Henrik Lantz

Henrik Lantz
Uppsala University | UU · Department of Medical Biochemistry and Microbiology

PhD in Systematics

About

80
Publications
12,719
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1,325
Citations

Publications

Publications (80)
Article
Full-text available
Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,07...
Article
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Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chro- mosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucle- o...
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List of genes without variants in CBS 11270. (TXT)
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Copy number variation in CBS 11270. (TXT)
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List of genes with reduced coverage. (TXT)
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Characterization of repeats in CBS 11270. (TXT)
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Characterization of variants in CBS 2499. (TXT)
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Clustering of genes with reduced coverage in CBS 11270. (DOCX)
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Haplotype sampling of CBS 11270. (DOCX)
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Distribution of SNPs per Kbp gene. (DOCX)
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Variation in coverage of chromosomes in CBS 11270. (DOCX)
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Characterization of variants in CBS 11270. (TXT)
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List of genes in CBS 11270 with variants. (TXT)
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List of genes in CBS 2499 with variants. (TXT)
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List of genes without variants in CBS 2499. (TXT)
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List of genes present in CBS 11270 but not in CBS 2499. (DOCX)
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Distribution of genes with different numbers of variants in heterozygous sites in the genome of CBS 11270 and between genomes of CBS 11270 and CBS 2499. (DOCX)
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List of genes present in CBS 2499 but not in CBS 11270. (DOCX)
Article
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A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work pr...
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The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies...
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As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic...
Article
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Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms d...
Preprint
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Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wi...
Preprint
Full-text available
Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wi...
Article
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After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts,...
Article
Significance: This paper outlines a novel strategy for combining genomics and quantitative DIA-MS proteomics data. We demonstrate a DIA-MS-based proteogenomics strategy for quantifying conserved and non-conserved peptides across clinical isolates of Streptococcus pyogenes from non-invasive and invasive infections. We suggest a strategy for constru...
Article
Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approx. 22Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X. bisporus appears to have relinquishe...
Article
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Background Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensi...
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The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene e...
Article
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On the basis of a study of ITS sequences, Vidal et al. (Rev. Iber. Micol. 17: 22, 2000) recommended that the genus Chrysosporium be restricted to species belonging to Onygenales. Using nrLSU genes, we studied the majority of clades examined by Vidal et al. and showed that currently accepted species in Chrysosporium phylogenetically belong in six cl...
Article
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Background Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified a...
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Article
The filamentous ascomycete Xeromyces bisporus is an extreme xerophile able to grow down to a water activity of 0.62. We have inferred the phylogenetic position of Xeromyces in relation to other xerophilic and xerotolerant fungi in the order Eurotiales. Using nrDNA and betatubulin sequences, we show that it is more closely related to the xerophilic...
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Hypoderma siculum is described and illustrated as a new species from southeast Sicily (Italy) that occurs on remnants of Ferula communis (Apiaceae). Its ecology and taxonomic and phylogenetic relationships are discussed
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Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and i...
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New generic circumscriptions of the Paleotropical tribe Vanguerieae in the subfamily Ixoroideae s.l. (Rubiaceae) have recently been established as a result of a series of phylogenetic studies conducted by Lantz and Bremer. The genus Canthium Lam. was shown in their study to be highly polyphyletic, and a largely dioecious group was for the first tim...
Article
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The newly circumscribed dioecious group (sensu Razafimandimbison et al.) of tribe Vanguerieae in the subfamily Ixoroideae (Rubiaceae) comprises over 200 species classified in four morphologically distinct genera: Cyclophyllum Hooker f., Peponidium (Baillon) Arènes, Pyrostria Commerson ex Jussieu, and one new genus affined to species of Canthium sub...
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Three new species of the tribe Vanguerieae (Rubiaceae) from Madagascar are described with illustrations. Two species are placed in Pyrostria, one in Peponidium. Peponidium crassifolium is recognized by its thick and slightly succulent leaves, Pyrostria pendula by the pendulous flowers and persistent pedicels, and Pyrostria serpentina by a serpentin...
Article
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The phylogeny of the Vanguerieae genera Fadogia, Rytigynia, Vangueria, and closely related genera is investigated using nuclear rDNA ITS sequences and plastid trnT-F and rpl16 sequences. Individual and combined analyses reveal several strongly supported clades. There are indications that Fadogia, Rytigynia, Tapiphyllum, and Vangueria are para- or p...
Article
The biologically interesting ant-plant association, myrmecophytism, occurs in ca. 140 of the 11,000 species and 22 of the 630 genera of the coffee family (Rubiaceae). These myrmecophytic Rubiaceae species are predominantly distributed in Southeast Asia, especially the Malesian region, with comparatively few species in mainland Africa and the Neotro...
Article
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The biologically interesting ant–plant association, myrmecophytism, occurs in ca. 140 of the 11,000 species and 22 of the 630 genera of the coffee family (Rubiaceae). These myrmecophytic Rubiaceae species are predominantly distributed in Southeast Asia, especially the Malesian region, with comparatively few species in mainland Africa and the Neotro...
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We discuss the history and circumscription of the genus Rytigynia (Rubiaceae. Vanguerieae) and present the morphological characters used for the delimitation of the genus in a new, restricted sense. We describe Rytigynia dichasialis, a new species from northeastern Tanzania that is unique in the genus by having long-pedunculate and dichasially cymo...
Article
The Vanguerieae is a species-rich tribe of the Rubiaceae with problematic generic circumscriptions. Here we address this issue by presenting a phylogeny in which strongly supported groups are identified. We use DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region, trnT-F sequences from the chloroplast genome, and 30...