Abstract
Morella rubra (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 M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra 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 infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. 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 (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG, and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future research characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry.
Highlights
Chloroplasts are essential organelles in plant cells for photosynthesis and perform other functions comprising synthesizing starch, fatty acids, pigments and amino acids (Neuhaus and Emes, 2000)
We generated a total of 8.5 million paired-end (PE) reads (200 million nucleotides) for M. rubra-GZMZ, and trimmed and assembled them using the CLC genome assembler pipeline (CLC Bio, Aarhus, Denmark)
A total of 290,501 PE reads were concordantly mapped to the final assembly and the mapped cp contigs were selected to merge for constructing a complete M. rubra-GZMZ cp genome map using BLAST (NCBI BLAST v2.2.31)
Summary
Chloroplasts (cp) are essential organelles in plant cells for photosynthesis and perform other functions comprising synthesizing starch, fatty acids, pigments and amino acids (Neuhaus and Emes, 2000). Compared with nuclear and mitochondrial genomes, chloroplast genomes are largely conserved in term of gene content, organization and structure (Raubeson and Jansen, 2005), and the nucleotide substitution rate of chloroplast genes is higher than that of mitochondrial genes, but lower than that of nuclear genes (Wolfe et al, 1987; Drouin et al, 2008) Evolutionary events such as mutations, duplications, losses and rearrangements of genes have been reported in a number of studies (Lee et al, 2007; Dong et al, 2013; Choi et al, 2016). Single nucleotide polymorphsims (SNPs) and indels, resulting from translocations, inversions, copy number variation of tandem repeats and rearrangements, are suitable for applying to phylogeny reconstruction (De Las Rivas et al, 2002), DNA barcoding (Hollingsworth et al, 2011), as well as investigating the geographic origin of some important domesticated crops (Arroyo-Garcia et al, 2006; Londo et al, 2006; Delplancke et al, 2013)
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