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Article ; Online: Spinach genomes reveal migration history and candidate genes for important crop traits.

Nguyen-Hoang, An / Sandell, Felix L / Himmelbauer, Heinz / Dohm, Juliane C

NAR genomics and bioinformatics

2024 Volume 6, Issue 2, Page(s) lqae034

Abstract: Spinach ( ...

Abstract	Spinach (
Language	English
Publishing date	2024-04-17
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqae034
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Article ; Online: Genomic variation in the genus Beta based on 656 sequenced beet genomes.

Felkel, Sabine / Dohm, Juliane C / Himmelbauer, Heinz

Scientific reports

2023 Volume 13, Issue 1, Page(s) 8654

Abstract: Cultivated beets (Beta vulgaris ssp. vulgaris) constitute important crop plants, in particular sugar beet as an indispensable source of sucrose. Several species of wild beets of the genus Beta with distribution along the European Atlantic coast, ... ...

Abstract	Cultivated beets (Beta vulgaris ssp. vulgaris) constitute important crop plants, in particular sugar beet as an indispensable source of sucrose. Several species of wild beets of the genus Beta with distribution along the European Atlantic coast, Macaronesia, and throughout the Mediterranean area exist. Thorough characterization of beet genomes is required for straightforward access to genes promoting genetic resistance against biotic and abiotic stress. Analysing short-read data of 656 sequenced beet genomes, we identified 10 million variant positions in comparison to the sugar beet reference genome RefBeet-1.2. The main groups of species and subspecies were distinguishable based on shared variation, and the separation of sea beets (Beta vulgaris ssp. maritima) into a Mediterranean and an Atlantic subgroup as suggested by previous studies could be confirmed. Complementary approaches of variant-based clustering were employed based on PCA, genotype likelihoods, tree calculations, and admixture analysis. Outliers suggested the occurrence of inter(sub)specific hybridisation, independently confirmed by different analyses. Screens for regions under artificial selection in the sugar beet genome identified 15 Mbp of the genome as variation-poor, enriched for genes involved in shoot system development, stress response, and carbohydrate metabolism. The resources presented herein will be valuable for crop improvement and wild species monitoring and conservation efforts, and for studies on beet genealogy, population structure and population dynamics. Our study provides a wealth of data for in-depth analyses of further aspects of the beet genome towards a thorough understanding of the biology of this important complex of a crop species and its wild relatives.
MeSH term(s)	Beta vulgaris/genetics ; Crops, Agricultural/genetics ; Base Sequence ; Genomics ; Sugars
Chemical Substances	Sugars
Language	English
Publishing date	2023-05-27
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/s41598-023-35691-7
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Article ; Online: Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting.

Sandell, Felix L / Holzweber, Thomas / Street, Nathaniel R / Dohm, Juliane C / Himmelbauer, Heinz

Plant biotechnology journal

2024 Volume 22, Issue 5, Page(s) 1312–1324

Abstract: Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a ... ...

Abstract	Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.
MeSH term(s)	Chenopodium quinoa/genetics ; Chenopodium quinoa/metabolism ; Color ; Genome-Wide Association Study ; Betalains/metabolism ; Genomics ; Seeds/genetics
Chemical Substances	Betalains (37279-84-8)
Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7652
ISSN (online)	1467-7652
ISSN	1467-7652
DOI	10.1111/pbi.14267
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Article ; Online: Prediction of NB-LRR resistance genes based on full-length sequence homology.

Andolfo, Giuseppe / Dohm, Juliane C / Himmelbauer, Heinz

The Plant journal : for cell and molecular biology

2022 Volume 110, Issue 6, Page(s) 1592–1602

Abstract: The activation of plant immunity is mediated by resistance (R)-gene receptors, also known as nucleotide-binding leucine-rich repeat (NB-LRR) genes, which in turn trigger the authentic defense response. R-gene identification is a crucial goal for both ... ...

