Pacific Biosciences of California Inc (PACB)

[Paulieme]

"(We found that the Illumina Synthetic Long Reads assembly failed in the Mst77Y region,The PacBio MHAP assembly of the Mst77Y region seems to be very accurate)" -- Long-Read Single Molecule Sequencing To Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome

Flavia J. Krsticevic1,
Carlos G. Schrago2 and
A. Bernardo Carvalho2,*


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Author Affiliations
1 Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas - CONICET;
2 Universidade Federal do Rio de Janeiro
?*To whom correspondence should be addressed. E-mail: [e-mail]


Abstract

The autosomal gene Mst77F of Drosophila melanogaster is essential for male fertility. In 2010 Krsticevic et al. found 18 Y-linked copies of Mst77F ("Mst77Y"), which collectively account for 20% of the functional Mst77F-like mRNA. The Mst77Y genes were severely misassembled in the then available genome assembly, and were identified by cloning and sequencing PCR products. The genomic structure of the Mst77Y region, and the possible existence of additional copies remained unknown. The recent publication of two long-read assemblies of D. melanogaster prompted us to re-investigate this challenging region of the Y chromosome. We found that the Illumina Synthetic Long Reads assembly failed in the Mst77Y region, most likely due to its tandem duplication structure. The PacBio MHAP assembly of the Mst77Y region seems to be very accurate, as revealed by comparisons with the previously found Mst77Y genes, a BAC sequence, and Illumina reads of the same strain. We found that the Mst77Y region spans 96 kb and originated from a 3.4 kb transposition from chromosome 3L to the Y chromosome, followed by tandem duplications inside the Y chromosome and invasion of transposable elements, which account for 48% of its length. Twelve of the 18 Mst77Y genes found in 2010 were confirmed in the PacBio assembly, the remaining six being PCR-induced artifacts. There are several identical copies of some Mst77Y genes, coincidentally bringing the total copy number to 18. Besides providing a detailed picture of the Mst77Y region, our results highlight the utility of PacBio technology in assembling difficult genomic regions such as tandemly repeated genes.
http://www.g3journal.org/content/early/2015/04/09/g3.115.017277.abstract