Biology subjects

Knitlhoffer, V.

Publications and source records attributed to Knitlhoffer, V..

3 recordsLinked to original sources

bioRxiv2024

Trans-generational adaptation to maternal climate through hormone transport in plants

Whether organisms can inherit parental adaptations to the environment is a major question in evolutionary biology. Plant development is highly plastic and dependent on the seasonal cues which are used to control growth and reproduction. Seed dormancy and germination are key traits which respond strongly to temperature during seed development and here we show that progeny adaptation to seasonal climate is inherited from the mother plant. Loss of maternal LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) causes an inability of progeny seeds to sense temperature and this is linked mechanistically to reduced ABA levels in seeds and activation of the primary nitrate response. At the single cell level, small changes in temperature activate nitrate signalling specifically in the mother, and ABA biosensor imaging reveals temperature-dependent fluxes of ABA into seeds necessary for dormancy induction. Thus, we reveal that progeny seeds inherit the climate adaptation of mother plants via active hormone transport during seed set.

plant biology↗

bioRxiv2024

A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition

Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics. We identified and removed Hi-C reads between homologous unitigs to facilitate their scaffolding and employed methods for the manual curation of rearrangements and misassemblies. Our final phased assembly included the four haplotypes in 36 chromosomes. We found that 18 chromosomes originated from diploid U. brizantha and the other 18 from either U. ruziziensis or diploid U. decumbens. We also identified a chromosomal translocation between chromosomes 5 and 32, as well as evidence of pairing exclusively within subgenomes, except for a homoeologous exchange in chromosome 21. Our results demonstrate that haplotype-aware assemblies accurately capture the allelic diversity in heterozygous species, making them the preferred option over collapsed-haplotype assemblies.

plant biology↗

bioRxiv2024

Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones

BackgroundThe identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing. ResultsIncreases in BrdU incorporation allow us to measure DNA replication dynamics, including identification of replication initiation, fork direction and termination on individual nanopore sequencing reads. Importantly, initiation and termination events are identified on single-molecules with high resolution, throughout S-phase, genome-wide and at high coverage at specific loci using targeted enrichment. We find a significant enrichment of initiation sites within the broad initiation zones identified by population level studies. However, these focused initiation sites only account for [~]20% of all identified replication initiation events. Most initiation events are dispersed throughout the genome and are missed by cell population approaches. This indicates that most initiation occurs at sites that, individually, are rarely used. These dispersed initiation sites contrast with the focused sites identified by population studies, in that they do not show a strong relationship to transcription or a particular epigenetic signature. ConclusionsWe show here that single-molecule sequencing enables unbiased detection and characterisation of DNA replication initiation events, including the numerous dispersed initiation events that replicate most of the human genome.

genomics↗