A5064637442- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Plant Disease Resistance and Genetics
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- Invertebrate Taxonomy and Ecology
- Genetics and Plant Breeding
- Molecular Biology Techniques and Applications
- Viral Infectious Diseases and Gene Expression in Insects
- Cancer-related molecular mechanisms research
- Genomics and Rare Diseases
- Plant tissue culture and regeneration
- RNA and protein synthesis mechanisms
- Nematode management and characterization studies
- Plant Virus Research Studies
- Animal Genetics and Reproduction
Iowa State University
2018-2024
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. results demonstrate ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres revealed additional variation major...
Abstract Background The domestic pig (Sus scrofa) is important both as a food source and biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, pharmacology to humans. draft reference genome (Sscrofa10.2) of purebred Duroc female established using older clone-based sequencing methods was incomplete, unresolved redundancies, short-range order orientation errors, associated misassembled genes limited utility. Results We present 2 annotated highly contiguous...
Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support sequenced genomes of many maize inbred lines in addition B73 reference genome assembly. Curation development efforts have targeted high quality datasets tools trait analysis, germplasm genetic studies, breeding. MaizeGDB hosts a wide range data including recent new types metadata, RNA-seq, proteomics, synteny, large-scale diversity. To improve access visualization several been implemented to:...
Abstract Creating gapless telomere-to-telomere assemblies of complex genomes is one the ultimate challenges in genomics. We use two independent and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed 63 contigs contig N50 162 Mb. This includes chromosome 3 (236 Mb) 9 (162 Mb), 53 Mb Ab10 meiotic drive haplotype. The data also reveal internal structure seven centromeres five heterochromatic knobs, showing that major tandem repeat arrays (CentC, knob180, TR-1)...
Genome assemblies are foundational for understanding the biology of a species. They provide physical framework mapping additional sequences, thereby enabling characterization of, example, genomic diversity and differences in gene expression across individuals tissue types. Quality metrics genome gauge both completeness contiguity an assembly help confidence downstream biological insights. To compare quality multiple assemblies, set common typically calculated then compared to one or more...
Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore extent TE within species, we developed an optimized open-source algorithm, panEDTA, de novo annotate TEs a pangenome context. We then generated unified annotation for maize derived from 26 reference-quality genomes, which reveals excess 35.1 Mb sequences per tropical relative temperate maize. A small number ( n = 216) families, mainly LTR retrotransposons, drive these...
Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina (RNA-seq) from a single White cross-bred pig.Across tissues, total 67,746 unique transcripts were observed, including 60.5% predicted protein-coding, 36.2% long non-coding 3.3% nonsense-mediated decay transcripts. On average, 90% splice junctions supported by RNA-seq within tissue. A large...
Abstract Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment critical sequence depth read length is important allocating limited resources. To this end, we generated eight the genome maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic with N50 subread lengths 11–21 kb. Assemblies ≤30 11 kb are highly fragmented, even low-copy genic regions showing...
Abstract The domestic pig ( Sus scrofa ) is important both as a food source and biomedical model with high anatomical immunological similarity to humans. draft reference genome (Sscrofa10.2) of purebred Duroc female established using older clone-based sequencing methods was incomplete unresolved redundancies, short range order orientation errors associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level assemblies created more recent long...
Abstract Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore extent TE within species, we developed an optimized open-source algorithm, panEDTA, de novo annotate TEs a pan-genome context. We then generated unified annotation for maize derived from 26 reference-quality genomes, which revealed excess 35.1 Mb sequences per tropical relative temperate maize. A small number (n = 216) families, mainly LTR retrotransposons,...
Abstract We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The data indicate number of pan-genes exceeds 103,000 ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres further reveal locations internal structures major cytological landmarks. show combining structural variation...
Abstract Background Genome assemblies are foundational for understanding the biology of a species. They provide physical framework mapping additional sequences, thereby enabling characterization of, example, genomic diversity and differences in gene expression across individuals tissue types. Quality metrics genome gauge both completeness contiguity an assembly help confidence downstream biological insights. To compare quality multiple assemblies, set common typically calculated then...
Abstract Recent improvements in the quality and yield of long-read data scaffolding technology have made it possible to rapidly generate reference-quality assemblies for complex genomes. Still, generating these is costly, an assessment critical sequence depth read length obtain high-quality important allocating limited resources. To this end, we generated eight independent genome maize inbred line NC358 using PacBio datasets ranging from 20-75x genomic N50 lengths 11-21 kb. Assemblies with...
Creating gapless telomere-to-telomere assemblies of complex genomes is one the ultimate challenges in genomics. We used long read technologies and an optical map based approach to produce a maize genome assembly composed only 63 contigs. The B73-Ab10 includes chromosome 3 (236 Mb) 9 (162 Mb), multiple highly repetitive centromeres heterochromatic knobs, 53 Mb Ab10 meiotic drive haplotype.