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Updated assembly resource of Phytophthora ramorum Pr102 isolate incorporating long reads from PacBio sequencing.

Abstract

The NA1 clonal lineage of Phytophthora ramorum is responsible for Sudden Oak Death, an epidemic that has devastated California's coastal forest ecosystems. An NA1 isolate Pr102 derived from coast live oak in California was previously sequenced and reported with 65 Mb assembly containing 12 Mb gaps in 2576 scaffolds. Here we report an improved 70 Mb genome in 1512 scaffolds with 6752 bp gaps after incorporating PacBio P5-C3 longreads. This assembly contains 19494 gene models (average gene length 2515 bp) compared to 16134 genes (average gene length of 1673 bp) in the previous version. We predicted 29 new RXLRs and 76 new paralogs of a total 392 RXLRs from this assembly. We predicted 35 CRNs compared to 19 in earlier version with six paralogs. Our lncRNAs prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.

Authors+Show Affiliations

Indian Institute of Chemical Technology, 62391, Structural Biology and Bioinformatics Division, Kolkata, West Bengal, India. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India , New Delhi, India ; mmadhubioinfo@gmail.com.University of California, Davis, California, Department of Plant Pathology, California, California, United States. USDA-ARS, Davis, California, California, California, United States ; jdyuzon@ucdavis.edu.Indian Institute of Chemical Technology, 62391, Structural Biology and Bioinformatics Division, Kolkata, West Bengal, India. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India , New Delhi, India ; arijpanda@gmail.com.University of California, Davis, California, Department of Plant Pathology, California, California, United States. USDA-ARS, Davis, California, California, California, United States ; tkasuga@ucdavis.edu.Indian Institute of Chemical Technology, 62391, Structural Biology and Bioinformatics Division , 4 Raja S C Mullick Road , Jadavpur , Kolkata , Kolkata, West Bengal, India , 700032 ; tsucheta@gmail.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31306082

Citation

Malar C, Mathu, et al. "Updated Assembly Resource of Phytophthora Ramorum Pr102 Isolate Incorporating Long Reads From PacBio Sequencing." Molecular Plant-microbe Interactions : MPMI, 2019.
Malar C M, Yuzon JD, Panda A, et al. Updated assembly resource of Phytophthora ramorum Pr102 isolate incorporating long reads from PacBio sequencing. Mol Plant Microbe Interact. 2019.
Malar C, M., Yuzon, J. D., Panda, A., Kasuga, T., & Tripathy, S. (2019). Updated assembly resource of Phytophthora ramorum Pr102 isolate incorporating long reads from PacBio sequencing. Molecular Plant-microbe Interactions : MPMI, doi:10.1094/MPMI-05-19-0147-A.
Malar C M, et al. Updated Assembly Resource of Phytophthora Ramorum Pr102 Isolate Incorporating Long Reads From PacBio Sequencing. Mol Plant Microbe Interact. 2019 Jul 15; PubMed PMID: 31306082.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Updated assembly resource of Phytophthora ramorum Pr102 isolate incorporating long reads from PacBio sequencing. AU - Malar C,Mathu, AU - Yuzon,Jennifer D, AU - Panda,Arijit, AU - Kasuga,Takao, AU - Tripathy,Sucheta, Y1 - 2019/07/15/ PY - 2019/7/16/entrez PY - 2019/7/16/pubmed PY - 2019/7/16/medline JF - Molecular plant-microbe interactions : MPMI JO - Mol. Plant Microbe Interact. N2 - The NA1 clonal lineage of Phytophthora ramorum is responsible for Sudden Oak Death, an epidemic that has devastated California's coastal forest ecosystems. An NA1 isolate Pr102 derived from coast live oak in California was previously sequenced and reported with 65 Mb assembly containing 12 Mb gaps in 2576 scaffolds. Here we report an improved 70 Mb genome in 1512 scaffolds with 6752 bp gaps after incorporating PacBio P5-C3 longreads. This assembly contains 19494 gene models (average gene length 2515 bp) compared to 16134 genes (average gene length of 1673 bp) in the previous version. We predicted 29 new RXLRs and 76 new paralogs of a total 392 RXLRs from this assembly. We predicted 35 CRNs compared to 19 in earlier version with six paralogs. Our lncRNAs 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 -