The complete chloroplast genome of Torreya parvifolia, a species with extremely small population in China

Abstract

Torreya parvifolia ( Torreya , Taxaceae) is endemic in Sichuan, China. It consisted of an extremely small population with less than 100 wild individuals. In this study, the complete chloroplast genome of T. parvifolia was assembled using the Illumina data. The complete chloroplast genome of T. parvifolia is 137,106 bp in length. The genome consists of 119 genes in total, including 82 protein-coding genes (PCGs), 4 ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes. Phylogenetic analysis indicated that T. parvifolia was closely related to T. fargesii , T. nucifera , and T. fargesii var. yunnanensis with strong support.

Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants

“…A plastome phylogeny showed a discordant phylogenetic position of T. jackii, which shifted to a position as sister to the rest of all other species [14]. However, also based on the complete plastome, the interspecific relationships differed from the above study in which T. jackii was also recovered as the earliest divergent species, but followed by T. taxifolia, rather than a sister clade consisting of NA species clade and other EA species clade [30,31,34,35]; other relationships saw T. californica as sister to T. grandis [30,31,34,35], and T. yunnanense was resolved as sister to a clade of T. parvifolia (T. fargesii + T. nucifera), and these two clades form a sister relationship [30,34]. These species formed a clade but had inconsistent relationships in Miao et al [35] and Ji et al [31].…”

“…Therefore, more caution should be taken when using cultivated plants from botanic gardens/arboretums for biological study, and there is a need for the verification of their species identification. In previous molecular studies [30,34,35], sequences were downloaded from GenBank or obtained from cultivated plants directly without concerns of species identification, which may have affected their phylogenetic inferences. The use of multiple samples per species in this respect cannot be overemphasized as only this allowed an independent check for correct species identifications [11].…”

“…As several species in Torreya are listed as endangered species with small distribution ranges, the plant material of some species used for previous molecular phylogenies came from cultivated plants in botanical gardens/arboretums, and only a single accession for each species was sampled in previous studies [30,31,[33][34][35]. The misidentification of this cultivated plant material may have led to the discordances between the previous studies.…”