Biology subjects

Mariene, G. M.

Publications and source records attributed to Mariene, G. M..

3 recordsLinked to original sources

bioRxiv2024

Genome assembly variation and its implications for gene discovery in nematode species

Genome assemblers are a critical component of genome science, but the choice of assembly software and protocols can be daunting. Here, we investigate genome assembly variation and its implications for gene discovery across three nematode species--Caenorhabditis bovis, Haemonchus contortus, and Heligmosomoides bakeri--highlighting the critical interplay between assembly choice and downstream genomic analysis. Selecting popular genome assemblers, we generated multiple assemblies for each species, analyzing their structure, completeness, and effect on gene family analysis. Our findings demonstrate that assembly variations can significantly affect gene family composition, with notable differences in critical gene families like cyp, gst, ugt, and nhr. Despite broadly similar performance using various assembly metrics, comparisons of assemblies with a single species revealed underlying structural rearrangements and inconsistencies in gene content. This emphasizes the imperative for continuous refinement of genomic resources. Our findings advocate for a cautious and informed approach to genome assembly and annotation to ensure reliable and insightful genomic interpretations.

genomics↗

bioRxiv2022

Accurate detection of structural variation is hard

The accurate characterization of structural variation is crucial for our understanding of how large chromosomal alterations affect phenotypic differences and contribute to genome evolution. Whole-genome sequencing is a popular approach for identifying structural variants, but the accuracy of popular tools remains unclear due to the limitations of existing benchmarks. Moreover, the performance of these tools for predicting variants in non-human genomes is less certain, as most tools were developed and benchmarked using data from the human genome. To address this problem, multiple short- and long-read tools were benchmarked using real and simulated Caenorhabditis elegans whole-genome sequence data. To evaluate the use of long-read data for the validation of short-read predictions, the agreement between predictions from a short-read ensemble learning method and long-read tools were compared. The results obtained from simulated data indicate that the best performing tool is contingent on the type and size of the variant, as well as the sequencing depth of coverage. These results also highlight the need for reference datasets generated from real data that can be used as ground truth in benchmarks.

genomics↗

bioRxiv2018

One species, two genomes: A critical assessment of inter isolate variation and identification of assembly incongruence in Haemonchus contortus

BackgroundNumerous quality issues may compromise genomic datas representation of its underlying organism. In this study, we compared two genomes published by different research groups for the parasitic nematode Haemonchus contortus, corresponding to divergent isolates. We analyzed differences between the genomes, attempting to ascertain which were attributable to legitimate biological differences, and which to technical error in one or both genomes.\n\nResultsWe found discrepancies between the H. contortus genomes in both assembly and annotation. The genomes differed in representation of genes that are highly conserved across eukaryotes, with clear evidence of misassembly underlying conserved genes missing from one genome or the other. Only 45% of genes in one genome were orthologous to genes in the other genome, with one genome exhibiting almost as much orthology to C. elegans as its counterpart H. contortus strain. The two genomes differed substantially in probable causes underlying this unexpectedly low orthology. One genome included many more inparalogues than the other, and more frequently assembled inparalogues together on the same portions of contiguous sequence. It also exhibited cases of better-conserved gene position relative to C. elegans.\n\nConclusionThe discrepancies between the two genomes far exceeded those expected as a consequence of biological differences between the two H. contortus isolates. This implies substantial quality issues in one or both genomes, suggesting that researchers must exercise caution when using genomic data for newly sequenced species.

genomics↗