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  1. Article ; Online: Subgenome evolution in allotetraploid plants.

    Schiavinato, Matteo / Bodrug-Schepers, Alexandrina / Dohm, Juliane C / Himmelbauer, Heinz

    The Plant journal : for cell and molecular biology

    2021  Volume 106, Issue 3, Page(s) 672–688

    Abstract: Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is ... ...

    Abstract Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.
    MeSH term(s) Brassica/genetics ; Chenopodium quinoa/genetics ; Domestication ; Evolution, Molecular ; Genome, Plant/genetics ; Hybridization, Genetic/genetics ; Plants/genetics ; Tetraploidy ; Nicotiana/genetics
    Language English
    Publishing date 2021-03-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1088037-9
    ISSN 1365-313X ; 0960-7412
    ISSN (online) 1365-313X
    ISSN 0960-7412
    DOI 10.1111/tpj.15190
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    Z 6071: Show issues

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  2. Article: Subgenome evolution in allotetraploid plants

    Schiavinato, Matteo / Bodrug‐Schepers, Alexandrina / Dohm, Juliane C / Himmelbauer, Heinz

    plant journal. 2021 May, v. 106, no. 3

    2021  

    Abstract: Polyploidization is a well‐known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is ... ...

    Abstract Polyploidization is a well‐known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.
    Keywords Chenopodium quinoa ; Nicotiana benthamiana ; allotetraploidy ; data collection ; domestication ; evolution ; fractionation ; genome ; hybrids ; interspecific hybridization ; tobacco
    Language English
    Dates of publication 2021-05
    Size p. 672-688.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note NAL-AP-2-clean ; JOURNAL ARTICLE
    ZDB-ID 1088037-9
    ISSN 1365-313X ; 0960-7412
    ISSN (online) 1365-313X
    ISSN 0960-7412
    DOI 10.1111/tpj.15190
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  3. Article: Quinoa genome assembly employing genomic variation for guided scaffolding

    Bodrug-Schepers, Alexandrina / Stralis-Pavese, Nancy / Buerstmayr, Hermann / Dohm, Juliane C. / Himmelbauer, Heinz

    Theoretical and applied genetics. 2021 Nov., v. 134, no. 11

    2021  

    Abstract: KEY MESSAGE: We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today’s genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve genome ...

    Abstract KEY MESSAGE: We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today’s genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve genome assemblies is attractive both cost-wise as well as scientifically, because the value of an assembly increases with its contiguity. We conclude that haplotype information is a valuable resource to group and order contigs toward the generation of pseudomolecules. Quinoa (Chenopodium quinoa) has been under cultivation in Latin America for more than 7500 years. Recently, quinoa has gained increasing attention due to its stress resistance and its nutritional value. We generated a novel quinoa genome assembly for the Bolivian accession CHEN125 using PacBio long-read sequencing data (assembly size 1.32 Gbp, initial N50 size 608 kbp). Next, we re-sequenced 50 quinoa accessions from Peru and Bolivia. This set of accessions differed at 4.4 million single-nucleotide variant (SNV) positions compared to CHEN125 (1.4 million SNV positions on average per accession). We show how to exploit variation in accessions that are distantly related to establish a genome-wide ordered set of contigs for guided scaffolding of a reference assembly. The method is based on detecting shared haplotypes and their expected continuity throughout the genome (i.e., the effect of linkage disequilibrium), as an extension of what is expected in mapping populations where only a few haplotypes are present. We test the approach using Arabidopsis thaliana data from different populations. After applying the method on our CHEN125 quinoa assembly we validated the results with mate-pairs, genetic markers, and another quinoa assembly originating from a Chilean cultivar. We show consistency between these information sources and the haplotype-based relations as determined by us and obtain an improved assembly with an N50 size of 1079 kbp and ordered contig groups of up to 39.7 Mbp. We conclude that haplotype information in distantly related individuals of the same species is a valuable resource to group and order contigs according to their adjacency in the genome toward the generation of pseudomolecules.
    Keywords Arabidopsis thaliana ; Chenopodium quinoa ; cultivars ; genetic variation ; genome ; genome assembly ; haplotypes ; linkage disequilibrium ; nutritive value ; stress tolerance ; Bolivia ; Latin America ; Peru
    Language English
    Dates of publication 2021-11
    Size p. 3577-3594.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ZDB-ID 2170-2
    ISSN 1432-2242 ; 0040-5752
    ISSN (online) 1432-2242
    ISSN 0040-5752
    DOI 10.1007/s00122-021-03915-x
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Quinoa genome assembly employing genomic variation for guided scaffolding.

    Bodrug-Schepers, Alexandrina / Stralis-Pavese, Nancy / Buerstmayr, Hermann / Dohm, Juliane C / Himmelbauer, Heinz

    TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

    2021  Volume 134, Issue 11, Page(s) 3577–3594

    Abstract: Key message: We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today's genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve ... ...

