Distantly related maize (Zea mays, L.) inbred lines exhibit an exceptional degree of structural genomic diversity, which is probably unique among plants. This study systematically investigated the developmental and genotype-dependent regulation of the primary root transcriptomes of a genetically diverse panel of maize F1-hybrids and their parental inbred lines. While we observed substantial transcriptomic changes during primary root development, we demonstrated that hybrid-associated gene expression patterns, including differential, non-additive, and allele-specific transcriptome profiles, are particularly robust to these developmental fluctuations.

doi:10.1093/jxb/erz452

@article{Vedder2020a,
    abstract = {Distantly related maize (Zea mays, L.) inbred lines exhibit an exceptional degree of structural genomic diversity, which is probably unique among plants. This study systematically investigated the developmental and genotype-dependent regulation of the primary root transcriptomes of a genetically diverse panel of maize F1-hybrids and their parental inbred lines. While we observed substantial transcriptomic changes during primary root development, we demonstrated that hybrid-associated gene expression patterns, including differential, non-additive, and allele-specific transcriptome profiles, are particularly robust to these developmental fluctuations.},
    author = {Baldauf, Jutta A. and Vedder, Lucia and Schoof, Heiko and Hochholdinger, Frank},
    doi = {10.1093/jxb/erz452},
    journal = {Journal of Experimental Botany},
    number = {3},
    pages = {865--876},
    title = {Robust non-syntenic gene expression patterns in diverse maize hybrids during root development},
    volume = {71},
    year = {2020}
}

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

doi:10.1093/gbe/evaa106

@article{Vedder2020b,
    abstract = {The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.},
    author = {Oeyen, Jan Philip and Baa-Puyoulet, Patrice and Benoit, Joshua B. and Beukeboom, Leo W. and Bornberg-Bauer, Erich and Buttstedt, Anja and Calevro, Federica and Cash, Elizabeth I. and Chao, Hsu and Charles, Hubert and Chen, Mei-Ju May and Childers, Christopher and Cridge, Andrew G. and Dearden, Peter and Dinh, Huyen and Doddapaneni, Harsha Vardhan and Dolan, Amanda and Donath, Alexander and Dowling, Daniel and Dugan, Shannon and Duncan, Elizabeth and Elpidina, Elena N. and Friedrich, Markus and Geuverink, Elzemiek and Gibson, Joshua D. and Grath, Sonja and Grimmelikhuijzen, Cornelis J. P. and Gro{\ss}e-Wilde, Ewald and Gudobba, Cameron and Han, Yi and Hansson, Bill S. and Hauser, Frank and Hughes, Daniel S. T. and Ioannidis, Panagiotis and Jacquin-Joly, Emmanuelle and Jennings, Emily C. and Jones, Jeffery W. and Klasberg, Steffen and Lee, Sandra L. and Lesn{\'y}, Peter and Lovegrove, Mackenzie and Martin, Sebastian and Martynov, Alexander G. and Mayer, Christoph and Montagn{\'e}, Nicolas and Moris, Victoria C. and Munoz-Torres, Monica and Murali, Shwetha Canchi and Muzny, Donna M. and Oppert, Brenda and Parisot, Nicolas and Pauli, Thomas and Peters, Ralph S. and Petersen, Malte and Pick, Christian and Persyn, Emma and Podsiadlowski, Lars and Poelchau, Monica F. and Provataris, Panagiotis and Qu, Jiaxin and Reijnders, Maarten J. M. F. and von Reumont, Bj{\"o}rn Marcus and Rosendale, Andrew J. and Simao, Felipe A. and Skelly, John and Sotiropoulos, Alexandros G. and Stahl, Aaron L. and Sumitani, Megumi and Szuter, Elise M. and Tidswell, Olivia and Tsitlakidis, Evangelos and Vedder, Lucia and Waterhouse, Robert M. and Werren, John H. and Wilbrandt, Jeanne and Worley, Kim C. and Yamamoto, Daisuke S. and {van de Zande}, Louis and Zdobnov, Evgeny M. and Ziesmann, Tanja and Gibbs, Richard A. and Richards, Stephen and Hatakeyama, Masatsugu and Misof, Bernhard and Niehuis, Oliver},
    doi = {10.1093/gbe/evaa106},
    journal = {Genome biology and evolution},
    number = {7},
    pages = {1099--1188},
    title = {Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera},
    volume = {12},
    year = {2020}
}

Maize (Zea mays, L.) displays an exceptional degree of structural genomic diversity. In addition, variation in gene expression further contributes to the extraordinary phenotypic diversity and plasticity of maize. This study provides a systematic investigation on how distantly related homozygous maize inbred lines affect the transcriptomic plasticity of their highly heterozygous F1 hybrids.

doi:10.1016/j.cub.2017.12.027

@article{Vedder2018,
    abstract = {Maize (Zea mays, L.) displays an exceptional degree of structural genomic diversity. In addition, variation in gene expression further contributes to the extraordinary phenotypic diversity and plasticity of maize. This study provides a systematic investigation on how distantly related homozygous maize inbred lines affect the transcriptomic plasticity of their highly heterozygous F1 hybrids.},
    author = {Baldauf, Jutta A. and Marcon, Caroline and Lithio, Andrew and Vedder, Lucia and Altrogge, Lena and Piepho, Hans-Peter and Schoof, Heiko and Nettleton, Dan and Hochholdinger, Frank},
    doi = {10.1016/j.cub.2017.12.027},
    journal = {Current Biology},
    number = {3},
    pages = {431--437},
    title = {Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids},
    volume = {28},
    year = {2018}
}

Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods.

doi:10.1186/s12864-016-3205-1

@article{Vedder2016,
    abstract = {Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods.},
    author = {Pauli, Thomas and Vedder, Lucia and Dowling, Daniel and Petersen, Malte and Meusemann, Karen and Donath, Alexander and Peters, Ralph S. and Podsiadlowski, Lars and Mayer, Christoph and Liu, Shanlin and Zhou, Xin and Heger, Peter and Wiehe, Thomas and Hering, Lars and Mayer, Georg and Misof, Bernhard and Niehuis, Oliver},
    doi = {10.1186/s12864-016-3205-1},
    issn = {1471-2164},
    journal = {BMC Genomics},
    number = {1},
    pages = {861},
    title = {Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins},
    url = {https://link.springer.com/article/10.1186/s12864-016-3205-1},
    volume = {17},
    year = {2016}
}