Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process.
Ontology highlight
ABSTRACT:
SUBMITTER: Martinez O
PROVIDER: S-EPMC8003350 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Gene expression is the primary molecular phenotype and can be estimated in specific organs or tissues at particular times. Here we analyzed genome-wide inheritance of gene expression in fruits of chili pepper (Capsicum annuum L.) in reciprocal crosses between a domesticated and a wild accession, estimating this parameter during fruit development. We defined a general hierarchical schema to classify gene expression inheritance which can be employed for any quantitative trait. We found that inheritance of gene expression is affected by both, the time of fruit development as well as the direction of the cross, and propose that such variations could be common in many developmental processes. We conclude that classification of inheritance patterns is important to have a better understanding of the mechanisms underlying gene expression regulation, and demonstrate that sets of genes with specific inheritance pattern at particular times of fruit development are enriched in different biological processes, molecular functions and cell components. All curated data and functions for analysis and visualization are publicly available as an R package.
| S-EPMC8609037 | biostudies-literature
Project description:BACKGROUND: The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. RESULTS: RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueño 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. CONCLUSIONS: In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.
| S-EPMC3936869 | biostudies-literature
Project description:The process of domestication requires the rapid transformation of the wild morphology into the cultivated forms that humans select for. This process often takes place through changes in the regulation of genes, yet, there is no definite pattern on the role of cis- and trans-acting regulatory variations in the domestication of the fruit among crops. Using allele-specific expression and network analyses, we characterized the regulatory patterns and the inheritance of gene expression in wild and cultivated accessions of chili pepper, a crop with remarkable fruit morphological variation. We propose that gene expression differences associated to the cultivated form are best explained by cis-regulatory hubs acting through trans-regulatory cascades. We show that in cultivated chili, the expression of genes associated with fruit morphology is partially recessive with respect to those in the wild relative, consistent with the hybrid fruit phenotype. Decreased expression of fruit maturation and growth genes in cultivated chili suggest that selection for loss-of-function took place in its domestication. Trans-regulatory changes underlie the majority of the genes showing regulatory divergence and had larger effect sizes on gene expression than cis-regulatory variants. Network analysis of selected cis-regulated genes, including ARP9 and MED25, indicated their interaction with many transcription factors involved in organ growth and fruit ripening. Differentially expressed genes linked to cis-regulatory variants and their interactions with downstream trans-acting genes have the potential to drive the morphological differences observed between wild and cultivated fruits and provide an attractive mechanism of morphological transformation during the domestication of the chili pepper.
| S-EPMC7253206 | biostudies-literature
Project description:Background The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Chili pepper is an economically and culturally important horticultural crop as well as a good model for the study of secondary metabolism during fruit development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. Results RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueno 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. Subsets of genes were expressed only at a single time point sampled (1,278, 1,596, 1,519 and 1,583 genes at 10, 20, 40 and 60 DAA, respectively). We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. Conclusions In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.
2014-02-21 | GSE54123 | GEO
Project description:The pepper weevil, Anthonomus eugenii, Cano (Coleoptera: Curculionidae), is one of the most destructive pests of chili pepper. It causes extensive damage on varieties selected for consumption. However, the occurrence of this pest on wild and ornamental peppers remains unknown. We investigated the consequences of chili domestication on the feeding and oviposition of A. eugenii on fruits and flowers. We used plants of one wild accession, Bird Eye Pepper, five ornamental varieties (Pops Yellow, Black Pearl, Sedona Sun, Chilli Chilli, and Salsa Deep), and two domesticated varieties selected for consumption (Scotch Bonnet and Jalapeño). First, we characterized the plants according to their fruit and flower sizes, pericarp thickness, capsaicin level, fruit position, and flower color. Then, we evaluated the susceptibility of fruits and flowers to A. eugenii. Overall, domestication increased fruit and flower sizes and pericarp thickness, altered capsaicin levels, and altered fruit position and flower color. Weevils laid more eggs and caused more feeding damage on varieties selected for consumption than on wild and ornamental plants. Our results add to the growing literature on the consequences of crop domestication on herbivores. This knowledge could be integrated into breeding programs to select varieties resistant against the pepper weevil.
