Other than the novel transcripts that demonstrate sequence similarity to other plant and/or non plant genes, the remaining novel transcripts encode deduced peptides that share no sequence similarity to every other proteins on the E value cutoff 1e 5. They may be likely from banana precise genes. More file 2, Table S2 lists 151 transcripts that are derived from these putative banana unique genes. The list only consists of the ones which have a minimum length of 259 nt plus a minimal abundance of 0. 56 FPKM by RNA seq. Supplemental file 3, Figure S1A plots the distri bution of length of these putative banana unique tran scripts and their encoded peptides. Amongst them, 15 transcripts consist of a predicted ORF that encodes a pep tide of at the least 150 amino acids, however the predicted peptides encoded by the vast majority of those putative banana unique transcripts are shorter, suggesting that many of them might be non coding RNAs.
Nearly all of the 151 banana exact transcripts had been expressed with less than 5 FPKM, but 44 of them have a FPKM larger than five. It wants to be noted selleckchem Quizartinib “ that also on the novel tran scripts listed in Extra file 1, Table S1, a lot of the other RNA seq sequences that map to un annotated genes could also be transcribed from genuine genes. Each one of these assembled RNA seq sequences are publically ac cessible by way of GenBank. Identification of single nucleotide polymorphisms and brief insertions/deletions The genome of cultivated Cavendish style banana is be lieved to be extremely heterozygous as it was derived from an intra species cross of Musa acuminata, a cross pollinating species.
The Musa genome sequence was obtained via sequencing the doubled haploid M. acuminata genotype. Thus, allelic polymorphisms that exist from the cultivated triploid banana cultivars couldn’t be re vealed from the sequenced genome information alone. Identification of SNPs and indels will reveal allelic polymorphisms, description handy information for breeding programs and for studying their origins. The transcriptome sequences from the Cavendish cultivar really are a superior supply to determine this kind of poly morphisms in genes. Using SAMtools, a total of 21,451 SNPs and three,207 indels were identified from our transcriptome data. We only listed the SNPs/ indels that have been identified by no less than two sequence reads. If it had been hit only by a single study, it can be much more very likely from a sequencing error and consequently not thought to be a serious SNP/indel within this report. Moreover, we only examined SNPs/indels within the transcripts that map to the annotated banana genes or the 842 novel transcripts described earl ier that have not been annotated while in the genome.