Comparative Chloroplast Genomics of <i>Fritillaria</i> (Liliaceae), Inferences for Phylogenetic Relationships between <i>Fritillaria</i> and <i>Lilium</i> and Plastome Evolution

• Main Authors: Jiao Huang, Yan Yu, Yan-Mei Liu, Deng-Feng Xie, Xing-Jin He, Song-Dong Zhou
• Format: Article
• Language: English
• Published: MDPI AG 2020-01-01
• Series: Plants
• Subjects: <i>fritillaria</i>; liliaceae; plastome genome; genome structure; phylogenomics
• Online Access: https://www.mdpi.com/2223-7747/9/2/133

<i>Fritillaria</i> is a genus that has important medicinal and horticultural values. The study involved the most comprehensive chloroplast genome samples referring to Old and New World clades of <i>Fritillaria</i> for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome sequences of <i>Fritillaria</i> which proved highly similar in overall size (151,652&#8722;152,434 bp), genome structure, gene content, and order. Comparing them with other species of Liliales (6 out of 10 families) indicated the same similarity but showed some structural variations due to the contraction or expansion of the inverted repeat (IR) regions. A/T mononucleotides, palindromic, and forward repeats were the most common types. Six hypervariable regions (<i>rps16</i>-<i>trnQ, rbcL</i>-<i>accD, accD</i>-<i>psaI, psaJ</i>-<i>rpl33, petD</i>-<i>rpoA</i>, and <i>rpl32</i>-<i>trnL</i>) were discovered based on 26 <i>Fritillaria</i> whole-plastomes to be potential molecular markers. Based on the plastome data that were collected from 26 <i>Fritillaria</i> and 21 <i>Lilium</i> species, a phylogenomic study was carried out with three <i>Cardiocrinum</i> species as outgroups. <i>Fritillaria</i> was sister to <i>Lilium</i> with a high support value, and the interspecies relationships within subgenus <i>Fritillaria</i> were resolved very well. The six hypervariable regions can be used as candidate DNA barcodes of <i>Fritillaria</i> and the phylogenomic framework can guide extensive genomic sampling for further phylogenetic analyses.