A chromosome-scale assembly for ‘d’Anjou' pear

Authors: YOCCA, ALAN - Hudsonalpha Institute For Biotechnology; AKINYUWA, MARY - Auburn University; BAILEY, NICHOLAS - Auburn University; CLIVER, BRANNAN - Auburn University; ESTES, HARRISON - Auburn University; GUILLEMETTE, ABIGAIL - Auburn University; HASANNIN, OMAR - Auburn University; HUTCHISON, JENNIFER - Auburn University; JENKINS, WREN - Auburn University; KAUR, ISHVEEN - Auburn University; KHANNA, RISHEEK - Auburn University; LOFTIN, MADELENE - Auburn University; LOPES, LAUREN - Auburn University; MOORE-POLLARD, ERIKA - University Of Tennessee; OLOFINTILA, OLUWAKEMISOLA - Auburn University; OYEBODE, GIDEON - Auburn University; PATEL, JINESH - Auburn University; THAPA, PARBATI - Auburn University; WALDINGER, MARTIN - Auburn University; ZHANG, JIE - Auburn University; ZHANG, QIONG - Auburn University; GOERTZEN, LESLIE - Auburn University; CAREY, SARAH - Hudsonalpha Institute For Biotechnology; Hargarten, Heidi; MATTHEIS, JAMES - Retired ARS Employee; ZHANG, HUITING - Washington State University; JONES, TERESA - Hudsonalpha Institute For Biotechnology; BOSTON, LORIBETH - Hudsonalpha Institute For Biotechnology; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; FICKLIN, STEPHEN - Washington State University; Honaas, Loren; HARKESS, ALEX - Hudsonalpha Institute For Biotechnology

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2023
Publication Date: 1/8/2024
Citation: Yocca, A., Akinyuwa, M., Bailey, N., Cliver, B., Estes, H., Guillemette, A., Hasannin, O., Hutchison, J., Jenkins, W., Kaur, I., Khanna, R., Loftin, M., Lopes, L., Moore-Pollard, E., Olofintila, O., Oyebode, G., Patel, J., Thapa, P., Waldinger, M., Zhang, J., Zhang, Q., Goertzen, L., Carey, S., Hargarten, H.L., Mattheis, J., Zhang, H., Jones, T., Boston, L., Grimwood, J., Ficklin, S., Honaas, L.A., Harkess, A. 2024. A chromosome-scale assembly for ‘d’Anjou' pear. G3, Genes/Genomes/Genetics. 14(3). Article jkae003. https://doi.org/10.1093/g3journal/jkae003.
DOI: https://doi.org/10.1093/g3journal/jkae003

Interpretive Summary: The domestic pear industry produces over 1B lbs of pears with a total economic impact of $1.6B. As a long-lived tree species, breeding cycles greatly exceed that of other crops such as corn and soybean. Further, protracted fruit storage periods of up to 1 year create many opportunities for fruit spoilage. Therefore, knowledge of the pear genetics that influence important traits (like disease resistance and storability) stands to greatly increase the pace of pear improvement, both for future cultivars and trees in the ground. Owing to recent advances in sequencing technologies, we can now access virtually all of the genetic information (collectively called the genome) in European pear. Whereas roughly half of the genetic information was obscured in previous pear genomes, we now present a high-resolution, and complete genome map of the major European pear cultivar “d’Anjou”. We confirm major structural genome changes that are shared with apple, a relative of pear, that occurred in the deep history of this fruit lineage. While this work adds significantly to resources for pear, it also contributes to valuable resources for the pear family which includes rose, cherry, blackberry, apricot, almond, strawberry, and more.

Technical Abstract: Cultivated pear consists of several Pyrus species with P. 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 cv. ‘d’Anjou’. Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totalling 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 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.