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A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)

Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic reso...

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Autores principales: Brůna, Tomáš, Aryal, Rishi, Dudchenko, Olga, Sargent, Daniel James, Mead, Daniel, Buti, Matteo, Cavallini, Andrea, Hytönen, Timo, Andrés, Javier, Pham, Melanie, Weisz, David, Mascagni, Flavia, Usai, Gabriele, Natali, Lucia, Bassil, Nahla, Fernandez, Gina E, Lomsadze, Alexandre, Armour, Mitchell, Olukolu, Bode, Poorten, Thomas, Britton, Caitlin, Davik, Jahn, Ashrafi, Hamid, Aiden, Erez Lieberman, Borodovsky, Mark, Worthington, Margaret
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9911083/
https://www.ncbi.nlm.nih.gov/pubmed/36331334
http://dx.doi.org/10.1093/g3journal/jkac289
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author Brůna, Tomáš
Aryal, Rishi
Dudchenko, Olga
Sargent, Daniel James
Mead, Daniel
Buti, Matteo
Cavallini, Andrea
Hytönen, Timo
Andrés, Javier
Pham, Melanie
Weisz, David
Mascagni, Flavia
Usai, Gabriele
Natali, Lucia
Bassil, Nahla
Fernandez, Gina E
Lomsadze, Alexandre
Armour, Mitchell
Olukolu, Bode
Poorten, Thomas
Britton, Caitlin
Davik, Jahn
Ashrafi, Hamid
Aiden, Erez Lieberman
Borodovsky, Mark
Worthington, Margaret
author_facet Brůna, Tomáš
Aryal, Rishi
Dudchenko, Olga
Sargent, Daniel James
Mead, Daniel
Buti, Matteo
Cavallini, Andrea
Hytönen, Timo
Andrés, Javier
Pham, Melanie
Weisz, David
Mascagni, Flavia
Usai, Gabriele
Natali, Lucia
Bassil, Nahla
Fernandez, Gina E
Lomsadze, Alexandre
Armour, Mitchell
Olukolu, Bode
Poorten, Thomas
Britton, Caitlin
Davik, Jahn
Ashrafi, Hamid
Aiden, Erez Lieberman
Borodovsky, Mark
Worthington, Margaret
author_sort Brůna, Tomáš
collection PubMed
description Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
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spelling pubmed-99110832023-02-13 A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”) Brůna, Tomáš Aryal, Rishi Dudchenko, Olga Sargent, Daniel James Mead, Daniel Buti, Matteo Cavallini, Andrea Hytönen, Timo Andrés, Javier Pham, Melanie Weisz, David Mascagni, Flavia Usai, Gabriele Natali, Lucia Bassil, Nahla Fernandez, Gina E Lomsadze, Alexandre Armour, Mitchell Olukolu, Bode Poorten, Thomas Britton, Caitlin Davik, Jahn Ashrafi, Hamid Aiden, Erez Lieberman Borodovsky, Mark Worthington, Margaret G3 (Bethesda) Plant Genetics and Genomics Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs. Oxford University Press 2022-11-04 /pmc/articles/PMC9911083/ /pubmed/36331334 http://dx.doi.org/10.1093/g3journal/jkac289 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Plant Genetics and Genomics
Brůna, Tomáš
Aryal, Rishi
Dudchenko, Olga
Sargent, Daniel James
Mead, Daniel
Buti, Matteo
Cavallini, Andrea
Hytönen, Timo
Andrés, Javier
Pham, Melanie
Weisz, David
Mascagni, Flavia
Usai, Gabriele
Natali, Lucia
Bassil, Nahla
Fernandez, Gina E
Lomsadze, Alexandre
Armour, Mitchell
Olukolu, Bode
Poorten, Thomas
Britton, Caitlin
Davik, Jahn
Ashrafi, Hamid
Aiden, Erez Lieberman
Borodovsky, Mark
Worthington, Margaret
A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)
title A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)
title_full A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)
title_fullStr A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)
title_full_unstemmed A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)
title_short A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)
title_sort chromosome-length genome assembly and annotation of blackberry (rubus argutus, cv. “hillquist”)
topic Plant Genetics and Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9911083/
https://www.ncbi.nlm.nih.gov/pubmed/36331334
http://dx.doi.org/10.1093/g3journal/jkac289
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