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      Genome Sequence of Fusarium oxysporum f. sp. conglutinans, the Etiological Agent of Cabbage Fusarium Wilt

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          Abstract

          Fusarium oxysporum f. sp. conglutinans is the causal agent of Fusarium wilt of cabbage (Brassica oleracea var. capitata L.), which results in severe yield loss. Here, we report a high-quality genome sequence of a race 1 strain (IVC-1) of F. oxysporum f. sp. conglutinans, which was assembled using a combination of PacBio long-read and Illumina short-read sequences. The assembled IVC-1 genome has a total size of 71.18 Mb, with a contig N50 length of 4.59 Mb, and encodes 23,374 predicted protein-coding genes. The high-quality genome of IVC-1 provides a valuable resource for facilitating our understanding of F. oxysporum f. sp. conglutinans–cabbage interaction.

          [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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          Most cited references21

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          BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

          Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
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            The Top 10 fungal pathogens in molecular plant pathology.

            The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10. © 2012 THE AUTHORS. MOLECULAR PLANT PATHOLOGY © 2012 BSPP AND BLACKWELL PUBLISHING LTD.
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              Phased diploid genome assembly with single-molecule real-time sequencing.

              While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata, samples that have challenged short-read assembly approaches. The FALCON-based assemblies are substantially more contiguous and complete than alternate short- or long-read approaches. The phased diploid assembly enabled the study of haplotype structure and heterozygosities between homologous chromosomes, including the identification of widespread heterozygous structural variation within coding sequences.
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                Author and article information

                Contributors
                Journal
                Molecular Plant-Microbe Interactions®
                MPMI
                Scientific Societies
                0894-0282
                1943-7706
                February 2021
                February 2021
                : 34
                : 2
                : 210-213
                Affiliations
                [1 ]Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
                [2 ]Jiangsu Agricultural Technology Extension Station, Nanjing 210036, China
                [3 ]Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, U.S.A.
                Article
                10.1094/MPMI-08-20-0245-A
                cd0e7c31-5732-4e78-8cdf-7a93a6bfe98c
                © 2021
                History

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