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Functional & Integrative Genomics

, Volume 18, Issue 2, pp 211–223 | Cite as

Transcriptomic profiling of developing fiber in levant cotton (Gossypium herbaceum L.)

  • Mithil J. Parekh
  • Sushil Kumar
  • Ranbir S. Fougat
  • Harshvardhan N. Zala
  • Ramesh J. Pandit
Original Article

Abstract

Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G. herbaceum on pyrosequencing and its analysis. About 1.38 million raw and 1.12 million quality trimmed reads were obtained followed by de novo assembly-generated 20,125 unigenes containing 14,882 coding sequences (CDs). BLASTx-based test of homology indicated that A1-derived transcripts shared a high similarity with Gossypium arboreum (A2). Functional annotation of the CDs using the UniProt categorized them into biological processes, cellular components, and molecular function, COG classification showed that a large number of CDs have significant homology in COG database (6215 CDs), and mapping of CDs with Kyoto Encyclopedia of Genes and Genomes (KEGG) database generated 200 pathways ultimately showing predominant engagement in the fiber development process. Transcription factors were predicted by comparison with Plant Transcription Factor Database, and their differential expression between stages exposed their important regulatory role in fiber development. Differential expression analysis based on reads per kilobase of transcript per million mapped reads (RPKM) value revealed activities of specific gene related to carbohydrate and lipid synthesis, carbon metabolism, energy metabolism, signal transduction, etc., at four stages of fiber development, and was validated by qPCR. Overall, this study will help as a valuable foundation for diploid cotton fiber improvement.

Keywords

Differential gene expression Diploid cotton Fiber quality Next-generation sequencing Transcriptome 

Notes

Acknowledgments

The authors would like to acknowledge funding support from Gujarat State Biotechnology Mission (GSBTM), Gujarat (Grant No. GSBTM/MD/PROJECTS/SSA/3382/2012-13). We thank the Professor and Head, Department of Animal Biotechnology, AAU for providing the NGS facility.

Author contribution

SK and RSF conceived of the experiment. MJP and SK carried out the work. MJP, HZ, and RP analyzed and interpreted the data. MJP and SK prepared the manuscript. SK and RSF contributed by designing the experiment, supervising the whole experiment, and preparing the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10142_2017_586_Fig10_ESM.gif (574 kb)
Supplementary Figure S1

Heat map of all differentially expressed fiber development related genes in diploid cotton (GIF 574 kb)

10142_2017_586_MOESM1_ESM.tif (1020 kb)
High Resolution Image (TIFF 1020 kb)
10142_2017_586_MOESM2_ESM.docx (34 kb)
ESM 1 (DOCX 33.9 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Mithil J. Parekh
    • 1
  • Sushil Kumar
    • 1
  • Ranbir S. Fougat
    • 1
  • Harshvardhan N. Zala
    • 1
  • Ramesh J. Pandit
    • 2
  1. 1.Department of Agricultural BiotechnologyAnand Agricultural UniversityAnandIndia
  2. 2.Department of Animal BiotechnologyAnand Agricultural UniversityAnandIndia

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