Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Huijuan Zhou; Yiheng Hu; Aziz Ebrahimi; Peiliang Liu; Keith Woeste; Peng Zhao; Shuoxin Zhang

doi:10.1186/s12862-021-01917-3

Whole genome based insights into the phylogeny and evolution of the Juglandaceae

BMC Ecol Evol. 2021 Oct 21;21(1):191. doi: 10.1186/s12862-021-01917-3.

Authors

Huijuan Zhou^#^{1

2}, Yiheng Hu^#², Aziz Ebrahimi³, Peiliang Liu², Keith Woeste³, Peng Zhao⁴, Shuoxin Zhang⁵

Affiliations

¹ College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
² Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
³ USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA.
⁴ Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China. pengzhao@nwu.edu.cn.
⁵ College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China. sxzhang@nwsuaf.edu.cn.

^# Contributed equally.

Abstract

Background: The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes.

Results: We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae.

Conclusions: A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).

Keywords: Divergence time; Diversification; Genome; Juglandaceae; Phylogenomics; Plastome.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Fossils
Genome, Chloroplast*
Juglandaceae* / genetics
Phylogeny
Plastids