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The complete plastome of real yellow wood (Podocarpus latifolius): gene organization and comparison with related species

Saina, Josphat K., Li, Zhi-Zhong, Gichira, Andrew W., Avoga, Sheila, Wang, Qing-Feng, Kuo, Liao
Holzforschung 2019 v.73 no.6 pp. 525-536
Cladrastis lutea, Podocarpus latifolius, genomics, introns, microsatellite repeats, molecular biology, phylogeny, population genetics, ribosomal RNA, transfer RNA, wood, wood pulp
Podocarpus latifolius [(Thunb.) R.Br. ex Mirb.], also known as real yellow wood, is a large evergreen tree with exceptionally high-quality wood. It is a member of the Podocarpaceae family, which includes many species widely grown for wood pulp as well as timber for construction. Despite its importance, studies focusing on its genetic characterization and molecular biology are limited. Therefore, this study reports the complete plastome of P. latifolius, which is a circular molecule of 134 020 base pairs (bp) in length, lacking a quadripartite structure. The P. latifolius plastome encodes 117 unique genes, consisting of 82 protein-coding genes, 31 transfer RNA genes and four ribosomal RNA genes. The analysis showed that the Podocarpaceae plastomes have experienced some intron and gene losses, inversions, and inverted repeat (IR) loss resulting in a diverse plastome organization at the species and genus levels. Therefore, to understand the extent of these genomic rearrangements, more sampling of the Podocarpaceae plastomes is necessary. A total of 149 editing sites were predicted in 28 genes, all of which were C to U conversions. Moreover, a total of 164 simple sequence repeats (SSRs) were identified in the P. latifolius plastome, the majority being mononucleotide repeat motifs with A/T sequence predominance. Overall, the data obtained in this study will be useful for population genetics, evolutionary history and phylogenetic studies of the species in this genus.