Abstract
The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly.
Highlights
Dear Dr Zauner: We thank you and the reviewers for your feedback on our manuscript
I am happy to say that the reviewers are positive overall and support publication as a Data Note. They have raised a number of points which we believe need to be addressed in a revised manuscript
We provide a point-by-point response explaining our revisions in the text below
Summary
Dear Dr Zauner: We thank you and the reviewers for your feedback on our manuscript. We have made revisions to address each of the comments from the referees. Comments from Editor: Dear Dr Salzberg, Your data note "An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing" (GIGA-D-16-00111) has been assessed by two reviewers.
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