Abstract	The activation of plant immunity is mediated by resistance (R)-gene receptors, also known as nucleotide-binding leucine-rich repeat (NB-LRR) genes, which in turn trigger the authentic defense response. R-gene identification is a crucial goal for both classic and modern plant breeding strategies for disease resistance. The conventional method identifies NB-LRR genes using a protein motif/domain-based search (PDS) within an automatically predicted gene set of the respective genome assembly. PDS proved to be imprecise since repeat masking prior to automatic genome annotation unwittingly prevented comprehensive NB-LRR gene detection. Furthermore, R-genes have diversified in a species-specific manner, so that NB-LRR gene identification cannot be universally standardized. Here, we present the full-length Homology-based R-gene Prediction (HRP) method for the comprehensive identification and annotation of a genome's R-gene repertoire. Our method has substantially addressed the complex genomic organization of tomato (Solanum lycopersicum) NB-LRR gene loci, proving to be more performant than the well-established RenSeq approach. HRP efficiency was also tested on three differently assembled and annotated Beta sp. genomes. Indeed, HRP identified up to 45% more full-length NB-LRR genes compared to previous approaches. HRP also turned out to be a more refined strategy for R-gene allele mining, testified by the identification of hitherto undiscovered Fom-2 homologs in five Cucurbita sp. genomes. In summary, our high-performance method for full-length NB-LRR gene discovery will propel the identification of novel R-genes towards development of improved cultivars.
MeSH term(s)	Disease Resistance/genetics ; Genes, Plant/genetics ; Lycopersicon esculentum/genetics ; Lycopersicon esculentum/metabolism ; Plant Breeding ; Plant Diseases/genetics ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Sequence Homology
Chemical Substances	Plant Proteins
Language	English
Publishing date	2022-04-18
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.15756
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Article: Prediction of NB‐LRR resistance genes based on full‐length sequence homology

Andolfo, Giuseppe / Dohm, Juliane C. / Himmelbauer, Heinz

plant journal. 2022 June, v. 110, no. 6

2022

Abstract: The activation of plant immunity is mediated by resistance (R)‐gene receptors, also known as nucleotide‐binding leucine‐rich repeat (NB‐LRR) genes, which in turn trigger the authentic defense response. R‐gene identification is a crucial goal for both ... ...

Abstract	The activation of plant immunity is mediated by resistance (R)‐gene receptors, also known as nucleotide‐binding leucine‐rich repeat (NB‐LRR) genes, which in turn trigger the authentic defense response. R‐gene identification is a crucial goal for both classic and modern plant breeding strategies for disease resistance. The conventional method identifies NB‐LRR genes using a protein motif/domain‐based search (PDS) within an automatically predicted gene set of the respective genome assembly. PDS proved to be imprecise since repeat masking prior to automatic genome annotation unwittingly prevented comprehensive NB‐LRR gene detection. Furthermore, R‐genes have diversified in a species‐specific manner, so that NB‐LRR gene identification cannot be universally standardized. Here, we present the full‐length Homology‐based R‐gene Prediction (HRP) method for the comprehensive identification and annotation of a genome's R‐gene repertoire. Our method has substantially addressed the complex genomic organization of tomato (Solanum lycopersicum) NB‐LRR gene loci, proving to be more performant than the well‐established RenSeq approach. HRP efficiency was also tested on three differently assembled and annotated Beta sp. genomes. Indeed, HRP identified up to 45% more full‐length NB‐LRR genes compared to previous approaches. HRP also turned out to be a more refined strategy for R‐gene allele mining, testified by the identification of hitherto undiscovered Fom‐2 homologs in five Cucurbita sp. genomes. In summary, our high‐performance method for full‐length NB‐LRR gene discovery will propel the identification of novel R‐genes towards development of improved cultivars.
Keywords	Cucurbita ; Solanum lycopersicum ; alleles ; cultivars ; disease resistance ; genome assembly ; immunity ; nucleotide sequences ; prediction ; sequence homology ; tomatoes
Language	English
Dates of publication	2022-06
Size	p. 1592-1602.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.15756
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Author Correction: Genomic distances reveal relationships of wild and cultivated beets.

Sandell, Felix L / Stralis-Pavese, Nancy / McGrath, J Mitchell / Schulz, Britta / Himmelbauer, Heinz / Dohm, Juliane C

Nature communications

2024 Volume 15, Issue 1, Page(s) 1078

Language	English
Publishing date	2024-02-05
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45401-0
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Article ; Online: Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach.

