Haplotype-Phased Genome Assembly of Virulent Phytophthora ramorum Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation

Molecular Plant-microbe Interactions : MPMI
Mathu Malar CSucheta Tripathy

Abstract

Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for P. ramorum, we performed long-read sequencing of highly aggressive P. ramorum isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of...Continue Reading

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Citations

Sep 4, 2019·Molecular Plant-microbe Interactions : MPMI·Chenming CuiDavid C Haak
Jun 26, 2020·Microorganisms·Jennifer David YuzonTakao Kasuga
Jul 16, 2019·Molecular Plant-microbe Interactions : MPMI·Mathu Malar CSucheta Tripathy
Apr 21, 2020·Molecular Plant-microbe Interactions : MPMI·Yoonyoung LeeMaxim Prokchorchik

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