Comparative genomics and phylogenetic perspectives of six fertile Lycoris species endemic to East Asia based on plastome characterization

Abstract

The genus Lycoris Herb. (Amaryllidaceae) is endemic to East Asia and comprises approximately 20 taxa of which most are confirmed to be sterile hybrids. Here, we report the complete plastome genome (plastome) sequences of six fertile Lycoris species using Illumina sequencing technology. The plastomes of the six species range from 158 436 bp to 158 761 bp in length, and they all contain 112 unique genes consisting of 78 protein coding genes, 30 transfer RNA genes and 4 ribosomal RNA genes. Gene structure, gene order and GC content are highly conserved among the six Lycoris plastomes, yet their lengths vary owing to the contraction and expansion of the IR/SC borders. Sixteen hypervariable regions with nucleotide variability > 0.9% were found, among which seven markers (trnS‐trnG, ndhF‐rpl32, rpl32‐trnL, psaA‐ycf3, clpP intron1, trnK‐rps16 and psaJ‐rpl33) were longer than 500 bp. Two marker regions (trnS‐trnG and rpl32‐trnL), randomly selected and validated, showed 2–3 folds higher nucleotide variability than four universal marker regions within populations of L. radiata. Pairwise sequence comparisons detected multiple simple sequence repeat (SSR) sites, and the richest SSRs are A/T mononucleotides in these Lycoris plastomes. The robust phylogenies inferred from the plastomes and coding region sequences consistently divided the six species into two well supported clades. One consisted of L. sanguinea and L. sprengeri, the other included the remaining four species (L. longituba, L. aurea, L. chinensis and L. radiata). These plastome markers will be useful in further taxonomic and phylogenetic studies of Lycoris. The obtained plastomes may facilitate the development of biotechnological applications for these herb bulbs with considerable ornamental and medical values, and offer genetic information for studying the phylogenetics and taxonomy of the genus.