Chloroplast genomes of two extant species of Tertiary relict Cercidiphyllum (Cercidiphyllaceae): comparative genomic and phylogenetic analyses

Abstract

Cercidiphyllum, the only member of Cercidiphyllaceae, contains two extant species: Cercidiphyllum japonicum and Cercidiphyllum magnificum. Here, we reported their complete chloroplast genomes by de novo assembly. The chloroplast genome sizes of C. japonicum and C. magnificum were 159,871 and 159,899 bp, respectively. The two chloroplast genomes have 99.7% sequence identity and were highly conserved in GC content (37.9%), gene content (132 genes), and gene order. Phylogenetic analysis of the chloroplast genomes confirmed the monophyly of Cercidiphyllum and recovered Cercidiphyllaceae as a member of the 'woody clade' of Saxifragales.

Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

“…Based on nuclear genome data generated by target-capture sequencing and RNA-seq, Folk et al [28] recovered the phylogenetic backbone of the WCS with high-resolution and well-supported interfamilial relationships. In contrast, previous plastome-based phylogenetic analyses of the WCS taxa have demonstrated tree topologies with low support [52,53] and inconsistent inter-familial relationships [32,33]. Consequently, the family-level maternal relationships within the WCS remain ambiguous, providing weak evidence for detecting cytonuclear discordance in the deep relationships within the WCS.…”

“…The interfamilial relationships are consistent with those revealed by Jian et al [21], Soltis et al [27], Xiang et al [30], Tarullo et al [31], and Bi et al [33]. Nevertheless, the interfamilial relationships recovered in this study are inconsistent with those obtained by analyzing plastid sequence data alone, which proposed topologies of (Daphniphyllaceae, (Altingiaceae, (Hamamelidaceae, Cercidiphyllaceae))) [32,77], (Altingiaceae, (Cercidiphyllaceae, (Daphniphyllaceae, Hamamelidaceae))) based on 83 plastid PCGs of four species [52], (Hamamelidaceae, (Cercidiphyllaceae, Daphniphyllaceae, Altingiaceae)) based on 83 protein-coding genes, and ((Daphniphyllaceae, Altingiaceae), (Hamamelidaceae, Cercidiphyllaceae)) based on plastome of nine species [53]. Due to the limited taxonomic sampling of the WCS, these studies likely suffered from phylogenetic errors.…”