, and exhibits broad-spectrum antimicrobial activity, producing the antibiotic penicillin at a concentration of 358 μg/mL. Genome sequencing and assembly revealed a genome size of 33.19 Mb with a GC content of 48.84%, containing 6959 coding genes. Comparative analysis with eight terrestrial strains identified 88 unique genes primarily associated with penicillin and aflatoxins biosynthesis, carbohydrate degradation, viral resistance, and three secondary metabolism gene clusters. Furthermore, significant expansions in gene families related to DNA repair were observed, likely linked to the strain's adaptation to its environmental niche.ConclusionsOur findings provide insights into the genomic and biological characteristics of P. chrysogenum adaptation to extreme anaerobic subseafloor sedimentary environments, such as high temperature and pressure.
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Project description:Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.
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Project description:Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.
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Project description:Prickles are common structures in plants that play a key role in defense against herbivores. In the Rosa genus, prickles are widely present with great diversity in terms of form and density. For cut rose production, prickles represent an important issue, as they can damage the flower and injure workers. Our objectives were to precisely describe the types of prickles that exist in roses, their tissues of origin and their development. We performed a detailed histological analysis of prickle initiation and development in a rose F1 population. Based on the prickle investigation of 110 roses, we proposed the first categorization of prickles in the Rosa genus. They are mainly divided into two categories, nonglandular prickles (NGPs) and glandular prickles (GPs), and subcategories were defined based on the presence/absence of hairs and branches. We demonstrated that NGPs and GPs both originate from multiple cells of the ground meristem beneath the protoderm. For GPs, the gland cells originate from the protoderm of the GP at the early developmental stage. Our findings clearly demonstrate that prickles are not modified trichomes (which originate from the protoderm). These conclusions are different from the current mainstream hypothesis. These results provide a foundation for further studies on prickle initiation and development in plants.
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