Analysis of Petunia vein clearing virus (PVCV) sequences, retroelements and tandem repeats in Petunia axillaris N and P. inflata S6

PetuniaNaturePVCVchromosomes.jpg325a. Schwarzacher T, Heslop-Harrison JS, Richert-Pöggeler KR. 2016. Analysis of Petunia vein clearing virus (PVCV) sequences, retroelements and tandem repeats in Petunia axillaris N and P. inflata S6. Supplementary manuscript 2. Nature Plants 2: article number 16074.

Link to manuscript: Petunia_PVCV_Repeats_SchwarzacherEtAl2016

Within the genome sequence assemblies of P. axillaris (PaxiN) and P. inflata (PinfS6) and unassembled reads, we analysed the occurrence of endogenous Petunia vein clearing virus (PVCV) sequences, other endogenous pararetrovirus (EPRV) sequences, LTR-retroelements, and tandem repeats. Petunia genomes show substantial diversity in their pararetroviral sequences as revealed in searches using the polymerase motif. Homologies to two genera of Caulimoviridae, Petu- and Florendoviruses, with more than 60% amino acid identity, were present in both species. Almost complete PVCV copies, fragments, and degenerate copies, sometimes in tandem arrays, were found. PVCV motifs were more frequent in P. axillaris, with the results seen in the assemblies confirmed by in situ hybridization of PVCV fragments to metaphase chromosomes indicating that P. axillaris is likely a more permissive host for EPRVs. LTR-retroelements are localised near centromeres; about 6500 full length elements were found in the PinfS6 assembly while 4500 were in PaxiN. Apart from rDNA, microsatellites and telomeric sequences, no highly abundant tandem repeats were identified in the assembly or raw reads. Repeat cluster analysis indicates that LTR-retroelements are associated with simple sequence repeats and low complexity DNA families and that repeats within Petunia are very diverse, with none having amplified to form a major proportion of the genome. The repeat landscape of Petunia is different from other species of Solanaceae, in particular the x=12 crown group including Solanum and Nicotiana, with a relative low proportion of total repeats for a genome size of 1.4Gb, x=7, and a high degree of genome plasticity.

Link to manuscript: Petunia_PVCV_Repeats_SchwarzacherEtAl2016

Supplementary manuscript 2 from

325b. Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS,  Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D’Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus S, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. 2016. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants 2: article number 16074. doi:10.1038/nplants.2016.74


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