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Molecular Biology Reports

, Volume 46, Issue 6, pp 6421–6434 | Cite as

Functional annotation of mulberry (Morus spp.) transcriptome, differential expression of genes related to growth and identification of putative genic SSRs, SNPs and InDels

  • M. S. Rukmangada
  • R. Sumathy
  • Vorkady Girish NaikEmail author
Original Article

Abstract

Growth is a complex trait associated with mulberry leaf yield and controlled by several genes. In this study, we have explored the molecular basis underlying growth using Transcriptome profiling of contrasting genotypes. A total of 66.6 Mbp of primary transcriptomes from high growth (HGG)—Jalalgarah-3 and M. laevigata (H) and, low growth genotypes (LGG)—Harmutty and Vadagaraparai-2; resulting in 24210, 27998, 28085 and 28764 final transcripts respectively. Out of the 34096 pooled transcripts, 20249 transcripts matched with at least one sequence of the non-redundant database. Functional annotation resulted in the categorization of 18970 transcripts into 3 gene ontology (GO) terms and 7440 were assigned to 23 Kyoto encyclopaedia of genes and genomes (KEGG) pathway. Based on the differentially expressed genes and gene enrichment analysis, over expression of photosynthetic related transcripts in HGG and defence related transcripts in LGG were noted. Simple sequence repeats were mined from unique transcripts and the most abundant motifs were tri- (1883) followed by di- (1710), tetra- (192), penta- (68) and hexa- (40) repeats. Further, a total of 390897 high quality SNPs and 8081 InDels were identified by mapping onto Morus notabilis reference genome. The study provides an insight into the expression of genes involved in growth and further research on utilization in gentic improvement of the crop.

Keywords

Mulberry growth Transcriptome profiling Differentially expressed genes GO/KEGG pathways Simple sequence repeats Single nucleotide polymorphisms 

Abbreviations

HGG

High growth genotypes

LGG

Low growth genotypes

DEGs

Differentially expressed genes

SSRs

Simple sequence repeats

SNPs

Single nucleotide polymorphisms

InDel

Insertion/deletion

GO

Gene ontology

KEGG

Kyoto encyclopaedia of genes and genomes

SFB

Shoot fresh biomass

SDB

Shoot dry biomass

A

Photosynthetic rate

Gs

Stomatal conductance

Tr

Transpiration rate

Notes

Acknowledgment

The authors gratefully acknowledge the Director, CSRTI, Mysuru for providing an opportunity to undertake the research work.

Author contribution

VGN provided the experimental materials. MSR designed the workflow and conducted the experiment. RS and MSR performed the bioinformatics analysis and drafted the manuscript. VGN guided the work, critically evaluated data interpretation and revised the manuscript. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Molecular Biology Laboratory – 1Central Sericultural Research and Training InstituteMysuruIndia
  2. 2.Bioinformatics Centre, Central Sericultural Research and Training InstituteMysuruIndia
  3. 3.Regional Sericultural Research StationCentral Silk Board, Ministry of Textiles - Govt. of IndiaChamarajanagaraIndia

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