Biology subjects

Corrales, A.

Publications and source records attributed to Corrales, A..

3 recordsLinked to original sources

bioRxiv2024

Benchmarking of bioinformatics tools for the hybrid de novo assembly of human whole-genome sequencing data

Accurate and complete de novo assembled genomes sustain variant identification and catalyze the discovery of new genomic features and biological functions. However, accurate and precise de novo assemblies of large and complex genomes remains a challenging task. Long-read sequencing data alone or in hybrid mode combined with more accurate short-read sequences facilitate the de novo assembly of genomes. A number of software exists for de novo genome assembly from long-read data although specific performance comparisons to assembly human genomes are lacking. Here we benchmarked 11 different pipelines including four long-read only assemblers and three hybrid assemblers, combined with four polishing schemes for de novo genome assembly of a human reference material sequenced with Oxford Nanopore Technologies and Illumina. In addition, the best performing choice was validated in a non-reference routine laboratory sample. Software performance was evaluated by assessing the quality of the assemblies with QUAST, BUSCO, and Merqury metrics, and the computational costs associated with each of the pipelines were also assessed. We found that Flye was superior to all other assemblers, especially when relying on Ratatosk error-corrected long-reads. Polishing improved the accuracy and continuity of the assemblies and the combination of two rounds of Racon and Pilon achieved the best results. The assembly of the non-reference sample showed comparable assembly metrics as those of the reference material. Based on the results, a complete optimal analysis pipeline for the assembly, polishing, and contig curation developed on Nextflow is provided to enable efficient parallelization and built-in dependency management to further advance in the generation of high-quality and chromosome-level human assemblies.

bioinformatics↗

bioRxiv2022

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unknown fungal taxa. We used a Global Soil Mycobiome consortium dataset to test relative performance of various sequencing depth standardization methods (calculation of residuals, exclusion of singletons, traditional and SRS rarefaction, use of Shannon index of diversity) to find optimal protocols for statistical analyses. Altogether, we used six global surveys to infer these patterns for soil-inhabiting fungi and their functional groups. We found that residuals of log-transformed richness (including singletons) against log-transformed sequencing depth yields significantly better model estimates compared with most other standardization methods. With respect to global patterns, fungal functional groups differed in the patterns of diversity, endemicity and vulnerability to main global change predictors. Unlike -diversity, endemicity and global-change vulnerability of fungi and most functional groups were greatest in the tropics. Fungi are vulnerable mostly to drought, heat, and land cover change. Fungal conservation areas of highest priority include wetlands and moist tropical ecosystems.

ecology↗

bioRxiv2020

Fungi of the Fortuna Forest Reserve: Taxonomy and ecology with emphasis on ectomycorrhizal communities

Panamanian montane forests harbor a high diversity of fungi, particularly of ectomycorrhizal (ECM) fungi, however their taxonomy and diversity patterns remain for the most part unexplored. Here we present state of the art fungal taxonomy and diversity patterns at Fortuna Forest Reserve based on morphological and molecular identification of over 1,000 fruiting body collections of macromycetes made over a period of five years. We compare these new results with previously published work based on environmental sampling of Oreomunnea mexicana root tips. We compiled a preliminary list of species and report 22 new genera and 29 new fungal species for Panama. Based on fruiting body collection data we compare the species composition of ECM fungal communities associated with Oreomunnea stands across sites differing in soil fertility and amount of rainfall. We also examine the effect of a long-term nitrogen addition treatment on the fruiting body production of ECM fungi. Finally, we discuss the biogeographic importance of Panama collections which fill in the knowledge gap of ECM fungal records between Costa Rica and Colombia. Given that the isthmus of Panama was an important migration route of ECM tree and fungal species from northern temperate areas to South America, the ECM fungal communities of Panama might show a high degree of isolation and therefore a high level of endemism. We expect that the forests at Fortuna will continue to yield new ECM macromycete data as we continue to study the collected specimens and describe new species.

ecology↗