Chinese Bulletin of Botany ›› 2015, Vol. 50 ›› Issue (5): 549-564.DOI: 10.11983/CBB15164

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Phylogenetic Reconstruction of Tribal Relationships in Asteroi- deae (Asteraceae) with Low-copy Nuclear Genes

Mian Liu1,2, Caifei Zhang1,2*, Chien-Hsun Huang1,2, Hong Ma1,2*   

  1. 1School of Life Sciences, Fudan University, Shanghai 200438, China
    2Institute of Plant Biology, Fudan University, Shanghai 200438, China
  • Received:2015-08-15 Accepted:2015-09-05 Online:2015-09-01 Published:2015-10-09
  • Contact: Zhang Caifei,Ma Hong
  • About author:? These authors contributed equally to this paper

Abstract:

Asteroideae is the largest subfamily of the daisy family, Asteraceae, with more species than most other angiosperm families. Previous phylogenetic relationships of Asteroideae tribes were mostly based on chloroplast genes, which are uniparentally inherited and could not reflect the entire evolutionary histories. Especially considering the widespread phenomenon of hybridization in Asteraceae, low-copy nuclear genes with biparental inheritance can better serve as phylogenetic markers, for a more complete understanding of their evolution. To resolve the intertribal relationships in Asteroideae, transcriptomic datasets were newly generated by sequencing 20 species and additional datasets for 11 species downloaded from NCBI, representing 13 tribes and all 3 supertribes of this subfamily. Extensive sequence analyses of the 31 datasets resulted in the selection of 47 orthologous nuclear genes for phylogenetic reconstruction. Using the supermatrix analyses and coalescent estimates, we obtained robust and highly supported species trees, which are in agreement with each other. New intertribal phylogenies of Asteroideae revealed that: (1) the supertribe Senecionodae should be merged into the supertribe Asterodae; (2) Anthemideae possibly originated from a hybrid of ancestors of Senecioneae and Astereae; and (3) Coreopsideae is probably also hybrid originated. This study demonstrates that low-copy nuclear genes are good markers for infra-familial phylogenetic reconstruction and provides a foundation for future studies of phylogeny of Asteraceae and other angiosperm families.

Key words: Asteraceae, Asteroideae, low-copy nuclear genes, phylogeny, transcriptome-sequencing