Comparative transcriptome analysis of TUCPs in Gossypium hirsutum Ligon-lintless-1 mutant and their proposed functions in cotton fiber development

Molecular Genetics and Genomics : MGG
Haron SalihXiong-Ming Du

Abstract

Transcripts of uncertain coding potential (TUCP) are part of the LncRNAs, which encode some polypeptides. However, the abundance of TUCP transcripts and their roles in Ligon-linless-1 (Li-1) cotton mutant during the early termination of fiber development are still not documented. Li-1 mutant is one of the excellent modules for investigating fiber elongation processes due to its unique fiber developmental stages. To examine the function of TUCP in cotton fiber development, it is important to identify TUCPs and their involvement in fiber development. In this study, we found that 11104 TUCP transcripts were removed by coding potential criteria of Pfam domain scan. Additionally, differential expression levels of TUCP transcripts were detected between Li-1 mutant and the wild-type (WT), which imply their possible functions in cotton fiber development. These results further revealed that a great number of differentially expressed TUCP transcripts in cotton were identified at 8 DPA, followed by 0 DPA and stem. However, these might explain an undesirable function in cotton fiber development. The gene ontology and pathway analysis, based on differential expression patterns of TUCP transcripts on targeted genes, identified the transport ...Continue Reading

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Methods Mentioned

BETA
physical treatments
RNA-seq
GTPase
phosphotransferase
GTPases
Assay
RNA Assay

Software Mentioned

Cuffdiff
WGCNA
R
Cuffmerge
Hierarchical Clustering Explorer
Cufflinks
house
Tophat2

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