A Dynamic Tandem Repeat in Monocotyledons Inferred from a Comparative Analysis of Chloroplast Genomes in Melanthiaceae

Abstract

Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore “hot spots” for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections (Veratrum and Fuscoveratrum) of Veratrum. Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3. Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.

Total duplication of the small single copy region in the angiosperm plastome: Rearrangement and inverted repeat instability in Asarum

“…Although dispersed tandem repeats are characteristic of plastomes (Ruhlman and Jansen, ) and duplications of these motifs in close proximity to one another have been reported elsewhere (Thomas et al., ), the mechanisms responsible for the generation of these repetitive motifs are not fully agreed upon (Vaughn and Bennetzen, ). Regardless of how repetitive regions are generated, we present evidence that is consistent with the work of other researchers (Guisinger et al., , ) who have hypothesized that replication fidelity and recombination can lead to plastome disruption on an evolutionary timescale (Do and Kim, ), in addition to generating the expected genomic variability that can be found between geographic or otherwise isolated populations of the same species (Gurdon and Maliga, ; Kim and Kim, ).…”

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

“…By contrast, the SSC-IR boundaries of Melanthiaceae (Veratrum) feature contractions when compared to Fritillaria and other Liliales ( Figure S1). Our results included 6 out of 10 families in the order Liliales (Table S2) and are in accordance with those of Do et al [33], who used four families in Liliaeles and Do et al [41], and five families in Liliales. Wang et al [42] suggested that trnH-rps19 clusters were located in the IR/LSC junctions within Liliales taxa, but different patterns of junction were found in Liliales from the present study ( Figure S1).…”

Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae)

“…In most angiosperms, the chloroplast genome (cpDNA) contains genes essential to photosynthesis ( Sugiura, 1992 ). Genomic events (i.e., gene deletion, inversion, or duplication) in cpDNA may provide information about species’ evolutionary history ( Cosner, Raubeson & Jansen, 2004 ; Do & Kim, 2017 ; Haberle et al, 2008 ). For example, the Fabaceae includes clades that are characterised by large inversions and the loss of inverted repeat regions ( Choi & Choi, 2017 ).…”