Even when the reads are assembled into contigs, there are still many contigs to align and annotate.
D. lowei was not considered in the synteny analysis since most of the genes in this species are flanked by genomic gaps, due to the shorter contig length of the D. lowei assembly (Table 1), which caused many contigs to contain only a single gene (Table 2), thus precluding proper synteny assignments.
Our carnation database included many contigs related to transcription factor activity (11% of the Molecular Function ESTs) in the GO function analysis.
In particular, many contigs assigned to various stress response pathways, including oxidative stress response, were down-regulated at 73HAT, as were contigs assigned to oxygen transport and carbon fixation.
Genbank BLAST and GSPC based on a microbial database both predict the origin of many Bear Paw contigs to have bacterial origin, while the viral database suggests the contigs are from bacteriophages (Additional file 3).
In contrast, Genbank BLAST and GSPC based on a microbial database predict many Octopus contigs to have archaeal origin, with the viral database indicating many contigs may belong to archaeal virus Families Fuselloviridae and Globuloviridae (Additional file 3).
These likely CDSs correspond to 23,245 (asymAD) and 22,941 (asym20h) original contigs because many contigs may correspond to two CDSs (both strands were considered in the CDS inference by TransDecoder).
Many contigs were similar to silk proteins from spiders, such as fibroin, dragline, flagelliform, major ampullate spidroin and flag silks.
Many contigs were similar to ubiquitin genes, and among the most strongly expressed genes, there was a tendency of lower expression in E. globulus.
Since many contigs are likely to be rare, with perhaps less than 1% of expressed genes accounting for 50% of cellular mRNA [ 68], a typical RNA-seq experiment will fail to record sequence from many transcripts.
The high abundance of these flagellar proteins based on RPKM value (ranging from top 25%to10%0%) and reads number (ranging from top 10%to2.5.5%), as well as the existence of many contigs (>440) related to dynein, also indicate the existence and importance of the flagellar system in C. moewusii (Additional file 5A, 5C).
