Plastomes of Betulaceae and phylogenetic implications

Abstract

Betulaceae is a well-defined family of Fagales, including six living genera and more than 160 modern species. Species of the family have high ecological and economic value for the abundant production of wood. However, phylogenetic relationships within Betulaceae have remained partly unresolved, likely due to the lack of a sufficient number of informative sites used in previous studies. Here, we re-investigate the Betulaceae phylogeny with whole chloroplast genomes from 24 species (17 newly assembled), representing all genera of the family. All the 24 plastomes are relatively conserved with four regions, and each genome is $158-161 kb long, with 111 genes. The six genera are all monophyletic in the plastome tree, whereas Ostrya Scop. is nested in the Carpinus clade in the internal transcribed spacer tree. Further incongruencies are also detected within some genera between species. Incomplete lineage sorting and/or hybrid introgression during the diversification of the family could account for such incongruencies. Our dating analysis, based on four fossils, suggests that the most recent common ancestors of the extant genera date back to the mid-to late Miocene, and confirms that Betulaceae started to diversify in the upper Cretaceous/early Paleocene. Our results highlight the significance of using more informative sites in resolving phylogenetic relationships. Plastome data and increased taxon sampling will help to better understand the evolutionary history of Betulaceae in the future.We would like to thank Dr. Zhiqiang Lu and Mingcheng Wang for their great help with collecting samples in the field and in Phylogenetics of Betulaceae 7 www.jse.ac.cn J. Syst. Evol. 9999 (9999): 1-11, 2019Yang et al.

Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

“…The generic relationships within Coryloideae were studied by molecular markers including matK and rbcL genes, and ITS regions [51, 65–67]. We found a similar grouping within the cp genome phylogeny, including that Corylus formed a monophyletic group and had a close relationship with Carpinus and Ostrya : the results of our analyses supported the previous studies [52]. Ostrya formed a sister group with Carpinus , and these genera together constituted a sister group to Corylus .…”

“…As stated in the literature, Corylus was closest to Carpinus and Ostrya species, and then relatively close to Betula , which is consistent with their taxonomic classification but provides greater insight into the relatedness of these genera (Fig. 4) [51, 52].

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Exploring the plastid genome disparity of liverworts

“…Thus, to achieve an excellent coverage of the phylogeny of land plant plastomes, attention should not only be given to the three lineages of bryophytes but also to selected lineages of angiosperms. Efforts focusing on the phylogenomics of economically important lineages, such as the grape genus Vitis (Wen et al, ) or the birch family Betulaceae (Yang et al, ), will enable us to fill some of the crucial gaps in our current understanding of the evolution of plastid genomes.…”

Involucre fossils of Carpinus, a northern temperate element, from the Miocene of China and the evolution of its species diversity in East Asia

“…However, understanding how temperate woody plant groups has accumulated diversity requires specific tests: time-calibrated molecular phylogenetic study and paleobotanical study. In recent years, many molecular phylogenetic studies on temperate woody plants have suggested that most of them originated in the Paleogene and diversified at different times throughout the Paleogene or Neogene ( Chin et al., 2014 , Forest et al., 2005 , Grimm and Renner, 2013 , Hinsinger et al., 2013 , Li et al., 2018 , Naciri et al., 2019 , Renner et al., 2008 , Yang et al., 2019a , Yang et al., 2019b ). Compared to molecular phylogenetic studies, paleobotanical studies provide more direct evidence of the evolutionary history of plants in East Asia; however, few paleobotanical studies have been conducted on the temperate woody plants.…”

“…Earlier studies based on single or multiple gene fragment(s) show that Carpinus is not monophyletic due to Ostrya Scop. being nested within it ( Chen et al., 1999 , Grimm and Renner, 2013 , Yang et al., 2019a , Yoo and Wen, 2002 ). However, a recent study based on the whole chloroplast genome indicates that the genus is monophyletic and sister to Ostrya ( Yang et al., 2019b ).…”