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Yocca A, Akinyuwa M, Bailey N, Cliver B, Estes H, Guillemette A, Hasannin O, Hutchison J, Jenkins W, Kaur I, Khanna RR, Loftin M, Lopes L, Moore-Pollard E, Olofintila O, Oyebode GO, Patel J, Thapa P, Waldinger M, Zhang J, Zhang Q, Goertzen L, Carey SB, Hargarten H, Mattheis J, Zhang H, Jones T, Boston L, Grimwood J, Ficklin S, Honaas L, Harkess A. A chromosome-scale assembly for 'd'Anjou' pear. G3 (Bethesda) 2024; 14:jkae003. [PMID: 38190814 PMCID: PMC10917493 DOI: 10.1093/g3journal/jkae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 07/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024]
Abstract
Cultivated pear consists of several Pyrus species with Pyrus communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully phased chromosome-scale genome assembly of P. communis 'd'Anjou.' Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totaling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other and to the Malus domestica 'Honeycrisp' apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d'Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.
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Affiliation(s)
- Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mary Akinyuwa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Nick Bailey
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Brannan Cliver
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Harrison Estes
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | | | - Omar Hasannin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer Hutchison
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wren Jenkins
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ishveen Kaur
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | | | - Madelene Loftin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Lauren Lopes
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Erika Moore-Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152-3530, USA
| | | | | | - Jinesh Patel
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Parbati Thapa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Martin Waldinger
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jie Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qiong Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Leslie Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Heidi Hargarten
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - James Mattheis
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Huiting Zhang
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Teresa Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - LoriBeth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Loren Honaas
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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