| S-EPMC8305446 | biostudies-literature
Project description:Background The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Chili pepper is an economically and culturally important horticultural crop as well as a good model for the study of secondary metabolism during fruit development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. Results RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueno 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. Subsets of genes were expressed only at a single time point sampled (1,278, 1,596, 1,519 and 1,583 genes at 10, 20, 40 and 60 DAA, respectively). We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. Conclusions In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled. RNA-seq libraries of whole chili pepper (Capsicum annuum Serrano 'Tampiqueno 74' landrace) were prepared from fruits at 10, 20, 40 and 60 days after anthesis (DAA). Two biological replicates of each fruit state were prepared (8 libraries in total). Libraries were sequenced in the Illumina MiSeq platform. The title of the libraries are: <DAA>repbio<#> where <DAA> are the days after anthesis (10, 20, 40 or 60) and <#> is the number of biological replicate, 1 or 2. Details follow. Biological material and RNA extraction Capsicum annuum Serrano 'Tampiqueno 74' seeds were germinated and the seedlings were cultivated until maturity under greenhouse conditions in a completely randomized experimental design at Cinvestav-Unidad Irapuato (Guanajuato, Mexico). The plants were grown during the spring and summer, and individual flowers were tagged at anthesis. Chili pepper fruits were randomly collected from different plants at 10, 20, 40 and 60 DAA. After sampling, the fruits were cleaned with ethanol immediately frozen in liquid nitrogen and stored at -80C until further use. For total RNA extractions, 10 fruits at the 10 DAA developmental stage and 5 fruits from each of the 20, 40 and 60 DAA stages were randomly selected from the pool of all harvested fruits. Whole fruits (pericarp, placenta and seeds) were ground in liquid nitrogen with a mortar and pestle to form a fine uniform powder. Samples were mixed vigorously and 100 mg aliquots were measured for each RNA extraction. The process was repeated with different sets of fruits in order to obtain two independent biological replicates at each developmental stage. A NucleoSpin RNA Plant kit (Macherey-Nagel) was used for total RNA extraction and contaminating genomic DNA was removed by DNase I (Macherey-Nagel) treatment following the manufacturers' protocols. Total RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer (Nano-Drop, Wilmington, DE, USA) and RNA quality was evaluated by gel electrophoresis on 1.0% denaturing agarose gels. In addition, aliquots of RNA were run on an Agilent 2100 Bioanalyzer using RNA 6000 chips (Agilent, Santa Clara, CA, USA) to test the RNA integrity number (RIN). All eight samples had RIN values higher than 8.7. Thirty ?g of total RNA from each of the eight samples (two biological replicates of four fruit developmental stages) was used for cDNA library preparation. Library construction and sequencing The eight total RNA samples (two biological replicates from chili pepper fruits at 10, 20, 40 and 60 DAA) were prepared for RNA-Seq using the Illumina TruSeq RNA Sample Preparation v2 Guide following the manufacturer's instructions. Briefly, mRNA was purified from 20?g of total RNA using poly-T oligo- attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, mRNA was fragmented using divalent cations under elevated temperature and primed for cDNA synthesis. The cleaved RNA fragments were primed with random hexamers and reverse transcribed into single-stranded cDNA using reverse transcriptase. In the next step, the RNA template was removed and the complementary cDNA strand was synthesized using RNAse H and DNA polymerase I, respectively. The overhangs that resulted from fragmentation were polished into blunt ends using an End Repair Mix (consisting of T4 DNA polymerase, Klenow fragment and T4 polynucleotide kinase). A single T nucleotide was added on the 3' end of the adapter for ligating the adapter to the cDNA fragments. Indexing adapters were ligated to the ends of the cDNAs using T4 DNA ligase, preparing them for hybridization onto a flow cell. Finally, the DNA fragments with adapter molecules at both ends were amplified by PCR to enrich the amount of DNA in the library. PCR was performed with a PCR primer cocktail that anneals to the ends of the adapters. Quantity and quality of the DNA libraries was assessed using Agilent DNA-1000 chips on an Agilent 2100 Bioanalyzer. The 8 cDNA libraries were pooled and simultaneously sequenced from both 5’ and 3’ ends using the Illumina MiSeq System platform according to the manufacturer's instructions. We performed three sequencing runs (technical replicates) with the aim of increase the sequencing depth. 150 bp paired-end reads were obtained in each sequencing run. Fluorescent image processing, base-calling and quality value calculations for each of the three runs were performed using Illumina MiSeq Control Software. Data were deposited at the NCBI (GEO database under series record GSE54123).
2014-02-21 | E-GEOD-54123 | biostudies-arrayexpress
Project description:BackgroundUnderstanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses.ResultsThe root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst = 0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication.ConclusionsWestern carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.
| S-EPMC4213543 | biostudies-literature
Project description:Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.
2021-03-16 | GSE165448 | GEO