Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

Genome Biology and Evolution, Год журнала: 2022, Номер 15(1)

Опубликована: Дек. 30, 2022

Abstract Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. associated loss of photosynthesis have evolved repeatedly in plants, particularly monocots. Although reductive evolution plastomes mycoheterotrophs well documented, the dynamics nuclear genome remains largely unknown. Transcriptome datasets were generated four three families (Orchidaceae, Burmanniaceae, Triuridaceae) related green used for phylogenomic analyses to resolve relationships among mycoheterotrophs, their relatives, representatives across Phylogenetic trees based on 602 genes mostly congruent with plastome phylogenies, except Asparagales + Liliales clade inferred trees. Reduction chlorophyll synthesis photosynthetic gene expression relaxation purifying selection retained progressive, greater older nonphotosynthetic lineages. One hundred seventy-four 1375 plant benchmark universally conserved orthologous undetected any mycoheterotroph transcriptome or mycoheterotrophic orchid Gastrodia but expressed providing evidence massively convergent We designate this set deleted Missing Mycoheterotrophs (MIM). MIM encode not only mainly plastid membrane proteins also a diverse processes, unknown function, mitochondrial, cellular processes. Transcription photosystem II (psb29) all lineages implies function mycoheterotrophs. Nonphotosynthetic enable novel insights into as shifts, loss, convergence genomes.

Язык: Английский

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A combination of conserved and diverged responses underlies Theobroma cacao’s defense response to Phytophthora palmivora

BMC Biology, Год журнала: 2024, Номер 22(1)

Опубликована: Фев. 16, 2024

Plants have complex and dynamic immune systems that evolved to resist pathogens. Humans worked enhance these defenses in crops through breeding. However, many harbor only a fraction of the genetic diversity present wild relatives. Increased utilization diverse germplasm search for desirable traits, such as disease resistance, is therefore valuable step towards breeding are adapted both current emerging threats. Here, we examine defense responses across four populations long-generation tree crop Theobroma cacao L., well non-cacao species, with goal identifying elements essential protection against oomycete pathogen Phytophthora palmivora.

Язык: Английский

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Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

PLoS ONE, Год журнала: 2024, Номер 19(3), С. e0297015 - e0297015

Опубликована: Март 6, 2024

Gene expression is highly impacted by the environment and can be reflective of past events that affected developmental processes. It therefore expected gene serve as a signal current or future phenotypic traits. In this paper we identify sets genes, which call Prognostic Transcriptomic Biomarkers (PTBs), predict firmness in Malus domestica (apple) fruits. apples, all individuals cultivar are clones, differences fruit quality due to environment. The apples transcriptome responds these environment, makes PTBs an attractive predictor quality. have potential enhance supply chain efficiency, reduce crop loss, provide higher more consistent for consumers. However, several questions must addressed. answer question two common modeling approaches, Random Forest ElasticNet, outperforms other. We if with few genes efficient at predicting This important because need perform qPCR, qPCR cost-effective assay input modeled using high-throughput RNA-seq. To do this, conducted pilot study texture ‘Gala’ variety across postharvest storage regiments. Fruit controllable post-harvest treatments good candidate explore use PTBs. find RandomForest model than ElasticNet predictive (r2 = 0.78) 15 genes. also show reasonably RNA-seq follow up experiment. Results promising PTBs, yet work needed ensure robust various environmental conditions treatments.

Язык: Английский

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Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit

G3 Genes Genomes Genetics, Год журнала: 2023, Номер 13(8)

Опубликована: Июнь 1, 2023

Apples grown in high heat, light, and low humidity environments are at risk for sun injury disorders like sunburn associated crop losses. Understanding the physiological molecular mechanisms underlying will support improvement of mitigation strategies breeding more resilient varieties. Numerous studies have highlighted key biochemical processes involved injury, such as phenylpropanoid reactive oxygen species (ROS) pathways, demonstrating both enzyme activities expression related genes response to conditions. Most previous focused on at-harvest activity a small number heat stress. Thus, it remains unclear how stress events earlier season affect physiology gene expression. Here, we applied mid-season apples field collected tissue along time course-24, 48, 72 h following stimulus-to investigate dynamic changes using transcriptomic lens. We found relatively differentially expressed (DEGs) enriched functional terms treatments. Only few these belonged pathways previously described be sunburn, AsA-GSH pathway, while most DEGs had not yet been implicated or pome fruit.

Язык: Английский

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kakapo: easy extraction and annotation of genes from raw RNA-seq reads

PeerJ, Год журнала: 2023, Номер 11, С. e16456 - e16456

Опубликована: Ноя. 27, 2023

kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes gene families. It flexibly uses original RNA-seq read GenBank SRA accession inputs without performing global assembly of entire transcriptomes metatranscriptomes. The identifies open reading frames in the assembled transcripts annotates them. optionally filters raw reads for ribosomal, plastid, mitochondrial reads, belonging non-target organisms ( e.g. , viral, bacterial, human). can be employed targeted assembly, arbitrary loci, such as those commonly used phylogenetic inference systematics candidate families phylogenomic metagenomic studies. We provide example applications discuss how its use offset declining value GenBank’s single-gene databases help datasets variety analyses.