Yosief, Roa'a H S / Lone, Iqbal M / Nachshon, Aharon / Himmelbauer, Heinz / Gat-Viks, Irit / Iraqi, Fuad A

Animal models and experimental medicine

2024 Volume 7, Issue 1, Page(s) 36–47

Abstract: Background: Aspergillus fumigatus (Af) is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic background. The aim of this study was to search for candidate genes associated with host ... ...

Abstract	Background: Aspergillus fumigatus (Af) is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic background. The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus (Af) using an RNAseq approach in CC lines and hepatic gene expression. Methods: We studied 31 male mice from 25 CC lines at 8 weeks old; the mice were infected with Af. Liver tissues were extracted from these mice 5 days post-infection, and next-generation RNA-sequencing (RNAseq) was performed. The GENE-E analysis platform was used to generate a clustered heat map matrix. Results: Significant variation in body weight changes between CC lines was observed. Hepatic gene expression revealed 12 top prioritized candidate genes differentially expressed in resistant versus susceptible mice based on body weight changes. Interestingly, three candidate genes are located within genomic intervals of the previously mapped quantitative trait loci (QTL), including Gm16270 and Stox1 on chromosome 10 and Gm11033 on chromosome 8. Conclusions: Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af. As a next step, eQTL analysis will be performed for our RNA-Seq data. Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.
MeSH term(s)	Humans ; Male ; Mice ; Animals ; Collaborative Cross Mice/genetics ; Chromosome Mapping ; Aspergillus fumigatus/genetics ; RNA-Seq ; Genetic Predisposition to Disease/genetics ; Quantitative Trait Loci/genetics ; Aspergillosis/genetics ; Body Weight/genetics
Language	English
Publishing date	2024-02-14
Publishing country	United States
Document type	Journal Article
ISSN	2576-2095
ISSN (online)	2576-2095
DOI	10.1002/ame2.12386
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Article ; Online: Genome-environment associations along elevation gradients in two snowbed species of the North-Eastern Calcareous Alps.

Felkel, Sabine / Tremetsberger, Karin / Moser, Dietmar / Dohm, Juliane C / Himmelbauer, Heinz / Winkler, Manuela

BMC plant biology

2023 Volume 23, Issue 1, Page(s) 203

Abstract: Background: Anthropogenic climate change leads to increasing temperatures and altered precipitation and snowmelt patterns, especially in alpine ecosystems. To understand species' responses to climate change, assessment of genetic structure and diversity ...

Abstract	Background: Anthropogenic climate change leads to increasing temperatures and altered precipitation and snowmelt patterns, especially in alpine ecosystems. To understand species' responses to climate change, assessment of genetic structure and diversity is crucial as the basis for the evaluation of migration patterns, genetic adaptation potential as well as the identification of adaptive alleles. Results: We studied genetic structure, diversity and genome-environment associations of two snowbed species endemic to the Eastern Alps with a large elevational range, Achillea clusiana Tausch and Campanula pulla L. Genotyping-by-sequencing was employed to assemble loci de novo, call variants and perform population genetic analyses. Populations of either species were distinguishable by mountain, and to some extent by elevation. We found evidence for gene flow between elevations. Results of genome-environment associations suggested similar selective pressures acting on both species, emanating mainly from precipitation and exposition rather than temperature. Conclusions: Given their genetic structure and amount of gene flow among populations the two study species are suitable to serve as a model for genetic monitoring of climate change adaptation along an elevation gradient. Consequences of climate change will predominantly manifest via changes in precipitation and, thus, duration of snow cover in the snowbeds and indirectly via shrub encroachment accompanied by increasing shading of snowbeds at lower range margins. Assembling genomes of the study species and studying larger sample sizes and time series will be necessary to functionally characterize and validate the herein identified genomic loci putatively involved in adaptive processes.
MeSH term(s)	Ecosystem ; Gene Flow ; Temperature ; Genomics ; Adaptation, Physiological ; Climate Change
Language	English
Publishing date	2023-04-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-023-04187-x
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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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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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