ArticleMolecular genetics and genomics : MGG2014
Towards an improved apple reference transcriptome using RNA-seq.
Article in Molecular genetics and genomics : MGG, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Unraveling the occasional occurrence of berry astringency in table grape cv. Scarlet Royal: a physiological and transcriptomic analysis.Frontiers in plant science · 2023Article
- Transcriptomic and metabolomic joint analysis reveals distinct flavonoid biosynthesis regulation for variegated testa color development in peanut (Arachis hypogaea L.).Scientific reports · 2021Article
- Transcriptome Profiling During Muscadine Berry Development Reveals the Dynamic of Polyphenols Metabolism.Frontiers in plant science · 2021Article
- An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals.Frontiers in plant science · 2021Review
- Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants.Scientific reports · 2020Article
- Article
- Exploring DNA Variant Segregation Types Enables Mapping Loci for Recessive Phenotypic Suppression of Columnar Growth in Apple.Frontiers in plant science · 2020Article
- Differential gene expression in non-transgenic and transgenic "M.26" apple overexpressing a peach CBF gene during the transition from eco-dormancy to bud break.Horticulture research · 2019Article
- Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus.Journal of experimental botany · 2018Article
- In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits.PloS one · 2017Article
- A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications.Nucleic acids research · 2016Article
- Comparative performance of transcriptome assembly methods for non-model organisms.BMC genomics · 2016Article
- Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation.Journal of experimental botany · 2015Article
- Uncovering co-expression gene network modules regulating fruit acidity in diverse apples.BMC genomics · 2015Article
- A co-expression gene network associated with developmental regulation of apple fruit acidity.Molecular genetics and genomics : MGG · 2015Article
- Elucidating the molecular responses of apple rootstock resistant to ARD pathogens: challenges and opportunities for development of genomics-assisted breeding tools.Horticulture research · 2014Review
- Understanding development and ripening of fruit crops in an 'omics' era.Horticulture research · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The reference genome of apple (Malus × domestica) has been available since 2010. Despite being a milestone in apple genomics, the reference genome is difficult to be used as a reference in RNA-seq (RNA sequencing) analysis, a widespread technology in transcriptomic studies. One of the major limitations appears to be the low coverage of the reference transcriptome in RNA-seq mapping of reads. To improve the reference transcriptome, we obtained 14 sets of strand-specific RNA-seq data of 168.5 million reads in total from fruit of Golden Delicious (GD, the source of the reference genome) in varying growth and developmental stages. Using a combination of genome-guided assembly and de novo assembly, the apple reference transcriptome was improved to a collection of 71,178 genes or transcripts, which includes 53,654 genes predicted originally (with MDP prefixed in their IDs) and 17,524 novel transcripts. Of these novel transcripts, 8,144 were identified from reads directly mapped to the reference genome while the remaining 9,380 were extracted from de novo assemblies of reads that could not be initially mapped to the reference genome. Evaluating the improved apple reference transcriptome with reads from Golden Delicious and other genotypes used in this and other studies showed that it allowed 62.5 ± 9.3-82.3 ± 2.7 % of reads to be mapped, a marked increase from the low rates of 37.4 ± 7.7-46.6 ± 7.1 % offered by the original reference transcriptome. The improved reference transcriptome therefore represents a step forward towards a complete reference transcriptome in apple.
Indexed as
Identifiers
24532088What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.