RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars
Abstract 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 expres...
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doaj-666001c675444707a4ae390db690a5462020-11-25T02:18:22ZengBMCBMC Genomics1471-21642020-07-0121111910.1186/s12864-020-06883-6RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivarsAmandeep Mittal0Inderjit Singh Yadav1Naresh Kumar Arora2Rajbir Singh Boora3Meenakshi Mittal4Parwinder Kaur5William Erskine6Parveen Chhuneja7Manav Indra Singh Gill8Kuldeep Singh9School of Agricultural Biotechnology, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, Punjab Agricultural UniversityDepartment of Fruit Science, Punjab Agricultural UniversityFruit Research Sub-Station, Punjab Agricultural UniversityPlant Breeding and Genetics, Punjab Agricultural UniversityCentre for Plant Genetics and Breeding, University of Western AustraliaCentre for Plant Genetics and Breeding, University of Western AustraliaSchool of Agricultural Biotechnology, Punjab Agricultural UniversityDepartment of Fruit Science, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, Punjab Agricultural UniversityAbstract 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 a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel. 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 a N50 of 3603 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. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored 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 color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.http://link.springer.com/article/10.1186/s12864-020-06883-6Guava RNA-SeqFruit development and ripeningAllahabad SafedaPunjab PinkApple ColorSecondary metabolites |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Amandeep Mittal Inderjit Singh Yadav Naresh Kumar Arora Rajbir Singh Boora Meenakshi Mittal Parwinder Kaur William Erskine Parveen Chhuneja Manav Indra Singh Gill Kuldeep Singh |
spellingShingle |
Amandeep Mittal Inderjit Singh Yadav Naresh Kumar Arora Rajbir Singh Boora Meenakshi Mittal Parwinder Kaur William Erskine Parveen Chhuneja Manav Indra Singh Gill Kuldeep Singh RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars BMC Genomics Guava RNA-Seq Fruit development and ripening Allahabad Safeda Punjab Pink Apple Color Secondary metabolites |
author_facet |
Amandeep Mittal Inderjit Singh Yadav Naresh Kumar Arora Rajbir Singh Boora Meenakshi Mittal Parwinder Kaur William Erskine Parveen Chhuneja Manav Indra Singh Gill Kuldeep Singh |
author_sort |
Amandeep Mittal |
title |
RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars |
title_short |
RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars |
title_full |
RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars |
title_fullStr |
RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars |
title_full_unstemmed |
RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars |
title_sort |
rna-sequencing based gene expression landscape of guava cv. allahabad safeda and comparative analysis to colored cultivars |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-07-01 |
description |
Abstract 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 a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel. 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 a N50 of 3603 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. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored 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 color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits. |
topic |
Guava RNA-Seq Fruit development and ripening Allahabad Safeda Punjab Pink Apple Color Secondary metabolites |
url |
http://link.springer.com/article/10.1186/s12864-020-06883-6 |
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