Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution.

Jiao Huang,Yan Yu,Xing-Jin He,Song-Dong Zhou,Deng-Feng Xie,Yan-Mei Liu

doi:10.3390/plants9020133

Jiao Huang, Yan Yu + Show 4 more

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https://doi.org/10.3390/plants9020133

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Abstract

Fritillaria 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 Fritillaria for marker selection and phylogenetic studies. We reported and compared eleven newly sequenced whole-plastome sequences of Fritillaria which proved highly similar in overall size (151,652–152,434 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 (rps16-trnQ, rbcL-accD, accD-psaI, psaJ-rpl33, petD-rpoA, and rpl32-trnL) were discovered based on 26 Fritillaria whole-plastomes to be potential molecular markers. Based on the plastome data that were collected from 26 Fritillaria and 21 Lilium species, a phylogenomic study was carried out with three Cardiocrinum species as outgroups. Fritillaria was sister to Lilium with a high support value, and the interspecies relationships within subgenus Fritillaria were resolved very well. The six hypervariable regions can be used as candidate DNA barcodes of Fritillaria and the phylogenomic framework can guide extensive genomic sampling for further phylogenetic analyses.

Highlights

Plastid genome of angiosperm have a typical quadripartite structure with a pair of inverted repeat (IR) regions separated by a small single-copy (SSC) region and a large single-copy (LSC) region [1,2].In contrast to mitochondrial and nuclear genomes, plastid genome is highly conserved and generally contains 110–130 distinct genes, ranging in size from 120–160 kb [3]
A total of 1.02–2.24 G clean base of the each Fritillaria species was collected and the plastomes size ranged from 151,652 bp (Fritillaria yuzhongensis) to 152,434 bp (Fritillaria maximowiczii) (Table 1)
Comparison of Fritillaria Plastomes and Phylogenetically Informative Markers were conserved in genome size, and in gene content, structure, and order (Figure 1), Our results revealed that the wholepublished plastome sequences of 11 newly sequenced

Summary

Introduction

Plastid genome of angiosperm have a typical quadripartite structure with a pair of inverted repeat (IR) regions separated by a small single-copy (SSC) region and a large single-copy (LSC) region [1,2].In contrast to mitochondrial and nuclear genomes, plastid genome is highly conserved and generally contains 110–130 distinct genes, ranging in size from 120–160 kb [3]. Plastid genome of angiosperm have a typical quadripartite structure with a pair of inverted repeat (IR) regions separated by a small single-copy (SSC) region and a large single-copy (LSC) region [1,2]. Plastid genomes are reported as a highly conserved sequence and structure in most angiosperms, they have been showed considerable variation in many taxa [2]. These structural variations are always involved in the contraction or extension of the IR region [1], appearance of large inversions or deletions [4,5], and genes gain or loss [2,6]. Due to low rates of nucleotide substitutions, lack of recombination, and uniparental inheritance, many plastid

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