Comparative transcriptome analysis of two cotton speices by RNA-seq

We obtained a total of 8.4 GB and 10.8 GB transcript sequence data from ‘Xuzhou142’ and ‘fl’ cultivars, respectively, which correspond to 43,532,778 and 55,844,768 reads. After quality assessment, the clean sequences where 43,036,504 and 55,325,412, respectively. Comparison of the RNA-seq data with genomic sequences revealed that 692 RNA editing sites were identified in mitochondrial genes, all of which were C-to-U conversions except for 13 U-to-C changes. we conducted a comparative transcriptome analysis of mitochondrial protein coding genes and investigated differences in RNA editing between the mitochondrial transcripts of G. hirsutum var. Xuzhou142 (WT) fiber and its near isogenic line, fuzzless-lintless mutant (fl) ovule. No significant difference was observed in the distribution of RNA editing sites in the non-coding regions between fiber and ovule cells. However, the editing efficiency of complex I, complex V, Ribosomal protein, and matR protein coding genes exhibited significant differences between fiber and ovule. Our results showed RNA editing events are abundant in the mitochondrial genome of cotton and some editing sites may closely associated with fiber elongation. Identify RNA editing sites in two cotton speices.