RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development and ripening

2019 ◽  
Vol 254 ◽  
pp. 26-34 ◽  
Author(s):  
Dante Travisany ◽  
Anibal Ayala-Raso ◽  
Alex Di Genova ◽  
Liliam Monsalve ◽  
Maricarmen Bernales ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fruit Development ◽  
Transcriptome Assembly ◽  
Rubus Idaeus ◽  
Rna Seq ◽  
Fruit Development And Ripening

scholarly journals Transcriptome analysis of oil palm inflorescences revealed candidate genes for an auxin signaling pathway involved in parthenocarpy

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5975
Author(s):  
Suthasinee Somyong ◽  
Kitti Walayaporn ◽  
Nukoon Jomchai ◽  
Chaiwat Naktang ◽  
Tanapong Yodyingyong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Palm ◽  
Fruit Development ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Parthenocarpic Fruit ◽  
Rna Seq ◽  
Auxin Treatment ◽  
Auxin Signaling Pathway ◽  
Average Size

Oil palm parthenocarpic fruits, which are produced without fertilization, can be targeted to increase oil content because the majority of the fruit is occupied by mesocarp, the part in which palm oil is stored. Consequently, gaining an understanding of the parthenocarpic mechanism would be instrumental for producing parthenocarpic oil palm. This study aims to determine effects of auxin treatment and analyze differentially expressed genes in oil palm pistils at the pollination/anthesis stage, using an RNA sequencing (RNA seq) approach. The auxin treatment caused 100% parthenocarpy when auxin was sprayed before stigmas opened. The parthenocarpy decreased to 55%, 8% and 5% when the auxin was sprayed 1, 2 and 3 days after the opening of stigmas, respectively. Oil palm plants used for RNA seq were plants untreated with auxin as controls and auxin-treated plants on the day before pollination and 1 day after pollination. The number of raw reads ranged from 8,425,859 to 11,811,166 reads, with an average size ranging from 99 to 137 base pairs (bp). When compared with the oil palm transcriptome, the mapped reads ranged from 8,179,948 to 11,320,799 reads, representing 95.85–98.01% of the oil palm matching. Based on five comparisons between RNA seq of treatments and controls, and confirmation using reverse transcription polymerase chain reaction and quantitative real-time RT-PCR expression, five candidate genes, including probable indole-3-acetic acid (IAA)-amido synthetase GH3.8 (EgGH3.8), IAA-amido synthetase GH3.1 (EgGH3.1), IAA induced ARG7 like (EgARG7), tryptophan amino transferase-related protein 3-like (EgTAA3) and flavin-containing monooxygenase 1 (EgFMO1), were differentially expressed between auxin-treated and untreated samples. This evidence suggests a pathway of parthenocarpic fruit development at the beginning of fruit development. However, more research is needed to identify which genes are definitely involved in parthenocarpy.

scholarly journals Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 19 ◽  
Author(s):  
Chao Feng ◽  
Ming Chen ◽  
Chang-jie Xu ◽  
Lin Bai ◽  
Xue-ren Yin ◽  
...  
Keyword(s):  
Fruit Development ◽  
Transcriptomic Analysis ◽  
Rna Seq ◽  
Chinese Bayberry ◽  
Myrica Rubra ◽  
Fruit Development And Ripening

iTRAQ and RNA-Seq analyses revealed the effects of grafting on fruit development and ripening of oriental melon (Cucumis melo L. var. makuwa)

Gene ◽  
2021 ◽  
Vol 766 ◽  
pp. 145142
Author(s):  
Sheng Chen ◽  
Yongyu Li ◽  
Yijie Zhao ◽  
Guanfa Li ◽  
Weiguang Zhang ◽  
...  
Keyword(s):  
Fruit Development ◽  
Cucumis Melo ◽  
Rna Seq ◽  
Oriental Melon ◽  
Fruit Development And Ripening ◽  
Cucumis Melo L

scholarly journals De Novo Transcriptome Assembly of Isatis indigotica at Reproductive Stages and Identification of Candidate Genes Associated with Flowering Pathways

2018 ◽  
Vol 143 (1) ◽  
pp. 56-66
Author(s):  
Yu Bai ◽  
Ying Zhou ◽  
Xiaoqing Tang ◽  
Yu Wang ◽  
Fangquan Wang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Orthologous Group ◽  
Rna Seq ◽  
Isatis Indigotica ◽  
Regulatory Pathways ◽  
Kegg Pathways ◽  
Bolting And Flowering

The appropriate timing of bolting and flowering is one of the keys to the reproductive success of Isatis indigotica. Several flowering regulatory pathways have been reported in plant species, but we know little about flowering regulatory in I. indigotica. In the present study, we performed RNA-seq and annotated I. indigotica transcriptome using RNA from five tissues (leaves, roots, flowers, fruit, and stems). Illumina sequencing generated 149,907,857 high-quality clean reads and 124,508 unigenes were assembled from the sequenced reads. Of these unigenes, 88,064 were functionally annotated by BLAST searches against the public protein databases. Functional classification and annotation assigned 55,991 and 23,072 unigenes to 52 gene ontology (GO) terms and 25 clusters of orthologous group (COG) categories, respectively. A total of 19,927 unigenes were assigned to 124 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 80 candidate genes related to plant circadian rhythm were identified. We also identified a number of differentially expressed genes (DEG) and 91 potential bolting and flowering-related genes from the RNA-seq data. This study is the first to identify bolting and flowering-related genes based on transcriptome sequencing and assembly in I. indigotica. The results provide foundations for the exploration of flowering pathways in I. indigotica and investigations of the molecular mechanisms of bolting and flowering in Brassicaceae plants.

scholarly journals RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vera Thole ◽  
Jean-Etienne Bassard ◽  
Ricardo Ramírez-González ◽  
Martin Trick ◽  
Bijan Ghasemi Afshar ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rubus Idaeus ◽  
Wild Plant ◽  
Anthocyanin Synthesis ◽  
Rna Seq ◽  
Link Type ◽  
Fruit Species ◽  
Wide Range

Abstract Background Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds. Results To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige. Conclusions We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.

scholarly journals Transcriptome profiling of Finnsheep ovaries during out-of-season breeding period

2015 ◽  
Vol 24 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Kisun Pokharel ◽  
Jaana Peippo ◽  
Göran Andersson ◽  
Meng-Hua Li ◽  
Juha Kantanen
Keyword(s):  
Candidate Genes ◽  
Reference Genome ◽  
Transcriptome Assembly ◽  
Transcriptome Profiling ◽  
Breeding Period ◽  
Rna Seq ◽  
Sequence Coverage ◽  
Bioinformatics Pipeline ◽  
Two Samples ◽  
The World

Finnsheep is one of the most prolific sheep breeds in the world. We sequenced RNA-Seq libraries from the ovaries of Finnsheep ewes collected during out of season breeding period at about 30X sequence coverage. A total of 86 966 348 and 105 587 994 reads from two samples were mapped against latest available ovine reference genome (Oarv3.1). The transcriptome assembly revealed 14 870 known ovine genes, including the 15 candidate genes for fertility and out-of-season breeding. In this study we successfully used our bioinformatics pipeline to assemble the first ovarian transcriptome of Finnsheep.

scholarly journals Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1423
Author(s):  
André Albuquerque ◽  
Cristina Óvilo ◽  
Yolanda Núñez ◽  
Rita Benítez ◽  
Adrián López-Garcia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Growth ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Pig Breeds ◽  
Nfkb Activation ◽  
Main Gene ◽  
Slow Type ◽  
Longissimus Lumborum ◽  
Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

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