Abstract
Pinaceae, the largest family of conifers, has a diversified organization of chloroplast (cp) genomes with two typical highly reduced inverted repeats (IRs). In the current study, we determined the complete sequence of the cp genome of an economically and ecologically important conifer tree, the loblolly pine (Pinus taeda L.), using Illumina paired-end sequencing and compared the sequence with those of other pine species. The results revealed a genome size of 121,531 base pairs (bp) containing a pair of 830-bp IR regions, distinguished by a small single copy (42,258 bp) and large single copy (77,614 bp) region. The chloroplast genome of P. taeda encodes 120 genes, comprising 81 protein-coding genes, four ribosomal RNA genes, and 35 tRNA genes, with 151 randomly distributed microsatellites. Approximately 6 palindromic, 34 forward, and 22 tandem repeats were found in the P. taeda cp genome. Whole cp genome comparison with those of other Pinus species exhibited an overall high degree of sequence similarity, with some divergence in intergenic spacers. Higher and lower numbers of indels and single-nucleotide polymorphism substitutions were observed relative to P. contorta and P. monophylla, respectively. Phylogenomic analyses based on the complete genome sequence revealed that 60 shared genes generated trees with the same topologies, and P. taeda was closely related to P. contorta in the subgenus Pinus. Thus, the complete P. taeda genome provided valuable resources for population and evolutionary studies of gymnosperms and can be used to identify related species.
Highlights
Gymnosperms are represented by a diverse and magnificent group of coniferous species distributed across eight families, consisting of 70 genera containing more than 630 species [1]
The P. taeda cp genome was assembled by mapping all Illumina sequence reads into a draft cp genome
The cp genome size of P. taeda was within the expected range (116–121 Kb) of other sequenced cp genomes of Pinaceae members [41, 68, 69]
Summary
Gymnosperms are represented by a diverse and magnificent group of coniferous species distributed across eight families, consisting of 70 genera containing more than 630 species [1]. They are thought to have arisen from seed plants approximately 300 million years ago and are one of the ancient main plant clades. Comparative studies revealed that transposable elements, repetitive sequences, and gene duplication are common in gymnosperm genomes [4, 6,7,8]. Conifers are the main representatives of the gymnosperms, predominant in various ecosystems and representing 82% of terrestrial biomass [9]
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