Genome research

Rice was the first major food crop to have its genome sequenced. The completion of the rice genome map was heralded for its potential to affect several billion human lives. The Torrey Mesa Research Institute shotgun DNA sequences from 2002 were merged with international data that led to the completion and assembly of the full-genome map of rice in 2007, which was the second high-resolution genome map available for plants.

As a member of the TMRI rice genome sequencing project committee, Cooper contributed and evaluated data for the overall genome sequencing effort. He has continued to advance genomics research by sequencing genes of plants and plant pathogens.

In 2014, Cooper first reported the artificial synthesis of the Tobacco mosaic virus.

Papers:

Genomic resources for Pseudomonas savastanoi pv. phaseolicola races 5 and 8 (2021). Bret Cooper and Ronghui Yang. Phytopathology. Published on-line before print December 14, 2020. DOI: c

Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies (2021). Ashwil Klein, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, and David L. Tabb. Plants 10, 765.

Proof by synthesis of Tobacco mosaic virus (2014). Bret Cooper. Genome Biology, 15, R67. Published on-line May 12, 2014.

The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families (2014). Tobias I. Link, Patrick Lang, Brian E. Scheffler, Mary V. Duke, Michelle A. Graham, Bret Cooper, Mark L. Tucker, Martijn van de Mortel, Ralf T. Voegele, Kurt Mendgen, Thomas J. Baum and Steven A. Whitham. Molecular Plant Pathology 15, 379-393. Published on-line before print Dec. 17, 2013. doi: 10.1111/mpp.12099.

Coding DNA Repeated throughout Intergenic Regions of the Arabidopsis thaliana Genome: Evolutionary Footprints of RNA Silencing (2009). Jian Feng, Daniel Q. Naiman, and Bret Cooper. Molecular BioSystems 5, 1679-1687. Published on-line before print April 30, 2009.

Generation of Phaseolus vulgaris ESTs and Investigation of their Regulation upon Uromyces appendiculatus Infection (2009). Sandra Thibivilliers, Trupti Joshi, Kimberly B. Campbell, Brian Scheffler, Dong Xu, Bret Cooper, Henry T. Nguyen, and Gary Stacey. BMC Plant Biology 9, 46. Published on-line before print April 27, 2009.

Analysis of Expressed Sequence Tags from Uromyces appendiculatus Hyphae and Haustoria and Their Comparison to Sequences from Other Rust Fungi (2008). David P. Puthoff, Anil Neelam, Mindy L. Ehrenfried, Brian Scheffler, Linda Ballard, Qijian Song, Kimberly B. Campbell, Bret Cooper, and Mark L. Tucker. Phytopathology 98, 1126-1135.

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica) (2002). Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S. Science 296, 92-100.