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Daphnia magna trol gene assembly with EvidentialGene

In fruitfly, this gene is trol for "Terribly reduced optic lobes", also known as Perlecan, see Uniprot Q9W4Y3 cluster or NCBI Gene ID: 45320

These are reference-free, de-novo gene assemblies, made without any other species gene information, genome-alignment, etc. They appeared in EvidentialGene outputs of the overassembly of Daph. magna mRNA-seq. This is one of the example complex gene loci that is rather difficult to model on genomes accurately. Genome modelling often makes partial models, models missing exons or containing all exons. See below maps of D. magna genes 2011m and D. pulex genes 2010, with gene-models showing these mistakes.

Note the apparent different gene structure on D. pulex genome and Fruitfly versus D. magna genome, at 3' left exon clusters. Only 60% of gene is mapped onto D. magna genome, due to gaps in D. magna draft genome (at bottom of D. magna map, DNA Content gap at left-3' end). The gene assembly is complete with 4200 aa (vs 4400 aa in fruitfly), The genome-model prediction of this gene is less than half size, 1500 aa, missing most of this gene due to gaps and complexity (see track Genes 2011m8).

This map view also shows a common problem of genome-free mRNA assembly, the several short, unattached exons of this long, complex gene, appearing as separate gene loci (top blue track). Most of these can be culled with genome map locations internal/adjacent to longer alternate transcripts.

Approx. 40 valid alternate transcripts were classified by EvidentialGene, from an over-assembly of 1850 transcripts of this locus, from one clonal mRNA set. Transcripts have 37 to 24 mapped-exons, more unmapped, with proteins of 4200 to 2500 aa. Of these, 24 are Velvet/Oases assembly, 5 from SOAP-denovo assembly, and 11 from Trinity. Longest protein transcripts were assembled from non-normalized RNA-seq with kmer size in the 91 to 77 range by Velvet/Oases (for 100bp paired-end Illumina reads). This is in contrast to DSCAM, which assembled well with smaller kmer ~50 and normalized data.


Daphnia magna trol gene on Dap. magna genome map.

trol_dmag7evg_alts

Daphnia magna trol gene on Dap. pulex genome map.

trol_dmag7evg_alts-dplxm

Compare to Fruitfly trol gene.

trol_frufly_alts_ncbi

Developed at the Genome Informatics Lab of Indiana University Biology Department