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      The de novo, chromosome-level genome assembly of the sweet chestnut ( Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio

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          Abstract

          Objectives

          The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety ‘Marrone di Chiusa Pesio’ using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads.

          Data description

          The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12863-024-01245-7.

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          GenomeScope: fast reference-free genome profiling from short reads.

          Gregory Vurture, Fritz Sedlazeck, Maria Nattestad … (2017)
          GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates.
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            NextPolish: a fast and efficient genome polishing tool for long-read assembly

            Jiang Hu, Junpeng Fan, Zongyi Sun … (2020)
            Although long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently corrects sequence errors in genomes assembled with long reads. This new tool consists of two interlinked modules that are designed to score and count K-mers from high quality short reads, and to polish genome assemblies containing large numbers of base errors. When evaluated for the speed and efficiency using human and a plant (Arabidopsis thaliana) genomes, NextPolish outperformed Pilon by correcting sequence errors faster, and with a higher correction accuracy. NextPolish is implemented in C and Python. The source code is available from https://github.com/Nextomics/NextPolish. Supplementary data are available at Bioinformatics online.
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              Intercontinental genetic divergence of Castanea species in eastern Asia and eastern North America

              Y. Fu, P. Lang, H. Huang … (2003)
              Article 0 comments Cited 14 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Luisa Palmieri: luisa.palmieri@fmach.it
                Journal
                Journal ID (nlm-ta): BMC Genom Data
                Journal ID (iso-abbrev): BMC Genom Data
                Title: BMC Genomic Data
                Publisher: BioMed Central (London )
                ISSN (Electronic): 2730-6844
                Publication date (Electronic): 22 June 2024
                Publication date PMC-release: 22 June 2024
                Publication date Collection: 2024
                Volume: 25
                Electronic Location Identifier: 64
                Affiliations
                [1 ]GRID grid.424414.3, ISNI 0000 0004 1755 6224, Research and Innovation Center, , Edmund Mach Foundation, ; via Mach 1, San Michele all’Adige, TN 38098 Italy
                [2 ]Research Institute on Terrestrial Ecosystem, National Research Council, ( https://ror.org/04zaypm56) Via Marconi 2, Porano, TR 05010 Italy
                [3 ]NBFC, National Biodiversity Future Center, Palermo, Italy
                [4 ]GRID grid.5326.2, ISNI 0000 0001 1940 4177, Institute for Sustainable Plant Protection, , National Research Council, ; Via Madonna del Piano 10, 50019, Sesto Fiorentino FI, Italy
                [5 ]Dept. of Agricultural and Food Sciences, University of Bologna, ( https://ror.org/01111rn36) Via Zamboni 33, Bologna, BO 40126 Italy
                [6 ]Dept. of Agricultural, Forest and Food Sci, University of Turin, ( https://ror.org/048tbm396) L.go P. Braccini 2, Grugliasco, TO 10095 Italy
                [7 ]Dep. of Agricultural, Food and Env.Sci, Marche Polytechnic University, ( https://ror.org/00x69rs40) via Brecce Bianche, Ancona, AN 60131 Italy
                Article
                Publisher ID: 1245
                DOI: 10.1186/s12863-024-01245-7
                PMC ID: 11193896
                PubMed ID: 38909221
                SO-VID: c8bfa3f5-dbda-4078-b988-9930d884b060
                Copyright © © The Author(s) 2024
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                Date received : 12 April 2024
                Date accepted : 17 June 2024
                Categories
                Subject: Data Note
                Custom metadata
                issue-copyright-statement © BioMed Central Ltd., part of Springer Nature 2024

                Keywords: european chestnut,genome sequence assembly,chromosome-scale
                Data availability:
                Keywords: european chestnut, genome sequence assembly, chromosome-scale

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