Biology subjects

Childs, K. L.

Publications and source records attributed to Childs, K. L..

5 recordsLinked to original sources

bioRxiv2025

A reference-quality NLRome for the hexaploid sweetpotato and diploid wild relatives

Breeding for sweetpotato (Ipomea batatas) resistance requires accelerating our understanding genomic of sources of resistance. Nucleotide-binding domain leucine-rich repeat receptors (NLRs) proteins represent a key component of the plant immune system that mediate plant immune responses. We cataloged the NLR diversity in 32 hexaploid sweetpotato genotypes and three diploid wild relatives using resistance gene enrichment sequencing (RenSeq) to capture and sequence full NLRs. A custom designed NLR bait-library enriched NLR genes with an average 97% target capture rate. We employed a curated database of cloned and functionally characterized NLRs to assign sequenced sweetpotato NLRs to canonical phylogenetic clades. We identified between 800 to 1,200 complete NLRs, highlighting the expanded diversity of coiled-coil NLRs (CNLs) across all genotypes. NLRs among sweetpotato genotypes exhibited large conservation across genotypes. Phylogenetic distance between 6X (hexaploid) and 2X (diploid) genotypes revealed that a small repertoire of I. batatas CNLs diverged from the sweetpotato wild relatives. Finally, we obtained chromosome coordinates in hexaploid (Beauregard) and diploid (Ipomoea trifida) genomes and recorded clustering of NLRs on chromosomes arms. Our study provides a catalog of NLR genes that can be used to accelerate breeding and increase our understanding of evolutionary dynamics of sweetpotato NLRs.

plant biology↗

bioRxiv2023

A chromosome-scale assembly for tetraploid sour cherry (Prunus cerasus L.) 'Montmorency' identifies three distinct ancestral Prunus genomes

BackgroundSour cherry (Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors most closely related to extant P. fruticosa (ground cherry) and P. avium (sweet cherry). Sour cherry is an allotetraploid with few genomic resources, so a genome sequence would greatly facilitate the improvement of this crop. In Prunus, two known classes of genes are of particular importance to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses and are critically important for successful fertilization and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. ResultsHere we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant sour cherry cultivar grown in the U.S. We also generated a draft assembly of P. fruticosa to use alongside a published P. avium sequence for syntelog-based subgenome assignments for Montmorency. Using hierarchal k-mer clustering and phylogenomics, we provide compelling evidence this allotetraploid is trigenomic, containing two distinct subgenomes inherited from a P. fruticosa-like ancestor (A and A) and two copies of the same subgenome inherited from a P. avium-like ancestor (BB). We therefore assigned the genome composition of Montmorency to be AABB and show little to no recombination has occurred between progenitor subgenomes (A/A and B). The S-alleles and DAMs in Montmorency and P. fruticosa were manually annotated and demonstrated to support the three subgenome assignments. Lastly, the hybridization event that Montmorency is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. ConclusionsThe genome of sour cherry cultivar Montmorency highlights the evolutionary complexity of the genus Prunus. These genomic resources will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.

genomics↗

bioRxiv2018

Evolutionary characteristics of intergenic transcribed regions indicate widespread noisy transcription in the Poaceae

Extensive transcriptional activity occurring in unannotated, intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conservation of intergenic transcribed regions (ITRs) in four Poaceae species. Most ITR sequences are species-specific. Those found across species tend to be more divergent in expression and have more recent duplicates compared to annotated genes. To assess if ITRs are functional (under selection), machine learning models were established in Oryza sativa (rice) that could distinguish between benchmark functional (phenotype genes) and nonfunctional (pseudogenes) sequences with high accuracy based on 44 evolutionary and biochemical features. Based on the prediction models, 584 rice ITRs (8%) are classified as likely functional that tend to have conserved expression and ancient retained duplicates. However, most ITRs do not exhibit sequence or expression conservation across species or following duplication, consistent with computational predictions that suggest 61% ITRs are not under selection. We outline key evolutionary characteristics that are tightly associated with likely-functional ITRs and provide a framework to identify novel genes to improve genome annotation and move toward connecting genotype to phenotype in crop and model systems.

genomics↗

bioRxiv2017

A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa

Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. We find that gene prediction programs trained on genes with random GC content do not completely predict all grass genes with extreme GC content. We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method in Oryza sativa.

bioinformatics↗

bioRxiv2016

Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower.

The importance and applications of polyploidy have long been recognized, from shaping the evolutionary success of flowering plants to improving agricultural productivity. Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. How quickly one subgenome dominates within a newly formed polyploid, if immediate or after millions of years, and the genomic features that determine which genome dominates remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of two divergent genomes and that subgenome expression dominance significantly increases over generations. Additionally, CHH methylation levels are significantly reduced in regions near genes and within transposons in the first generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and submissive subgenomes in the natural allopolyploid. Our analyses reveal that the subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following the hybridization. These findings not only provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events, but may also contribute to uncovering the mechanistic basis of heterosis and subgenomic dominance.

genomics↗