The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

Abstract

Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp). It consists of 112 unique genes from which 81 are protein-coding, 27 tRNA and four rRNA genes. All bittersweet plastid genes including non-functional ones and even intergenic spacer regions are transcribed in primary plastid transcripts covering 95.22% of the genome. These are later substantially edited in a post-transcriptional phase to activate gene functions. By comparing the bittersweet plastid genome with all available Solanaceae sequences we found that gene content and synteny are highly conserved across the family. During genome comparison we have identified several annotation errors, which we have corrected in a manual curation process then we have identified the major plastid genome structural changes in Solanaceae. Interpreted in a phylogenetic context they seem to provide additional support for larger clades. The plastid genome sequence of bittersweet could help to benchmark Solanaceae plastid genome annotations and could be used as a reference for further studies. Such reliable annotations are important for gene diversity calculations, synteny map constructions and assigning partitions for phylogenetic analysis with de novo sequenced plastomes of Solanaceae.

Fig 1. The berries and flowers of Solanum dulcamara L.

Fig 2. Map of the chloroplast genome of the Solanum dulcamara.

Genes lying inside of the outer circle are transcribed counterclockwise while those outside that circle are transcribed clockwise. Genes belonging to different functional groups are color coded differently and the GC, AT content of the genome are plotted on the inner circle as dark and light gray, respectively. The inverted repeats, large single copy, and small single copy regions are denoted by IR, LSC, and SSC, respectively.

Fig 3. Junction sites of the inverted repeats.

For each species, genes transcribed in positive strand are depicted on the top of their corresponding track with right to left direction, while the genes on the negative strand are depicted below from left to right. The arrows are showing the distance of the start or end coordinate of a given gene from the corresponding junction site. For the genes extending from a region to another, the T bar above or below them show the extent of their parts with their corresponding values in base pair while nothing is plotted for the genes tangent to the sites. The plotted genes and distances in the vicinity of the junction sites are the scaled projection of the genome. JLB (IRb /LSC), JSB (IRb/SSC), JSA (SSC/IRa) and JLA (IRa/LSC) denote the junction sites between each corresponding two regions on the genome.

Fig 4. Cladogram illustrating the phylogenetic relationships of Solanaceae based on complete chloroplast genome sequences.

Plastid genome rearrangement events are mapped on the branches of the best scoring maximum likelihood tree generated with RAxML-NG. Each node has 100% bootstrap support value. A node with lower support value indicated and those with support values below 50% collapsed. Currently recognized suprageneric groups are listed on the right.