AUTHOR=Liu Lu-Xian , Li Rui , Worth James R. P. , Li Xian , Li Pan , Cameron Kenneth M. , Fu Cheng-Xin 

TITLE=The Complete Chloroplast Genome of Chinese Bayberry (Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales

JOURNAL=Frontiers in Plant Science

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.00968

DOI=10.3389/fpls.2017.00968

ISSN=1664-462X

ABSTRACT=<p><italic>Morella rubra</italic> (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry’s domestication are still unresolved. In this study, we report the chloroplast (cp) genome of <italic>M. rubra</italic> and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three <italic>M. rubra</italic> individuals were 159,478, 159,568, and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014–26,069 bp) separated by a large single-copy (LSC) region (88,683–88,809 bp) and a small single-copy (SSC) region (18,676–18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the IRs. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of <italic>inf</italic>A and the pseudogenization of <italic>ycf</italic>15 in all analyzed species, and <italic>rpl</italic>22 has been pseudogenized in <italic>M. rubra</italic> and <italic>Castanea mollissima</italic>, but not in <italic>Juglans regia</italic> or <italic>Ostrya rehderiana</italic>. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (<italic>trn</italic>H-<italic>psb</italic>A, <italic>psb</italic>A-<italic>trn</italic>K, <italic>rps</italic>2-<italic>rpo</italic>C2, <italic>ycf</italic>4-<italic>cem</italic>A, <italic>pet</italic>D-<italic>rpo</italic>A, <italic>ndh</italic>E-<italic>ndh</italic>G, and <italic>ndh</italic>A intron) with relatively high levels of variation and variable cpSSR loci were identified within <italic>M. rubra</italic>, which will be useful in future research characterizing the population genetics of <italic>M. rubra</italic> and investigating the origin of domesticated Chinese bayberry.</p>