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Updated Assembly of Phytophthora ramorum pr102 Isolate Incorporating Long Reads from PacBio Sequencing.
Mol Plant Microbe Interact. 2019 Nov; 32(11):1472-1474.MP

Abstract

The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.

Authors+Show Affiliations

Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India. Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.Department of Plant Pathology, University of California, Davis, CA, U.S.A. USDA-ARS, Davis, CA, U.S.A.Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India. Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.Department of Plant Pathology, University of California, Davis, CA, U.S.A. USDA-ARS, Davis, CA, U.S.A.Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India. Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31306082

Citation

Malar C, Mathu, et al. "Updated Assembly of Phytophthora Ramorum Pr102 Isolate Incorporating Long Reads From PacBio Sequencing." Molecular Plant-microbe Interactions : MPMI, vol. 32, no. 11, 2019, pp. 1472-1474.
Malar C M, Yuzon JD, Panda A, et al. Updated Assembly of Phytophthora ramorum pr102 Isolate Incorporating Long Reads from PacBio Sequencing. Mol Plant Microbe Interact. 2019;32(11):1472-1474.
Malar C, M., Yuzon, J. D., Panda, A., Kasuga, T., & Tripathy, S. (2019). Updated Assembly of Phytophthora ramorum pr102 Isolate Incorporating Long Reads from PacBio Sequencing. Molecular Plant-microbe Interactions : MPMI, 32(11), 1472-1474. https://doi.org/10.1094/MPMI-05-19-0147-A
Malar C M, et al. Updated Assembly of Phytophthora Ramorum Pr102 Isolate Incorporating Long Reads From PacBio Sequencing. Mol Plant Microbe Interact. 2019;32(11):1472-1474. PubMed PMID: 31306082.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Updated Assembly of Phytophthora ramorum pr102 Isolate Incorporating Long Reads from PacBio Sequencing. AU - Malar C,Mathu, AU - Yuzon,Jennifer David, AU - Panda,Arijit, AU - Kasuga,Takao, AU - Tripathy,Sucheta, Y1 - 2019/09/27/ PY - 2019/7/16/pubmed PY - 2019/11/2/medline PY - 2019/7/16/entrez KW - Phytophthora ramorum KW - gaps KW - long read assembly KW - repeats KW - sudden oak death SP - 1472 EP - 1474 JF - Molecular plant-microbe interactions : MPMI JO - Mol. Plant Microbe Interact. VL - 32 IS - 11 N2 - The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen. SN - 0894-0282 UR - https://www.unboundmedicine.com/medline/citation/31306082/Updated_assembly_resource_of_Phytophthora_ramorum_Pr102_isolate_incorporating_long_reads_from_PacBio_sequencing L2 - http://apsjournals.apsnet.org/doi/full/10.1094/MPMI-05-19-0147-A?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -