Biology subjects

Niederhuth, C.

Publications and source records attributed to Niederhuth, C..

8 recordsLinked to original sources

bioRxiv2024

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

BackgroundTeinturier grapevine varieties were first described in the 16th century and have persisted due to their deep pigmentation. Unlike most other grapevine varieties, teinturier varieties produce berries with pigmented flesh due to anthocyanin production within the flesh. As a result, teinturier varieties are of interest not only for their ability to enhance the pigmentation of wine blends but also for their health benefits. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. FindingsFor Dakapo, we used a combination of Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine genome assembly to generate a final assembly of 508.5 Mbp with an N50 scaffold length of 25.6 Mbp and a BUSCO score of 98.0%. A combination approach of de novo annotation and lifting over annotations from the existing grapevine reference genome resulted in the annotation of 36,940 genes in the Dakapo assembly. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. The diploid genome has an N50 scaffold length of 24.9 Mbp and a BUSCO score of 98.7%, and both haplotype-specific genomes are of similar quality. De novo annotation of the diploid Rubired genome yielded annotations for 56,681 genes. ConclusionsThe Dakapo and Rubired genome assemblies and annotations will provide genetic resources for future investigations into berry flesh pigmentation and other traits of interest in grapevine.

genomics↗

bioRxiv2024

Small, but mitey: Investigating the molecular genetic basis for mite domatia development and intraspecific variation in Vitis riparia using transcriptomics

* Here, we investigated the molecular genetic basis of mite domatia, structures on the underside of leaves that house mutualistic mites, and intraspecific variation in domatia size in Vitis riparia (riverbank grape). * Domatia and leaf traits were measured, and the transcriptomes of mite domatia from two genotypes of V. riparia with distinct domatia sizes were sequenced to investigate the molecular genetic pathways that regulate domatia development and intraspecific variation in domatia traits. * Key trichome regulators as well as auxin and jasmonic acid are involved in domatia development. Genes involved in cell wall biosynthesis, biotic interactions, and molecule transport/metabolism are upregulated in domatia, consistent with their role in domatia development and function. * This work is one of the first to date that provides insight into the molecular genetic bases of mite domatia. We identified key genetic pathways involved in domatia development and function, and uncovered unexpected pathways that provide an avenue for future investigation. We also found that intraspecific variation in domatia size in V. riparia seems to be driven by differences in overall leaf development between genotypes.

plant biology↗

bioRxiv2023

From buds to shoots: Insights into grapevine development from the Witch's Broom bud sport

Premise of StudyDevelopment is relatively understudied in woody vines, such as grapevine (Vitis vinifera). We used the Witchs Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis of the bud sport. MethodsWe phenotyped shoots, buds, and leaves of two independent cases of the Witchs Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild-type counterparts of the same variety. We also performed Illumina and Oxford Nanopore sequencing on the two independent cases and two wild-type counterparts of the same variety. Key ResultsThe Dakapo and Merlot cases of Witchs Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witchs Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We were able to identify unique genetic mutations in our two Witchs Broom cases that are strong candidates for the genetic basis of the bud sports. ConclusionsThe Witchs Broom bud sport in grapevine serves as a useful natural mutant in which to study grapevine development. The Witchs Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another. Future work on Witchs Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.

plant biology↗

bioRxiv2023

Epigenomic divergence underlies sequence polymorphism and the evolutionary fate of duplicate paralogs in A. thaliana.

Processes affecting rates of sequence polymorphism are fundamental to molecular evolution and the evolutionary fate of gene duplicates. The relationship between gene activity and sequence polymorphism can influence the likelihood that functionally redundant gene copies are co-maintained in stable evolutionary equilibria versus other outcomes such as neo-functionalization. Here we investigate genic variation in epigenome-associated polymorphism rates in Arabidopsis thaliana and consider whether these affect the evolution of gene duplicates. We compared the frequency of sequence polymorphism and patterns of genetic differentiation between genes classified by exon methylation patterns: unmethylated (unM), gene-body methylated (gbM), and transposon-like methylated (teM) states, which reflect divergence in gene expression. We found that the frequency of polymorphism was higher in teM (transcriptionally repressed, tissue-specific) genes and lower in gbM (active, constitutively expressed) genes. Comparisons of gene duplicates were largely consistent with genome-wide patterns - gene copies that exhibit teM tend to accumulate higher sequence polymorphism, evolve faster, and are in chromatin states associated with reduced DNA repair. This relationship between expression, the epigenome, and polymorphism may lead to the breakdown of equilibrium states that would otherwise maintain genetic redundancies. Epigenome-mediated polymorphism rate variation may therefore aid the pseudogenization of duplicate paralogs or increase the evolution of novel gene functions in duplicate paralogs maintained over evolutionary time.

genomics↗

bioRxiv2021

Hypermethylation is associated with increased age in almond (Prunus dulcis D.A. Webb) accessions

O_LIThe focus of this study is to profile changes in DNA methylation and small RNA expression occurring with increased age in almond breeding germplasm to identify possible biomarkers of age that can be used to assess the potential of individuals to develop aging-related disorders. C_LIO_LITo profile DNA methylation in almond germplasm, 70 methylomes were generated from almond individuals representing three age cohorts (11, 7, and 2 years old) using an enzymatic methyl-seq approach followed by analysis to call differentially methylated regions (DMRs) within these cohorts. Small RNA (sRNA) expression was profiled in three breeding selections, each from two age cohorts (1 and 6 years old) using sRNA-Seq followed by differential expression analysis. C_LIO_LIWeighted chromosome-level methylation analysis reveals hypermethylation in 11-year old almond breeding selections when compared to 2-year-old selections in the CG and CHH contexts. Seventeen consensus DMRs were identified in all age contrasts. sRNA expression differed significantly between the two age cohorts tested, with significantly decreased expression in sRNAs in the 6-year-old selections compared to the 1-year-old. C_LIO_LIAlmond shows a pattern of hypermethylation and decreased sRNA expression with increased age. Identified DMRs and differentially expressed sRNAs could function as putative biomarkers of age following validation in additional age groups. C_LI

plant biology↗

bioRxiv2021

Integrated analysis of the methylome and transcriptome of twin almonds (Prunus dulcis D.A.Webb) reveals genomic features associated with non-infectious bud failure

I.Almond (Prunus dulcis [Mill.] D.A.Webb) exhibits an age-related disorder called non-infectious bud-failure (BF) affecting vegetative bud development and nut yield. The underlying cause of BF remains unknown but is hypothesized to be associated with heritable epigenetic mechanisms. To address this disorder and its epigenetic components, we utilized a monozygotic twin study model profiling genome-wide DNA methylation and gene expression in two sets of twin almonds discordant for BF-exhibition. Analysis of DNA methylation patterns show that BF-exhibition and methylation, namely hypomethylation, are not independent phenomena. Transcriptomic data generated from the twin pairs also shows genome-wide differential gene expression associated with BF-exhibition. After identifying differentially methylated regions (DMRs) in each twin pair, a comparison revealed 170 shared DMRs between the two twin pairs. These DMRs and the associated genetic components may play a role in BF-exhibition. A subset of 52 shared DMRs are in close proximity to genes involved in meristem maintenance, cell cycle regulation, and response to heat stress. Annotation of specific genes included involvement in processes like cell wall development, calcium ion signaling, and DNA methylation. Results of this work support the hypothesis that BF-exhibition is associated with hypomethylation in almond, and identified DMRs and differentially expressed genes can serve as potential biomarkers to assess BF-potential in almond germplasm. Our results contribute to an understanding of the contribution of epigenetic disorders in agricultural performance and biological fitness of perennials. II. SignificanceThis study examines epigenetic components underlying noninfectious bud failure, an aging-related disorder affecting almond. Results from this work contribute to our understanding of the implications of DNA methylation on agricultural production, namely perennial fruit and nut production, due to effects on growth, development, and reproduction. Describing the methylome of discordant, monozygotic twin almonds enables the study of genomic features underlying noninfectious bud failure in this economically important crop.

plant biology↗

bioRxiv2020

The molecular basis of Kale domestication: Transcription profiling of leaves and meristems provides new insights into the evolution of a Brassica oleracea vegetative morphotype

Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales ornate leaves, delayed flowering, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNAseq experiments were used to understand the global pattern of expressed genes during one single phase of development in kale, cabbage and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes, and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plan architecture, defense and nutrition were differentially expressed in kale. RNA-Seq experiments allow the discovery of novel candidate genes involved in the kale domestication syndrome. We identified candidate genes differentially expressed in kale that could be responsible for variation in flowering times, taste and herbivore defense, variation in leaf morphology, plant architecture, and nutritional value. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.

plant biology↗

bioRxiv2019

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploidBrassica napus

Interspecific hybridization and allopolyploidization merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant" over the other subgenome, having a greater number of reatined duplicate genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we "replayed the evolutionary tape" with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations. We found that the same subgenome was consistently more dominantly expressed in all lines and generations. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the Brassica oleracea derived C subgenome in all lines and generations. These differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting subgenome dominance is related to inherited parental genome differences rather than a byproduct of allopolyploidization. Gene network analyses indicated an enrichment for network interactions and several biological functions for C subgenome biased pairs, but no enrichment was observed for A subgenome biased pairs. These findings demonstrate that "replaying the evolutionary tape" in allopolyploids results in repeatable and predictable subgenome expression dominance patterns based on preexisting genetic differences among the parental species. These findings have major implications regarding the genotypic and phenotypic diversity observed following plant hybridization in both ecological and agricultural contexts.

evolutionary biology↗