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The complete chloroplast genome of Lilium brownii F.E.Brown var. viridulum Baker (Liliaceae).

ABSTRACT: Lilium brownii F.E.Brown var. viridulum Baker is a medicinal and food plant that is widely distributed in northern and eastern Asia. Here, we report on the complete chloroplast genome sequence of L. brownii var. viridulum. The chloroplast genome is 152,665 bp in size and includes two inverted repeat regions of 53,052 bp, which is separated by a large single-copy region of 82,085 bp and a small single-copy region of 17,528 bp. A total of 131 genes were predicted, including 38 tRNA, 8 rRNA, and 85 protein-coding genes. Phylogenetic analysis placed L. brownii var. viridulum under the family Liliaceae.

SUBMITTER: Jin J

PROVIDER: S-EPMC7748718 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.

Dataset Information

The complete chloroplast genome of Lilium brownii F.E.Brown var. viridulum Baker (Liliaceae).

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