文献类型：期刊文献

英文题名：Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees

作者：Zinkgraf, Matthew[1,2] Zhao, Shu-Tang[3] Canning, Courtney[1] Gerttula, Suzanne[1] Lu, Meng-Zhu[3] Filkov, Vladimir[4] Groover, Andrew[1,5]

第一作者：Zinkgraf, Matthew

通信作者：Groover, A[1];Lu, MZ[2];Filkov, V[3];Groover, A[4]

机构：[1]US Forest Serv, USDA, Pacific Southwest Res Stn, Davis, CA 95618 USA;[2]Western Washington Univ, Coll Sci & Engn, Bellingham, WA 98225 USA;[3]Chinese Acad Forestry, Res Inst Forestry, State Key Lab Tree Genet & Breeding, Beijing 100091, Peoples R China;[4]Univ Calif Davis, Comp Sci, Davis, CA 95618 USA;[5]Univ Calif Davis, Dept Plant Biol, Davis, CA 95616 USA

年份：2020

卷号：228

期号：6

起止页码：1811-1823

外文期刊名：NEW PHYTOLOGIST

收录：;Scopus(收录号：2-s2.0-85089376586);WOS:【SCI-EXPANDED(收录号:WOS:000559506800001)】；

基金：The authors thank Reginald King for assistance in plant propagation; Ajiinkkya Bhalerao and Tyson Lathem for assistance with bioinformatics analyses; Larry Smart for supplying cutting of Salix purpurea; Steve Strauss for Eucalyptus grandis; and the Arnold Arboretum for access to S. aegyptiaca, S. babylonica and S. chaenomeloides. All raw Illumina sequene data for this project have been submitted to the National Center for Biotechnology Information (NCBI) and associated with BioProject PRJNA556244. This study was supported by an Arnold Arboretum Sargent Fellowship to AG, USDA AFRI 2015-67013-22891 to AG and VF, a National Nonprofit Institute Research Grant of CAF (CAFYBB2012039) to SZ, and NSF PGRP Fellowship IOS-1402064 to MZ. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a US Department of Energy Office of Science User Facility operated under contract no. DE-AC02-05CH11231.

语种：英文

外文关键词：computational biology; evolutionary genomics; forest trees; gene coexpression networks; plants; wood formation

摘要：Wood formation was present in early angiosperms, but has been highly modified through evolution to generate the anatomical diversity seen in extant angiosperm lineages. In this project, we modeled changes in gene coexpression relationships associated with the evolution of wood formation in a phylogenetic survey of 13 angiosperm tree species. Gravitropic stimulation was used as an experimental treatment to alter wood formation and also perturb gene expression. Gene transcript abundances were determined using RNA sequencing of developing wood tissues from upright trees, and from the top (tension wood) and bottom (opposite wood) tissues of gravistimulated trees. A network-based approach was employed to align gene coexpression networks across species based on orthologous relationships. A large-scale, multilayer network was modeled that identified both lineage-specific gene coexpression modules and modules conserved across multiple species. Functional annotation and analysis of modules identified specific regulatory processes associated with conserved modules, including regulation of hormones, protein phosphorylation, meristem development and epigenetic processes. Our results provide novel insights into the evolution and development of wood formation, and demonstrate the ability to identify biological processes and genes important for the evolution of a foundational trait in nonmodel, undomesticated forest trees.