title: Genetic variations in the chloroplast genome and phylogenetic clustering of Lycoris species.
abstract: The genus Lycoris of Amaryllidaceae comprises approximately 20 species that are distributed only in the moist warm temperate woodlands of eastern Asia. The objectives of this study were: (1) to clarify the phylogeny of the Lycoris species by using the definitive DNA sequencing method and (2) to examine the possible maternal donor of the hybrid origin Lycoris species and the Japanese triploid strains of Lycoris radiata var. radiata. The nucleotide sequence of the maturase K (matK) gene and the noncoding intergenic spacer (IGS) between the atpB and rbcL genes in the chloroplast genome were determined in a total of 27 strains of 11 species of the genus Lycoris. Variation among taxa was mainly due to nucleotide substitution, although deletions and an insertion were found in the IGS. For two chloroplast regions, the phylogenetic trees showed essentially similar topology, indicating the existence of four clades, I, II, III, and IV. For all the species except L. radiata, intraspecific variation was smaller than interspecific variation. For L. radiata, triploid strains were divided into clades I and II, and diploid strains were divided into clades I and IV. This implies that the diploid species of L. radiata var. pumila is a probable ancestral species. The clustering indicated that the chloroplast genome has not evolved in parallel with the karyotype in genus Lycoris. Regarding the hybrid origin species, the maternal parents of L. squamigara, L. albiflora and L. rosea were revealed to be L. longituba, L. radiata and L. radiata var pumila, respectively. We also suggest that a diploid strain of L. radiata var. pumila in clade I might be a candidate of the maternal donor of the Japanese triploid strains. A possible model of the maternal donor of Lycoris species is proposed.
authors.affiliation: Transcriptome Profiling Group, National Institute of Radiological Sciences, Chiba, Japan. horitadaaki810@aol.com
authors.forename: Tada-aki
authors.initials: TA
authors.lastname: Hori
authors.forename: Akiko
authors.initials: A
authors.lastname: Hayashi
authors.forename: Tsuneo
authors.initials: T
authors.lastname: Sasanuma
authors.forename: Siro
authors.initials: S
authors.lastname: Kurita
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D018742:DNA, Chloroplast / Q000032:analysis*; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D031426:Lycoris / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018742:DNA, Chloroplast