    Abstract Key message: We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today's genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve genome assemblies is attractive both cost-wise as well as scientifically, because the value of an assembly increases with its contiguity. We conclude that haplotype information is a valuable resource to group and order contigs toward the generation of pseudomolecules. Quinoa (Chenopodium quinoa) has been under cultivation in Latin America for more than 7500 years. Recently, quinoa has gained increasing attention due to its stress resistance and its nutritional value. We generated a novel quinoa genome assembly for the Bolivian accession CHEN125 using PacBio long-read sequencing data (assembly size 1.32 Gbp, initial N50 size 608 kbp). Next, we re-sequenced 50 quinoa accessions from Peru and Bolivia. This set of accessions differed at 4.4 million single-nucleotide variant (SNV) positions compared to CHEN125 (1.4 million SNV positions on average per accession). We show how to exploit variation in accessions that are distantly related to establish a genome-wide ordered set of contigs for guided scaffolding of a reference assembly. The method is based on detecting shared haplotypes and their expected continuity throughout the genome (i.e., the effect of linkage disequilibrium), as an extension of what is expected in mapping populations where only a few haplotypes are present. We test the approach using Arabidopsis thaliana data from different populations. After applying the method on our CHEN125 quinoa assembly we validated the results with mate-pairs, genetic markers, and another quinoa assembly originating from a Chilean cultivar. We show consistency between these information sources and the haplotype-based relations as determined by us and obtain an improved assembly with an N50 size of 1079 kbp and ordered contig groups of up to 39.7 Mbp. We conclude that haplotype information in distantly related individuals of the same species is a valuable resource to group and order contigs according to their adjacency in the genome toward the generation of pseudomolecules.
    MeSH term(s) Arabidopsis/genetics ; Bolivia ; Chenopodium quinoa/genetics ; Chile ; Contig Mapping ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Genome, Plant ; Haplotypes ; Peru
    Chemical Substances Genetic Markers
    Language English
    Publishing date 2021-08-07
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2170-2
    ISSN 1432-2242 ; 0040-5752
    ISSN (online) 1432-2242
    ISSN 0040-5752
    DOI 10.1007/s00122-021-03915-x
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1692: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Molecular signatures of alternative reproductive strategies in a facultatively social hover wasp.

    Taylor, Benjamin A / Taylor, Daisy / Bodrug-Schepers, Alexandrina / Câmara Ferreira, Francisco / Stralis-Pavese, Nancy / Himmelbauer, Heinz / Guigó, Roderic / Reuter, Max / Sumner, Seirian

    Molecular ecology

    2023  Volume 33, Issue 2, Page(s) e17217

    Abstract: Social insect reproductives and non-reproductives represent ideal models with which to understand the expression and regulation of alternative phenotypes. Most research in this area has focused on the developmental regulation of reproductive phenotypes ... ...

    Abstract Social insect reproductives and non-reproductives represent ideal models with which to understand the expression and regulation of alternative phenotypes. Most research in this area has focused on the developmental regulation of reproductive phenotypes in obligately social taxa such as honey bees, while relatively few studies have addressed the molecular correlates of reproductive differentiation in species in which the division of reproductive labour is established only in plastic dominance hierarchies. To address this knowledge gap, we generate the first genome for any stenogastrine wasp and analyse brain transcriptomic data for non-reproductives and reproductives of the facultatively social species Liostenogaster flavolineata, a representative of one of the simplest forms of social living. By experimentally manipulating the reproductive 'queues' exhibited by social colonies of this species, we show that reproductive division of labour in this species is associated with transcriptomic signatures that are more subtle and variable than those observed in social taxa in which colony living has become obligate; that variation in gene expression among non-reproductives reflects their investment into foraging effort more than their social rank; and that genes associated with reproductive division of labour overlap to some extent with those underlying division of labour in the separate polistine origin of wasp sociality but only explain a small portion of overall variation in this trait. These results indicate that broad patterns of within-colony transcriptomic differentiation in this species are similar to those in Polistinae but offer little support for the existence of a strongly conserved 'toolkit' for sociality.
    MeSH term(s) Bees/genetics ; Animals ; Wasps/genetics ; Social Behavior ; Social Dominance ; Gene Expression Profiling ; Transcriptome/genetics ; Reproduction/genetics
    Language English
    Publishing date 2023-11-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.17217
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    Z 2005/723: Show issues

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  6. Article ; Online: Putting hornets on the genomic map.

    Favreau, Emeline / Cini, Alessandro / Taylor, Daisy / Câmara Ferreira, Francisco / Bentley, Michael A / Cappa, Federico / Cervo, Rita / Privman, Eyal / Schneider, Jadesada / Thiéry, Denis / Mashoodh, Rahia / Wyatt, Christopher D R / Brown, Robert L / Bodrug-Schepers, Alexandrina / Stralis-Pavese, Nancy / Dohm, Juliane C / Mead, Daniel / Himmelbauer, Heinz / Guigo, Roderic /
    Sumner, Seirian

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 6232

    Abstract: Hornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding ... ...

    Abstract Hornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding why these wasps are such successful invaders is critical to managing future introductions and minimising impact on native biodiversity. Critical to the management toolkit is a comprehensive genomic resource for these insects. Here we provide the annotated genomes for two hornets, Vespa crabro and Vespa velutina. We compare their genomes with those of other social Hymenoptera, including the northern giant hornet Vespa mandarinia. The three hornet genomes show evidence of selection pressure on genes associated with reproduction, which might facilitate the transition into invasive ranges. Vespa crabro has experienced positive selection on the highest number of genes, including those putatively associated with molecular binding and olfactory systems. Caste-specific brain transcriptomic analysis also revealed 133 differentially expressed genes, some of which are associated with olfactory functions. This report provides a spring-board for advancing our understanding of the evolution and ecology of hornets, and opens up opportunities for using molecular methods in the future management of both native and invasive populations of these over-looked insects.
    MeSH term(s) Animals ; Wasps/genetics ; Introduced Species ; Reproduction
    Language English
    Publishing date 2023-04-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-31932-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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