A de novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny

Pucker B, Holtgräwe D, Rosleff Sörensen T, Stracke R, Viehöver P, Weisshaar B. A de novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PLoS One. 2016;11(10): e0164321.Arabidopsis thaliana is the most important model organism for fundamental plant biology. The genome diversity of different accessions of this species has been intensively studied, for example in the 1001 genome project which led to the identification of many small nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels). In addition, presence/absence variation (PAV), copy number variation (CNV) and mobile genetic elements contribute to genomic differences between A. thaliana accessions. To address larger genome rearrangements between the A. thaliana reference accession Columbia-0 (Col-0) and another accession of about average distance to Col-0, we created a de novo next generation sequencing (NGS)-based assembly from the accession Niederzenz-1 (Nd-1). The result was evaluated with respect to assembly strategy and synteny to Col-0. We provide a high quality genome sequence of the A. thaliana accession (Nd-1, LXSY01000000). The assembly displays an N50 of 0.590 Mbp and covers 99% of the Col-0 reference sequence. Scaffolds from the de novo assembly were positioned on the basis of sequence similarity to the reference. Errors in this automatic scaffold anchoring were manually corrected based on analyzing reciprocal best BLAST hits (RBHs) of genes. Comparison of the final Nd-1 assembly to the reference revealed duplications and deletions (PAV). We identified 826 insertions and 746 deletions in Nd-1. Randomly selected candidates of PAV were experimentally validated. Our Nd-1 de novo assembly allowed reliable identification of larger genic and intergenic variants, which was difficult or error-prone by short read mapping approaches alone. While overall sequence similarity as well as synteny is very high, we detected short and larger (affecting more than 100 bp) differences between Col-0 and Nd-1 based on bi-directional comparisons. The de novo assembly provided here and additional assemblies that will certainly be published in the future will allow to describe the pan-genome of A. thaliana

Sugar Beet BeetMap-3, and Steps to Improve the Genome Assembly and Genome Sequence Annotation (W875)

Weisshaar B, Himmelbauer H, Schmidt T, et al. Sugar Beet BeetMap-3, and Steps to Improve the Genome Assembly and Genome Sequence Annotation (W875). Presented at the Plant and Animal Genome XXIV Conference, San Diego, USA

Functional Genomic Tools for Arabidopsis available at the MPIZ

Dekker KA, Rosleff Sörensen T, Saedler H, Weisshaar B. Functional Genomic Tools for Arabidopsis available at the MPIZ. Biotechnoligia. 2003;4(63):19-31.Summary This article summarizes the activities at the Max Planck Institute for Plant Breeding Research (Max-Planck-Institut für Züchtungsforschung, MPIZ) in the area of "Arabidopsis genomics". We describe the status of three Arabidopsis thaliana genomic projects at the MPIZ: 1) The Gene Knock-Out Facility ZIGIA (Zentrum zur Identifikation von Genfunktionen durch lnsertionsmutagenese bei A. thaliana, Center for Functional Genomics in A. thaliana) using lines tagged with the maize transposon En/Spm, 2) the GABI-Kat project that provides sequence indexed T-DNA tagged lines and 3) the GABI-MASC project that creates mapping tools based on single nucleotide polymorphisms (SNP) for efficient assessment of natural diversity in A. thaliana. The materials and tools developed by these projects are publicly available and used worldwide by scientist to explore the frontiers of plant sciences

Heterozygous SNVs between BoeWGS1.0 and PN40024

Holtgräwe D, Pucker B, Rosleff Sörensen T, Weisshaar B. Heterozygous SNVs between BoeWGS1.0 and PN40024. Bielefeld University; 2019.Belongs to the study 'A Partially Phase-separated Genome Sequence Assembly of the Vitis rootstock ‘Börner’ (_Vitis riparia_ x _Vitis cinerea_) and its Exploitation for Marker Development and Targeted Mapping' which contains additional information about this dataset

Description and mapping positions of BoeWGS1.0 contigs

Holtgräwe D, Pucker B, Rosleff Sörensen T, Weisshaar B. Description and mapping positions of BoeWGS1.0 contigs. Bielefeld University; 2019.Belongs to the study 'A Partially Phase-separated Genome Sequence Assembly of the Vitis rootstock ‘Börner’ (_Vitis riparia_ x _Vitis cinerea_) and its Exploitation for Marker Development and Targeted Mapping' which contains additional information about this dataset

Homozygous SNVs between BoeWGS1.0 and PN40024

Holtgräwe D, Pucker B, Rosleff Sörensen T, Weisshaar B. Homozygous SNVs between BoeWGS1.0 and PN40024. Bielefeld University; 2019.Belongs to the study 'A Partially Phase-separated Genome Sequence Assembly of the Vitis rootstock ‘Börner’ (_Vitis riparia_ x _Vitis cinerea_) and its Exploitation for Marker Development and Targeted Mapping' which contains additional information about this dataset

Contig sequences derived from selected ‘Börner’ BACs assigned to either of the two parental haplotypes *V. riparia* or *V. cinerea* of the *Vitis* rootstock ‘Börner’

Rosleff Sörensen T, Frommer B, Viehöver P, Weisshaar B, Holtgräwe D. Contig sequences derived from selected ‘Börner’ BACs assigned to either of the two parental haplotypes *V. riparia* or *V. cinerea* of the *Vitis* rootstock ‘Börner’. Bielefeld University; 2022.BAC sequences from ‘Börner’ assigned to the haplotype derived from *V. riparia* or to the haplotype derived from *V. cinerea* are offered as a dataset. Haplotype assignment is based on read mapping with read data from both parents of ‘Börner’. The BAC sequences were produced in the frame of the project GrapeReSeq and are further described in the paper 'A fully phased interspecific Grapevine Rootstock Genome sequence representing *V. riparia* and *V. cinerea* and allele-aware annotation of the phylloxera resistance locus *Rdv1*'

Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes

Wenke T, Dobel T, Rosleff Sörensen T, Junghans H, Weisshaar B, Schmidt T. Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes. The Plant Cell. 2011;23(9):3117-3128.Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5' truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3' end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families

Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet ( Beta vulgaris )

Stracke R, Holtgräwe D, Schneider J, Pucker B, Rosleff Sörensen T, Weisshaar B. Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet ( Beta vulgaris ). BMC Plant Biology. 2014;14(1): 249.Background: The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Although genome-wide analysis of this gene family has been carried out in some species, the R2R3-MYB genes in Beta vulgaris ssp. vulgaris (sugar beet) as the first sequenced member of the order Caryophyllales, have not been analysed heretofore. Results: We present a comprehensive, genome-wide analysis of the MYB genes from Beta vulgaris ssp. vulgaris (sugar beet) which is the first species of the order Caryophyllales with a sequenced genome. A total of 70 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Also, organ specific expression patterns were determined from RNA-seq data. The R2R3-MYB genes were functionally categorised which led to the identification of a sugar beet-specific clade with an atypical amino acid composition in the R3 domain, putatively encoding betalain regulators. The functional classification was verified by experimental confirmation of the prediction that the R2R3-MYB gene Bv_iogq encodes a flavonol regulator. Conclusions: This study provides the first step towards cloning and functional dissection of the role of MYB transcription factor genes in the nutritionally and evolutionarily interesting species B. vulgaris. In addition, it describes the flavonol regulator BvMYB12, being the first sugar beet R2R3-MYB with an experimentally proven function