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

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).

The first complete chloroplast genome in Engelhardia sensu stricto, Engelhardia hainanensis Chen: genome characterization and its phylogenetic relationships within the family Juglandaceae

“… 2020 ), Alfaropsis roxburghiana MH188300 (Zhou et al. 2021 ), Alfaropsis fenzelii MT991009 (Liu et al. 2021 ), Carya cathayensis MN892516 (Shen et al.…”

“… 2022 ), Carya hunanensis MH188303 (Zhou et al. 2021 ), Carya kweichowensis MH188301 (Zhou et al. 2021 ), Carya sinensis MW421595 (Xi et al.…”

“… 2021 ), Carya kweichowensis MH188301 (Zhou et al. 2021 ), Carya sinensis MW421595 (Xi et al. 2022 ), Carya poilanei ON568300 (Xi et al.…”

Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

“…5c and Supplementary Fig. 14e ) nor over the past 20 years 9 , 10 , 14 – 16 , 18 , 19 . This implies that the placement of Platycarya in either the genome-structure-based phylogeny or the DNA-alignment-based phylogenies must be wrong.…”

The Significances of Cretaceous Petrified Wood Fossils from Padangcermin, Lampung in Paleoenvironmental Perspectives

“…Generally, these taxa are associated with freshwater ecosystems, such as rivers and lacustrine [18]. This tree family is known to have existed since the Cretaceous [19]. Based on the aquatic plant fossils identified as graminoid aquatic plants, indicating a freshwater depositional environment surrounded by woody plants such as Junglandaceaea and grassy wetland plants, such as graminoid-aquatic plants occupied the area.…”