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Research article
Amandeep Mittal
Punjab Agricultural University
Corresponding Author
License:
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Background
Guava ( Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has potential to set the stage for the functional genomics for traits of commerce.
Results
Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with N50 of 3,603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues and 68 genes among colored tissue comparisons. Mapping the differentially expressed transcripts over molecular pathways indicate significant hormonal changes during fruit development. Comparisons of red vs green peel in guava cv. Apple Colour, white pulp vs red pulp in Punjab pink and fruit maturation vs ripening in non-coloured Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways.
Conclusions
Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting colour genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.
Keywords
Guava RNA-Seq, Fruit development and ripening, Allahabad Safeda, Punjab Pink, Apple Colour, Secondary metabolites, Candidate genes for fruit colour
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CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 1
Posted 07 Feb, 2020
No community comments so far
Editorial decision: Major revision
On 03 Mar, 2020
Reviewer #7 agreed
On 29 Feb, 2020
Review #2 received
Received 28 Feb, 2020
Review #3 received
Received 28 Feb, 2020
Reviewer #6 agreed
On 27 Feb, 2020
Reviewer #5 agreed
On 24 Feb, 2020
Review #4 received
Received 24 Feb, 2020
Review #1 received
Received 17 Feb, 2020
Reviewer #4 agreed
On 09 Feb, 2020
Reviewer #3 agreed
On 08 Feb, 2020
Reviewer #2 agreed
On 07 Feb, 2020
Reviewers invited
Invitations sent on 06 Feb, 2020
Reviewer #1 agreed
On 06 Feb, 2020
Editor invited
On 05 Feb, 2020
Editor assigned
On 31 Jan, 2020
Submission checks complete
On 30 Jan, 2020
First submitted
On 29 Jan, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Amandeep Mittal
Punjab Agricultural University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 1
Posted 07 Feb, 2020
No community comments so far
Editorial decision: Major revision
On 03 Mar, 2020
Reviewer #7 agreed
On 29 Feb, 2020
Review #2 received
Received 28 Feb, 2020
Review #3 received
Received 28 Feb, 2020
Reviewer #6 agreed
On 27 Feb, 2020
Reviewer #5 agreed
On 24 Feb, 2020
Review #4 received
Received 24 Feb, 2020
Review #1 received
Received 17 Feb, 2020
Reviewer #4 agreed
On 09 Feb, 2020
Reviewer #3 agreed
On 08 Feb, 2020
Reviewer #2 agreed
On 07 Feb, 2020
Reviewers invited
Invitations sent on 06 Feb, 2020
Reviewer #1 agreed
On 06 Feb, 2020
Editor invited
On 05 Feb, 2020
Editor assigned
On 31 Jan, 2020
Submission checks complete
On 30 Jan, 2020
First submitted
On 29 Jan, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background
Guava ( Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has potential to set the stage for the functional genomics for traits of commerce.
Results
Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with N50 of 3,603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues and 68 genes among colored tissue comparisons. Mapping the differentially expressed transcripts over molecular pathways indicate significant hormonal changes during fruit development. Comparisons of red vs green peel in guava cv. Apple Colour, white pulp vs red pulp in Punjab pink and fruit maturation vs ripening in non-coloured Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways.
Conclusions
Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting colour genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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