Comparative Genome Analysis and Phylogenetic Relationship of Order Liliales Insight from the Complete Plastid Genome Sequences of Two Lilies (Lilium longiflorum and Alstroemeria aurea)

Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp inLiliumlongiflorum( Liliaceae ) and 155,510bp inAlstroemeriaaurea( Alstroemeriaceae ). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales . The sister relationship of Liliales and Asparagales -commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae , Smilacaceae , and Alstroemeriaceae , and between two Lilium species ofL. longflorumandL. superbum . Gene content and order were conserved in the order Liliales except inf A loss in Smilax and Alstroemeria . IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria . Ka/Ks ratio was high in mat K among the pair-wise comparison of three families and the most variable genes were psa J, ycf 1, rpl 32, rpl 22, mat K, and ccs A among the three families and rps 15, rpo A, mat K, and ndh F between Lilium .