De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome
Abstract
Abstract Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Using the de novo annotations we identify cultivar-specific genes and define the core and dispensable genomes. Expression analysis across cultivars and tissues reveals conservation in expression between a large core set of homeologous genes, in addition to widespread changes in subgenome homeolog expression bias between cultivars and cultivar-specific expression profiles. We utilise both the newly constructed gene-based wheat pan-genome and pan-transcriptome, demonstrating variation in the prolamin superfamily and immune-reactive proteins across cultivars.
Article Details
Authors (127)
Benjamen White
Thomas Lux
Rachel Rusholme-Pilcher
Angéla Juhász
Gemy Kaithakottil
Susan Duncan
James Simmonds
Hannah Rees
Jonathan Wright
Joshua Colmer
Sabrina Ward
Ryan Joynson
Benedict Coombes
Naomi Irish
Suzanne Henderson
Tom Barker
Helen Chapman
Leah Catchpole
Karim Gharbi
Utpal Bose
Moeko Okada
Heidrun Gundlach
Daniel Lang
Guy Naamati
Erik J. Legg
Arvind K. Bharti
Michelle L. Colgrave
Wilfried Haerty
Cristobal Uauy
David Swarbreck
Philippa Borrill
Jesse A. Poland
Nils Stein
Klaus F. X. Mayer
Curtis Pozniak
Sean Walkowiak
Valentyna Klymiuk
Brook Byrns
Kirby Nilsen
Jennifer Ens
Krystalee Wiebe
Amidou N’Diaye
Pierre J. Hucl
Curtis J. Pozniak
Bin Xiao Fu
Liangliang Gao
Emily Delorean
Dal-Hoe Koo
Allen K. Fritz
Jesse Poland
Cecile Monat
Axel Himmelbach
Anne Fiebig
Sudharsan Padmarasu
Uwe Scholz
Martin Mascher
Georg Haberer
Mulualem T. Kassa
Pierre Fobert
Sateesh Kagale
Jemima Brinton
Ricardo H. Ramirez-Gonzalez
Michael Bevan
Neil McKenzie
Burkhard Steuernagel
Markus C. Kolodziej
Simon G. Krattinger
Beat Keller
Thomas Wicker
Dinushika Thambugala
Curt A. McCartney
Venkat Bandi
Jorge Nunez Siri
Carl Gutwin
Catharine Aquino
Masaomi Hatakeyama
Dario Copetti
Gwyneth Halstead-Nussloch
Timothy Paape
Rie Shimizu-Inatsugi
Kentaro K. Shimizu
Department of Evolutionary Biology and Environmental Studies, University of Zurich
Tomohiro Ban
Kanako Kawaura
Toshiaki Tameshige
Hiroyuki Tsuji
Luca Venturini
Matthew Clark
Division of Hematology/Oncology, Department of Medicine, University of California
Bernardo Clavijo
Christine Fosker
Gonzalo Garcia Accinelli
Darren Heavens
Ksenia Krasileva
Keith A. Gardner
Nick Fradgley
Lawrence Percival-Alwyn
James Cockram
Juan Gutierrez-Gonzalez
Gary Muehlbauer
Chu Shin Koh
Andrew G. Sharpe
Jasline Deek
Alejandro C. Costamagna
Hiroyuki Kanamori
Fuminori Kobayashi
Tsuyoshi Tanaka
Jianzhong Wu
Hirokazu Handa
Tony Kuo
Roche Informatics, F. Hoffmann-La Roche Ltd.
Jun Sese
Kazuki Murata
Yusuke Nabeka
Shuhei Nasuda
Philomin Juliana
Ravi Singh
Department of Chemistry, Gwangju Institute of Science and Technology (GIST) 1 , 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005,
Hikmet Budak
Ian Small
Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia
Joanna Melonek
Sylvie Cloutier
Gabriel Keeble-Gagnère
Josquin Tibbets
Erik Legg
Arvind Bharti
Peter Langridge
Ken Chalmers
Assaf Distelfeld
Manuel Spannagl
Anthony Hall