Abstract
Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.
Highlights
IntroductionLitsea contains around 408 species, with Litsea cubeba (Lour.) Pers
The complete chloroplast genome of L. auriculata was 152,377 bp in length and displayed a quadripartite structure consisting of a pair of inverted repeat regions (IR with 20,015 bp) divided by two single-copy regions (LSC, 93,533 bp, and SSC, 18,814 bp; Figure 1, Table 1)
Our results showed the high conservativeness of the plastid genomes of these 12 Litsea species regarding the canonical angiosperm quadripartite structure with no structural arrangement or gene inversion and the unbiased codon usage preferences
Summary
Litsea contains around 408 species, with Litsea cubeba (Lour.) Pers. Regarding the fossil records of Litsea, Dai et al [10] reported a well-preserved fossil leaf of Litsea cf chunii Cheng discovered in the Late Pliocene’s sediments of the Mangbang formation in Tengchong county, Yunnan Province, China, and a mummified fossil wood of Litseoxylon nanningensis gen. Nov. was identified from the Upper Oligocene Yongning Formation of the Nanning Basin, Guangxi Province, South China, by Huang et al [11]. Many of the species of Litsea have ethnobotanical or economic uses [13,14,15,16,17,18]. Many Litsea species are in urgent need of conservation: 98 species of this genus are listed in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species
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