The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes.

Jia Li,Ting Wang,Yingjuan Su

doi:10.3389/fpls.2018.00533

Abstract

The plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica, Taiwania cryptomerioides, Cephalotaxus, Taxus chinensis, and Podocarpus lambertii, and the main reason for this phenomenon was the existence of tandemly repeated sequences. However, it is still unknown whether the accD gene length in other cupressophytes has expanded. Here, in order to investigate how widespread this phenomenon was, 18 accD sequences and its surrounding regions of cupressophyte were sequenced and analyzed. Together with 39 GenBank sequence data, our taxon sampling covered all the extant gymnosperm orders. The repetitive elements and substitution rates of accD among 57 gymnosperm species were analyzed, the results show: (1) Reading frame length of accD gene in 18 cupressophytes species has also expanded. (2) Many repetitive elements were identified in accD gene of cupressophyte lineages. (3) The synonymous and non-synonymous substitution rates of accD were accelerated in cupressophytes. (4) accD was located in rearrangement endpoints. These results suggested that repetitive elements may mediate the chloroplast genome rearrangement and accelerated the substitution rates.

Highlights

IntroductionCupressophytes, called non-Pinaceae conifers, comprise about 380 species in 58 genera of five families: Araucariaceae, Podocarpaceae, Sciadopityaceae, Taxaceae (including Cephalotaxaceae), and Cupressaceae (including Taxodiaceae) (Christenhusz et al, 2011)
Cupressophytes, called non-Pinaceae conifers, comprise about 380 species in 58 genera of five families: Araucariaceae, Podocarpaceae, Sciadopityaceae, Taxaceae, and Cupressaceae (Christenhusz et al, 2011)
Many studies have suggested that highly rearranged chloroplast genome generally possess a great many repetitive sequences which are associated with rearrangement endpoints, and this phenomenon has been observed in some land plants: Douglas-fir (Pseudotsuga menziesii) (Tsai and Strauss, 1989), Pelargonium (Chumley et al, 2006), Trifolium (Cai et al, 2008), Trachelium (Haberle et al, 2008), Oleaceae (Lee et al, 2007), and Asteraceae (Kim et al, 2005; Timme et al, 2007)

Summary

Introduction

Cupressophytes, called non-Pinaceae conifers, comprise about 380 species in 58 genera of five families: Araucariaceae, Podocarpaceae, Sciadopityaceae, Taxaceae (including Cephalotaxaceae), and Cupressaceae (including Taxodiaceae) (Christenhusz et al, 2011). Dispersed repetitive DNA sequences are scattered throughout the chloroplast genome. Most of the studies concentrate on detecting repeat sequences on a chloroplast genome-wide degree (Saski et al, 2005; Guo et al, 2007; Haberle et al, 2008; Tangphatsornruang et al, 2011); while there are only very few reports about the presence and structure of the repetitive DNA of a specific gene among many lineages (Hipkins et al, 1995; Erixon and Oxelman, 2008). The genome containing the most frequency of long repeats is usually the most reorganized

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