Single-molecule sequencing of the Drosophila serrata genome

Allen, Scott L., Delaney, Emily K., Kopp, Artyom and Chenoweth, Stephen F. (2017) Single-molecule sequencing of the Drosophila serrata genome. G3 , 7 3: 781-788. doi:10.1534/g3.116.037598


Author Allen, Scott L.
Delaney, Emily K.
Kopp, Artyom
Chenoweth, Stephen F.
Title Single-molecule sequencing of the Drosophila serrata genome
Formatted title
Single-molecule sequencing of the Drosophila serrata genome
Journal name G3    Check publisher's open access policy
ISSN 2160-1836
Publication date 2017-03-01
Sub-type Article (original research)
DOI 10.1534/g3.116.037598
Open Access Status DOI
Volume 7
Issue 3
Start page 781
End page 788
Total pages 8
Place of publication Bethesda, MD, United States
Publisher Genetics Society of America
Language eng
Formatted abstract
Long-read sequencing technology promises to greatly enhance de novo assembly of genomes for nonmodel species. Although the error rates of long reads have been a stumbling block, sequencing at high coverage permits the self-correction of many errors. Here, we sequence and de novo assemble the genome of Drosophila serrata, a species from the montium subgroup that has been well-studied for latitudinal clines, sexual selection, and gene expression, but which lacks a reference genome. Using 11 Pac- Bio single-molecule real-time (SMRT cells), we generated 12 Gbp of raw sequence data comprising ~65 × whole-genome coverage. Read lengths averaged 8940 bp (NRead50 12,200) with the longest read at 53 kbp. We self-corrected reads using the PBDagCon algorithm and assembled the genome using the MHAP algorithm within the PBcR assembler. Total genome length was 198 Mbp with an N50 just under 1 Mbp. Contigs displayed a high degree of chromosome arm-level conservation with the D. melanogaster genome and many could be sensibly placed on the D. serrata physical map. We also provide an initial annotation for this genome using in silico gene predictions that were supported by RNA-seq data.
Keyword Assembly
Drosophila montium
Long reads genome
PacBio Celera
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
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School of Biological Sciences Publications
 
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