Simultaneous gene finding in multiple genomes

König, Stefanie; Romoth, Lars; Gerischer, Lizzy; Stanke, Mario

doi:10.1093/bioinformatics/btw494

Cited by 64 publications

(39 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Trimmed reads were mapped to the corresponding genome assembly using HISAT2 v2.0.4 ( Kim et al, 2015 ) specifying a max intron length of 5 kb and the “dta-cufflinks” option to report alignments tailored for cufflinks input. Cufflinks-guided annotations were generated using CodingQuarry pathogen-mode (CQPM, Testa et al, 2015 ) which were later provided to Augustus ( Stanke et al, 2006 ; König et al, 2016 ) as hints. Intron position hints were extracted from the mapped RNAseq reads using the bam2hints utility provided with Augustus and position hints from PTR Pt-1C-BFP proteins (assembly ASM14998v1) mapped to each genome using Exonerate v2.2.0 ( Slater and Birney, 2005 ).…”

Section: Methodsmentioning

confidence: 99%

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

et al. 2018

View full text Add to dashboard Cite

Pyrenophora teres, P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes. Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive genome than PTM and more recent transposon activity measured by the frequency and size of genome fissures. PTT has a longer cultivated host association and, notably, a greater range of host–pathogen genetic interactions compared to other Pyrenophora spp., a property which associates better with genome size than pathogen lifestyle. The two forms possess similar complements of TE families with Tc1/Mariner and LINE-like Tad-1 elements more abundant in PTT. Tad-1 was only detectable as vestigial fragments in PTM and, within the forms, differences in genome sizes and the presence and absence of several TE families indicated recent lineage invasions. Gene differences between P. teres forms are mainly associated with gene-sparse regions near or within TE-rich regions, with many genes possessing characteristics of fungal effectors. Instances of gene interruption by transposons resulting in pseudogenization were detected in PTT. In addition, both forms have a large complement of secondary metabolite gene clusters indicating significant capacity to produce an array of different molecules. This study provides genomic resources for functional genetics to help dissect factors underlying the host–pathogen interactions.

show abstract

Section: Methodsmentioning

confidence: 99%

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Species with an overlapping ORF longer than 50% of the D. melanogaster ORF were denoted as ORF harbouring. To generate a set of syntenic ORFs for evolutionary rate analysis, the same methodology was applied to a twelve-way whole genome alignment of the Drosophila clade (König et al 2016). In this case, the syntenic regions corresponding to all Drosophila single exon orphan genes, old genes and intergenic ORFs in the study set were extracted and syntenic ORFs were identified as before.…”

Section: Analysis Of Syntenic Genomic Regionsmentioning

confidence: 99%

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila

2020

View full text Add to dashboard Cite

Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Drosophila genus. Across the annotated proteomes of twelve species, we find 6297 orphan genes within 4953 taxon-specific clusters of orthologs. By inferring the ancestral DNA as non-coding for between 550 and 2467 (8.7-39.2%) of these genes, we describe for the first time how de novo emergence contributes to the abundance of clade-specific Drosophila genes. In support of them having functional roles, we show that de novo genes have robust expression and translational support. However, the distinct nucleotide sequences of de novo genes, which have characteristics intermediate between intergenic regions and conserved genes, reflect their recent birth from non-coding DNA. We find that de novo genes encode more disordered proteins than both older genes and intergenic regions. Together, our results suggest that gene emergence from non-coding DNA provides an abundant source of material for the evolution of new proteins. Following gene birth, gradual evolution over large evolutionary timescales moulds sequence properties towards those of conserved genes, resulting in a continuum of properties whose starting points depend on the nucleotide sequences of an initial pool of novel genes.

show abstract

“…Complementing direct evidence from transcriptional and translational data, comparative genomics allows finding functional genomic elements that are conserved between species. Genes, exons, and other DNA elements under natural selection are often highly conserved between close relatives and the core set of human genes are conserved in all bilateria …”

Section: Evidence For Protein‐coding Genes Comes From Multiple Sourcesmentioning

confidence: 99%

The Protein‐Coding Human Genome: Annotating High‐Hanging Fruits

et al. 2019

View full text Add to dashboard Cite

The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.

show abstract

Simultaneous gene finding in multiple genomes

Abstract: The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online.

Cited by 64 publications

References 24 publications

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila

The Protein‐Coding Human Genome: Annotating High‐Hanging Fruits

Contact Info

Product

Resources

About