AUTHOR=Li Jia , Su Yingjuan , Wang Ting 

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

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.00533

DOI=10.3389/fpls.2018.00533

ISSN=1664-462X

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