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Although some authors previously questioned the circumscription of Nicotiana benthamiana , it has never been treated taxonomically as more than a single widespread, variable species. A recent study employing phylogenetic and population genetic analyses has demonstrated that N. benthamiana comprises five species that are geographically and morphologically distinct. Here, we describe four new species in the N. benthamiana complex, namely, N. bilybara M.W.Chase & Christenh., N. candelabra M.W.Chase & Christenh., N. rupestris M.W.Chase & Christenh. and N. scopulorum M.W.Chase & Christenh., and illustrate all five. We provide descriptions, a diagnostic key and a table of morphological characters distinguishing these closely related species. The major morphological feature that distinguishes N. benthamiana from the other four species is its petiolate leaves that become sessile only near the apex of the inflorescence; N. candelabra is distinct in its bifacial branching, N. bilybara in its commonly winged petiole with an auriculate base, N. rupestris in the leafy apices of its calyx lobes, and N. scopulorum is the least morphologically divergent species, conforming most closely to the general description of the N. benthamiana species complex. A recent study employing phylogenetic and population genetic analyses has demonstrated that the important model plant, Nicotiana benthamiana , is not a single species but instead comprises five species that are geographically and morphologically distinct. Here, we describe four new species in the N. benthamiana complex and illustrate all five. [ABSTRACT FROM AUTHOR]

To provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridization between diploids D. fuchsii and D. incarnata. Our results first reveal that the paternal D. incarnata genome shows a marked increased content of LTR retrotransposons compared to the maternal species, reflected in its larger genome size and consistent with a previously hypothesized bottleneck. With regard to the allopolyploids, in the youngest D. purpurella both genome size and TE composition appear to be largely additive with respect to parents, whereas for polyploids of intermediate ages we uncover rampant genome expansion on a magnitude of multiple entire genomes of some plants such as Arabidopsis. The oldest allopolyploids in the series are not larger than the intermediate ones. A putative tandem repeat, potentially derived from a non-autonomous miniature inverted-repeat TE (MITE) drives much of the genome dynamics in the allopolyploids. The highly dynamic MITE-like element is found in higher proportions in the maternal diploid, D. fuchsii, but is observed to increase in copy number in both subgenomes of the allopolyploids. Altogether, the fate of repeats appears strongly regulated and therefore predictable across multiple independent allopolyploidization events in this system. Apart from the MITE-like element, we consistently document a mild genomic shock following the allopolyploidizations investigated here, which may be linked to their relatively large genome sizes, possibly associated with strong selection against further genome expansions. [ABSTRACT FROM AUTHOR]

SUMMARY: One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA‐dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remain relatively underexplored. Here, we have used multispecies coalescent methods on genome‐wide single nucleotide polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long‐isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development. Significance Statement: Nicotiana benthamiana, native to Australia, is an important model organism in plant/virus research because the single genotype known (LAB) has an insertion in the Rdr1 gene inactivating virus resistance. Here, we provide clear evidence that N. benthamiana comprises five species, one of which includes LAB and accessions from the northern Northern Territory in which the Rdr1 insertion is variable, leading us to conclude that the insertion is not related to the extremophile hypothesis for this species. [ABSTRACT FROM AUTHOR]