Plastome phylogenomic analysis of Torreya (Taxaceae)

Abstract

Torreya Arn., a small genus of Taxaceae, consists of six species occurring in North America and eastern Asia. Several phylogenetic studies have previously been undertaken to reveal relationships within this genus, although only a few DNA segments or species were used. In the present study, we sequenced five Torreya plastomes and combined these with two existing plastomes from the genus to investigate plastome evolution and phylogenetic relationships within Torreya. All sequenced Torreya plastomes shared the same complement of 82 protein‐coding genes, 4 ribosomal RNA genes, and 31 transfer RNA genes. Phylogenetic inference using a maximum likelihood framework consisted of an 82‐gene, 17‐taxon dataset, including all species of Torreya, resolved Torreya as a monophyletic clade. Strongly supported relationships within the genus include the position of the early diverging T. jackii Chun, the two sister pairs T. fargesii Franch.–T. nucifera (L.) Siebold & Zucc. and T. grandis Fortune ex Lindl.–T. californica Torr., and the monophyly of the clade including T. fargesii var. yunnanensis, T. fargesii, and T. nucifera. In addition to the inference of species relationships, divergence time estimation and biogeographical analysis were carried out. The diversification of Torreya was estimated to be approximately 8.9 Ma. Ancestral state reconstruction of the geographical area suggested China/eastern North America as the most likely ancestral region for the six extant Torreya species.

Plastome phylogenomic and biogeographic study on Thuja (Cupressaceae)

“…All plastomes of Thuja possess 116 unique genes arranged in the same order, including 82 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with trnI-CAU and trnQ-UUG having two copies. Previous studies have commonly reported that the plastomes of conifers are usually characterized by the loss of an IR [36][37][38][39][40][41][42][43][44], which is different from the typical quadripartite structure shared by most angiosperm plastomes [45]. As expected, the loss of an IR was evident in all Thuja plastomes.…”

“…Consistent with previous studies, we detected two repeated tRNA genes, trnI-CAU and trnQ-UUG, existing inall Thuja plastomes. As proposed previously [37,41,44], these types of repeated tRNA genes in direct or inverted copies are possibly the result of the incomplete loss of IR regions.…”

“…Previously, repeated tRNA genes in direct or inverted copies have been commonly discovered in conifer plastomes [37][38][39][40]44]. For instance, the duplicated gene trnI-CAU was discovered in Pinaceae [33,37], trnQ-UUG genehad two copies in Cupressophytes [38], the duplicated trnQ-UUG and trnI-CAU genes were reported in Taxus [46] and Cryptomeria [47], and three duplicated tRNA genes, trnI-CAU, trnQ-UUG, and trnN-GUU, were found in Torreya [44]. Consistent with previous studies, we detected two repeated tRNA genes, trnI-CAU and trnQ-UUG, existing inall Thuja plastomes.…”

Comparative Genomic Analysis Reveals the Mechanism Driving the Diversification of Plastomic Structure in Taxaceae Species

“…Dealing with the rearrangements of two specific inverted fragments, our study provides novel insights into the structural diversification of Taxaceae plastomes. Phylogeny of the Taxaceae genera has been controversial for many years (Lu et al, 2014;Wu and Chaw, 2016;Zhang et al, 2019). In this study, 73 shared protein-coding genes were used to determine the relationships among the four genera.…”

Advances in biogeography in the age of a new modern synthesis

“…The tribe Maleae of Rosaceae had an early New World diversification and subsequently diversified in Asia. Zhang et al () conduct plastome phylogenomic analyses of Torreya and infer the divergence between the eastern North American T. taxifolia with its eastern Asian relatives in the late Miocene, but a much younger disjunction is inferred between the western North American T. californica and the eastern Asian T. grandis . The authors argue for the climatic oscillations and environmental changes during and after the late Tertiary in shaping up the intercontinental biogeography of Torreya .…”