Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen

Abstract

We report the first plastome sequence of giant ragweed ( Ambrosia trifida ); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trn S-GCU and trn G-UCC genes, and the latter between trn E-UUC and trn T-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia , are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.

Sow Thistle Chloroplast Genomes: Insights into the Plastome Evolution and Relationship of Two Weedy Species, Sonchus asper and Sonchus oleraceus (Asteraceae)

“…Remarkably, there were low proportions of other SSR types, i.e., three mono-nucleotide SSRs (4%), four di-nucleotide SSRs (5%), and six tetra-nucleotide SSRs (7%) (Figure 4A). The abundance of tri-nucleotide SSRs was consistent with previous findings with similar parameter settings [54]; however, the frequency of mono-nucleotide SSRs was significantly lower because of the more stringent search parameter used in this study (i.e., minimum repeat of 15) than in previous studies (minimum repeat of 8 or 10) [47,54]. The most abundant repeat motif was “AAT/ATT” followed by “AAG/CTT” in all five genomes (Figure 4B, Table S1).…”

Plastid Phylogenomics of Dendroseris (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands

“…As for SSRs and large repeat sequences, Dendroseris showed patterns comparable to Dendrosonchus and Sonchus in the numbers and frequencies of repeat type ( Cho et al, 2019a , b ). In addition, all showed an abundance of tri-nucleotide SSRs (over 80%), which is also consistent with other weedy Asteraceae species such as Ambrosia trifida ( Sablok et al, 2019 ), and the highest frequencies of SSRs from the LSC region. Furthermore, the similar distribution pattern of large repeats was also observed for majority in forward (F) and palindromic (P) matches from Dendroseris ( F = 19∼22, P = 19∼23 out of a total of 50 pairs) and herbaceous weedy Sonchus ( F = 21, P = 21 out of total 49 pairs) ( Cho et al, 2019b ).…”

Exploring the phylogeny of the marattialean ferns

“…In ccs A, rpo B and rps 15 genes, we observed the use of the alternative start codon ACG instead of the common AUG in Marattia laxa . Genes with such exceptional start codons are RNA edited in Asteraceae (Sablok et al, 2019) and Solanaceae (Amiryousefi et al, 2018). The diversity of RNA editing in ferns is somewhat unclear, as the abundant U‐to‐C edits are lacking in major lineages.…”