Comparative genomics of six Juglans species reveals disease‐associated gene family contractions. (16th January 2020)

• Record Type: Journal Article
• Authors: Trouern‐Trend, Alexander J.; Falk, Taylor; Zaman, Sumaira; Caballero, Madison; Neale, David B.; Langley, Charles H.; Dandekar, Abhaya M.; Stevens, Kristian A.; Wegrzyn, Jill L.
• Is Part Of: Plant journal. Volume 102:Number 2(2020)
• Page Start: 410
• Page End: 423
• Publication Date: 2020-01-16
• Subjects: walnut -- wingnut -- Juglans -- Juglandaceae -- genome annotation -- comparative genomics -- whole‐genome duplication -- phenology -- disease resistance -- crop genomics; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14630
• Languages: English
• ISSNs: 0960-7412

Abstract

SUMMARY: Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood‐producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae ( Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera ) produced using BRAKER2 semi‐unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue‐specific J . regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi‐exonic and mono‐exonic putative genes to yield between 27 000 and 44 000 high‐confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high‐quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance‐related wall‐associated kinase (WAK), Catharanthus roseus receptor‐like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole‐genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis. Significance Statement: High‐quality full genome annotations for six species of walnut ( Juglans ) and a wingnut ( Pterocarya ) outgroup were constructed using semi‐unsupervised gene prediction followed by gene model filtering and functional characterization. The genomes and their annotations represent a set of unique species within a single hardwood genus. Comparative analyses based on the gene models uncovered rapid evolution in multiple gene families as well as contractions related to disease‐response. A whole‐genome duplication was also confirmed in a Juglandaceae common ancestor.