Язык: Английский

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Peach LAZY1 and DRO1 protein-protein interactions and co-expression with PRAF/RLD family support conserved gravity-related protein interactions across plants.

PubMed, Год журнала: 2024, Номер 2024

Опубликована: Янв. 1, 2024

IGT/LAZY proteins play a central role in determining gravitropic set point angle and orientation of lateral organs across plant species. Recent work model systems has demonstrated that interactions between BREVIS RADIX (BRX)-domain containing proteins, such as PH, RCC1, AND FYVE/RCC1-LIKE DOMAIN (PRAF/RLD), LIKE (BRXL) family members, are mechanistically important for setting angle. Here, we identified peach PRAF/RLD interactors the PpeLAZY1 DEEPER ROOTING 1 (PpeDRO1) from yeast-two-hybrid screen. We also show BRX domains these interacting have high sequence similarity with rice Arabidopsis. Further, all expressed at relatively levels leaf, meristem, shoot tip tissues. Together, this evidence supports importance conservation IGT/LAZY-BRX-domain interactions, which underlie angiosperms.

Язык: Английский

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Bioinformatics for Gene Identification and Crop Improvement in Wheat

Опубликована: Июль 19, 2024

In recent years, the availability of high-throughput genome/transcriptome sequencing data and sophisticated bioinformatics tools facilitated in silico identification novel genes for several crops including wheat using well-characterized from other species. The information thus generated may be used further validation marker-assisted selection (MAS), gene editing, cloning. this chapter, we summarize available developments field, three parts: (i) databases, tools, methodology corresponding proteins; (ii) present status families identified (including contribution authors own lab); (iii) use current future improvement programs. This chapter is a suitable reference students/scientists working field plant genomics cultivars.

Язык: Английский

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Genome-Wide Survey of the Potential Function of CrLBDs in Catharanthus roseus MIA Biosynthesis

Genes, Год журнала: 2024, Номер 15(9), С. 1140 - 1140

Опубликована: Авг. 29, 2024

Catharanthus roseus (C. roseus) can produce over 150 types of monoterpenoid indole alkaloids (MIAs), including vinblastine and vincristine, which are currently the primary sources these alkaloids. Exploring complex regulatory mechanisms C. is significant for resolving MIA biosynthesis. The Lateral Organ Boundaries Domain (LBD) a plant-specific transcription factor family that plays crucial roles in physiological processes plant growth, stress tolerance, specialized metabolism. However, LBD gene has not been extensively characterized roseus, whether its members involved biosynthesis still being determined. A total 34 (CrLBD) genes were identified. RNA-Seq data investigated to examine expression patterns CrLBD various tissues methyl jasmonate (MeJA) treatments. results revealed Class Ia member CrLBD4 positively correlated with iridoid biosynthetic (p < 0.05, r ≥ 0.8); IIb CrLBD11 negatively ≤ −0.8). Further validation leaves at different growth stages showed exhibited potential trends accumulation vindoline catharanthine. Yeast one-hybrid (Y1H) subcellular localization assays demonstrated could bind “aattatTCCGGccgc” cis-element localize nucleus. These findings suggest may be candidates regulating roseus. In this study, we systematically analyzed provided insights into certain CrLBDs

Язык: Английский

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Genome architecture of the heavy metal tolerant and accumulator Hirschfeldia incana: insights from genome sequencing, assembly, and comparative analysis

Environmental and Experimental Botany, Год журнала: 2024, Номер unknown, С. 105991 - 105991

Опубликована: Окт. 1, 2024

Язык: Английский

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The evolution of pectate lyase-like genes across land plants, and their roles in haustorium formation in parasitic plants

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 7, 2024

Abstract Parasitic plants in Orobanchaceae are noxious agricultural pests that severely impact crops worldwide. These acquire water and nutrients from their hosts through a specialized organ called the haustorium. A key step haustorium development involves cell wall modification. In this study, we identified analyzed evolutionary relationships of pectate lyase-like ( PLL ) genes across parasitic other non-parasitic land plant lineages. To support detailed examination gene models paralogous family members, used published genomes, as well recently generated draft genome assembly annotation Triphysaria versicolor . One particular gene, denoted PLL1 Orobanchaceae, emerged an important candidate for parasitism, highlighted by our previous comparative transcriptomics research; it belongs to largest sub-clade is highly upregulated haustoria. explore its function development, manipulated expression T. , model species using direct transformation parasite host-induced-gene-silencing (HIGS). For HIGS, transgenic Medicago truncatula Arabidopsis thaliana expressing hairpin RNAs targeting Both experimental approaches effectively reduced resulting increased frequency poorly adhered parasites. findings demonstrate plays crucial role suggest promising target managing weeds. Notably, success HIGS even before establishment functional highlights possibility early intervention against parasitism.

Язык: Английский

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