Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus Dipelta and Their Phylogenomic Implications.

Fangfang Peng,Zhan-Lin Liu,Jie Han,Zhe Zhao,Bin Tian,Yunjing Lei,Bei Xu,Qian Yang

doi:10.3389/fgene.2020.573226

Abstract

Dipelta (Caprifoliaceae) is a Tertiary relict genus endemic to China, comprising three species with horticultural and medicinal values. For the lack of genomic information, interspecific relationships and divergence times in the genus remain unresolved. In the present study, we assembled and characterized the complete plastomes, the partial mitogenomes, and nuclear internal transcribed spacer (ITS) fragments from genome skimming datasets of 14 Dipelta individuals. The plastomes were conserved in genomic structure, gene order, and gene content, but with highly variable repeat sequences. Three genes (rpl23, ycf1, ycf2) were examined with positive selection, and nine divergent hotpot regions (psbL, accD, rpl23, ycf2, ycf3, rbcL-accD, trnI-CAU-ycf2, ndhH-rps15, and rps18 intron) were potentially valuable for DNA barcodes. Contrasted to the variability in plastome sequences, mitogenomes contained 12 protein-coding genes with limited indels and nucleotide substitutions, and no gene was found under positive selection. Genes in organellar genomes tended to have a similar pattern of codon usage bias, with a preference of A/U ending codons. Phylogenetic trees constructed with plastomes, mitogenomes, and ITS sequences consistently supported that Dipelta was monophyletic, and Dipelta elegans was sister to the other two taxa. Interspecific divergences were estimated at about 33–37 Ma in the Eocene/Oligocene boundary, suggesting the paleo-endemism of the extant species as “living fossils” of the East Asian Flora. Our study well-exhibited that genome skimming could provide valuable genomic information to elucidate the evolutionary history of the complex group in a cost-efficient way.

Highlights

Dipelta (Caprifoliaceae), mainly distributed in southwest and central China, is a Tertiary relict woody genus with three extant species, Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans (Figure 1) (Wu et al, 2011)
Nuclear internal transcribed spacer (ITS) fragments of D. yunnanensis and D. floribunda were in similar sizes (613 bp or 61 bp), while D. elegant counterparts were longer (623–639 bp) with higher GC contents (Supplementary Table A2)
Partial mitogenomes of Dipelta were determined in this study, with the sizes of 218,040 bp (D. floribunda_GSWX)–242,194 bp (D. yunnanensis_YNKM)

Summary

Introduction

Dipelta (Caprifoliaceae), mainly distributed in southwest and central China, is a Tertiary relict woody genus with three extant species, Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans (Figure 1) (Wu et al, 2011). Either D. yunnanensis or D. elegans was possibly a sister to the other two taxa (Liu et al, 2013; Wang et al, 2015). The low resolution of chloroplast fragments even produced a completely polytomous phylogenetic tree of the genus (Liu et al, 2013). Chloroplast DNA fragments suggested that infrageneric taxa diverged in the Miocene (9.92 Ma) (Wang et al, 2015), indicating the paleo-endemism of the living species. To elucidate the phylogenetic incongruence and divergence issues, additional genomic data are indispensably needed

Objectives

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Conclusion