Bombarely et al. 2016. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida Nature Plants

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 genomes. 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 (60-65%) of total repeats for a genome size of 1.4Gb, x=7, and a high degree of genome plasticity.

[1]  S. Elena,et al.  Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes. , 2015, Virology.

[2]  M. Zytnicki,et al.  Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution , 2014, Nature Communications.

[3]  S. Bonatto,et al.  Novel Transposable Elements in Solanaceae: Evolutionary Relationships among Tnt1-related Sequences in Wild Petunia Species , 2014, Plant Molecular Biology Reporter.

[4]  Yeisoo Yu,et al.  Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species , 2014, Nature Genetics.

[5]  R. Brlansky,et al.  Population of Endogenous Pararetrovirus Genomes in Carrizo Citrange , 2014, Genome Announcements.

[6]  Alexander Goesmann,et al.  The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) , 2013, Nature.

[7]  T. Schwarzacher,et al.  Nucleosomes and centromeric DNA packaging , 2013, Proceedings of the National Academy of Sciences.

[8]  R. Olmstead,et al.  A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree , 2013, BMC Evolutionary Biology.

[9]  Q. Cronk,et al.  Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species , 2013, BMC Genomics.

[10]  J. Stoye,et al.  Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[11]  M. Peitsch,et al.  Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis , 2013, Genome Biology.

[12]  Petr Novák,et al.  RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads , 2013, Bioinform..

[13]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[14]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[15]  U. Grossniklaus,et al.  Analysis of plant germline development by high-throughput RNA profiling: technical advances and new insights. , 2012, The Plant journal : for cell and molecular biology.

[16]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[17]  J. Poulain,et al.  The genome of the mesopolyploid crop species Brassica rapa , 2011, Nature Genetics.

[18]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[19]  J. Macas,et al.  Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data , 2010, BMC Bioinformatics.

[20]  Asan,et al.  The genome of the cucumber, Cucumis sativus L. , 2009, Nature Genetics.

[21]  J. Hamacher,et al.  Plant Virus Diseases: Ornamental Plants , 2008 .

[22]  T. Hohn,et al.  Distinct expression of endogenous Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production. , 2007, The Plant journal : for cell and molecular biology.

[23]  K. Richert-Pöggeler,et al.  Endogenous pararetroviruses: two-faced travelers in the plant genome. , 2006, Trends in plant science.

[24]  Hitoshi Watanabe,et al.  Two novel transposable elements in a cytochrome P450 gene govern anthocyanin biosynthesis of commercial petunias. , 2005, Gene.

[25]  M. Matzke,et al.  A Distinct Endogenous Pararetrovirus Family in Nicotiana tomentosiformis, a Diploid Progenitor of Polyploid Tobacco1[w] , 2004, Plant Physiology.

[26]  T. Hohn,et al.  Induction of infectious petunia vein clearing (pararetro) virus from endogenous provirus in petunia , 2003, The EMBO journal.

[27]  John F. McDonald,et al.  LTR_STRUC: a novel search and identification program for LTR retrotransposons , 2003, Bioinform..

[28]  Zhong Yang,et al.  Sequence Analysis of a 282-Kilobase Region Surrounding the Citrus Tristeza Virus Resistance Gene (Ctv) Locus inPoncirus trifoliata L. Raf.1 , 2003, Plant Physiology.

[29]  K. Mishiba,et al.  Nuclear DNA Content as an Index Character Discriminating Taxa in the Genus Petunia sensu Jussieu (Solanaceae) , 2000 .

[30]  K. Richert-Pöggeler,et al.  Petunia vein-clearing virus: a plant pararetrovirus with the core sequences for an integrase function. , 1997, Virology.

[31]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..

[32]  A. Geering,et al.  Endogenous viral sequences in plant genomes , 2011 .

[33]  T. Gerats.  Identification and Exploitation of Petunia Transposable Elements: A Brief History , 2009 .

[34]  K. Richert-Pöggeler,et al.  Impact of Retroelements in Shaping the Petunia Genome , 2009 .

[35]  T. Hohn,et al.  Evolution of Integrated Plant Viruses , 2008 .

[36]  C. Hansen,et al.  Sequences and Phylogenies of Plant Pararetroviruses, Viruses, and Transposable Elements , 2004 .

[37]  S. Halford.  Practical In Situ Hybridization , 2000, Heredity.

[38]  M. Mayo,et al.  Virus Taxonomy , 1991, Archives of Virology Supplement 10.