The Chloroplast Genome of Hyoscyamus niger and a Phylogenetic Study of the Tribe Hyoscyameae (Solanaceae)

Abstract

The tribe Hyoscyameae (Solanaceae) is restricted to Eurasia and includes the genera Archihyoscyamus, Anisodus, Atropa, Atropanthe, Hyoscyamus, Physochlaina, Przewalskia and Scopolia. Even though the monophyly of Hyoscyameae is strongly supported, the relationships of the taxa within the tribe remain unclear. Chloroplast markers have been widely used to elucidate plant relationships at low taxonomic levels. Identification of variable chloroplast intergenic regions has been developed based on comparative genomics of chloroplast genomes, but these regions have a narrow phylogenetic utility. In this study, we present the chloroplast genome sequence of Hyoscyamus niger and make comparisons to other solanaceous plastid genomes in terms of gene order, gene and intron content, editing sites, origins of replication, repeats, and hypothetical open reading frames. We developed and sequenced three variable plastid markers from eight species to elucidate relationships within the tribe Hyoscyameae. The presence of a horizontally transferred intron in the mitochondrial cox1 gene of some species of the tribe is considered here a likely synapomorphy uniting five genera of the Hyoscyameae. Alternatively, the cox1 intron could be a homoplasious character acquired twice within the tribe. A homoplasious inversion in the intergenic plastid spacer trnC-psbM was recognized as a source of bias and removed from the data set used in the phylogenetic analyses. Almost 12 kb of plastid sequence data were not sufficient to completely resolve relationships among genera of Hyoscyameae but some clades were identified. Two alternative hypotheses of the evolution of the genera within the tribe are proposed.

Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant

“…This editing is controlled by the nuclear genome, opening the door to nuclear-cytoplasmic incompatibilities (Schmitz-Linneweber et al, 2005). The Nt-derived nuclear-encoded editing machinery in the cybrid Nt(+Hn) faces the challenge of editing three Hn-specific sites of chloroplast RNA editing, one in each of three genes ( ndhA , ndhD , and rpoB ) in which the cybrid (this study) and Hn (Sanchez-Puerta & Abbona, 2014) cpDNAs are predicted to undergo RNA editing at sites at which Nt cpDNA encodes a T and does not require editing. Those edits restore what would otherwise be non-synonymous changes at highly conserved amino acids.…”

“…Graphical genome maps were generated using OGDraw software (Lohse et al, 2007). The cybrid cpDNA was not annotated because it is identical to that of H. niger (Sanchez-Puerta & Abbona, 2014). Non-synonymous sites of RNA editing were predicted using PREP-Mt (Mower, 2005) with a cutoff value of 0.5.…”

“…All chloroplast contigs from the set of Velvet runs of the cybrid were combined, as were all mitochondrial contigs of Hn and of the cybrid. The published cpDNA sequence of H. niger (Sanchez-Puerta & Abbona, 2014) is available in Gen-Bank (KF248009). Genome assemblies and read-pair mapping patterns were visually inspected using Consed v26 (Gordon & Green, 2013).…”

RNA editing in the chloroplast of Asian Palmyra palm (Borassus flabellifer)

“…RNA editing sites obtained from B. flabellifer (this study), Cocos nucifera (identified by Next Generations Sequencing or NGS; Huang et al, 2013) and Elaeis guineensis (by NGS; Uthaipaisanwong et al, 2012), in total 53 sites, were compared to those of other 15 plant species. These included six monocots: S. polyrhiza (21 sites by NGS), P. aphrodite (13 sites by direct cDNA sequencing), Z. mays (13 sites by direct cDNA sequencing), O. sativa (14 sites by direct cDNA sequencing), S. officinarum (12 sites by NGS) and H. vulgare (8 sites by direct cDNA sequencing), six dicots: A. thaliana (10 sites by direct cDNA sequencing), P. sativum (7 sites by direct cDNA sequencing), A. belladonna (8 sites by direct cDNA sequencing), H. niger (8 sites by NGS), J. curcas (7 sites by NGS), N. tabacum (10 sites by direct cDNA sequencing) and two gymnosperms: C. taitungensis (5 sites by using CURE-Chloroplast software and direct sequencing) and Pinus thunbergii (0 sites by direct cDNA sequencing) (Wakasugi et al, 1996;Corneille et al, 2000;Sasaki et al, 2003;Inada et al, 2004;Zeng et al, 2007;Asif et al, 2010;Uthaipaisanwong et al, 2012;Huang et al, 2013;Sanchez-Puerta and Abbona, 2014;Wang et al, 2015;He et al, 2016). The list of genes is presented in Table S2.…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…The genes psbT, rpl2, and ndhD had the alternative start codon ACG, and rps19 started with GTG. Use of ACG and GTG as start codons is common for a variety of genes in the chloroplast genomes of land plants [17][18][19][20]. Finally, the cemA gene was identified as a pseudogene with a premature stop codon in the F. cirrhosa cp genome.…”