This study examined introns in three litostome species. Two (Myriokaryon sp., Apodileptus visscheri) have short and tightly distributed intron lengths (between 20 and 40 bp), while a third (Monodinium sp.) has a wider length distribution (see their Figure 7). All were GT-AG bound, with conserved A at position 3.
Two points were not clear to me:
- Why only these three species were chosen for intron analysis. Transcriptomes were sequenced for at least three other species, and new data for a total of 14 species were produced in this study. Their Table 1 (assembly stats) does not distinguish between genomes and transcriptomes (?). Their data are not yet public on SRA.
- The modal intron length for Monodinium sp. was reported as 200 bp. This seems like an error, presumably they meant that the majority of introns were >=200 bp, not that they were exactly 200 bp. However, only accessions for the raw sequencing reads were provided, no links to assemblies were given.
I am unsure about their gene predictions because it appears that they used Augustus trained on Litonotus pictus for all the new genomes. For the intron analysis, however, they used RNAseq mapping so that is likely to be reliable.
Ideally I would add their RNAseq data and genomes to this pipeline, but I am not keen on having to reassemble their data.
This study examined introns in three litostome species. Two (Myriokaryon sp., Apodileptus visscheri) have short and tightly distributed intron lengths (between 20 and 40 bp), while a third (Monodinium sp.) has a wider length distribution (see their Figure 7). All were GT-AG bound, with conserved A at position 3.
Two points were not clear to me:
I am unsure about their gene predictions because it appears that they used Augustus trained on Litonotus pictus for all the new genomes. For the intron analysis, however, they used RNAseq mapping so that is likely to be reliable.
Ideally I would add their RNAseq data and genomes to this pipeline, but I am not keen on having to reassemble their data.