Biology subjects

Elbers, J. P.

Publications and source records attributed to Elbers, J. P..

3 recordsLinked to original sources

bioRxiv2024

Using readmers and hapmers in assessing phase switching after read error correction of Oxford Nanopore Sequences

AO_SCPLOWBSTRACTC_SCPLOWMethods for sequence error correction can improve sequence accuracy; however, there can be unintended errors added during error correction. One such example is phase switching, whereby sequences derived from genomes containing more than one parental copy have contributions from more than one parental haplotype. Such switches are mistakes that can confound downstream analyses especially de novo genome assembly. While DNA sequences do not possess words such as linguistic languages, one can partition a DNA sequence into word-like objects called k-mers. K-mers include pieces of DNA sequence of k length that can describe various properties of DNA sequences. With regard to phase switching, there are k-mers present in one parental haplotype not found in other(s). These so-called hapmers can represent inaccuracies in that parental haplotypes assembly but also correct, unique DNA variation. Here we investigated the effect of DNA sequence error correction on phase switching at the sequence/read level. Using several error-correction methods, we find all methods tested are similar to raw, presumably, phase-switch-free Oxford Nanopore Technologies (ONT) sequences in the percentage of readmers (k-mers from the ONT sequences) matching one parental haplotypes hapmers. This work demonstrates an efficient method to assess if an error-correction method has introduced phase switching implemented in the Julia programming language.

bioinformatics↗

bioRxiv2024

Unraveling Genome- and Immunome-wide Genetic Diversity in Jaguars (Panthera onca): Implications for Targeted Conservation

Our study examines the declining Jaguar populations in Central and South America, assessing the impact of habitat loss and fragmentation on genetic diversity and local adaptation. We investigated population structure and immunome variability in 25 jaguars to identify unique genetic diversity for informed, targeted conservation. Our genome-wide analyses revealed three distinct geographic populations corresponding to Central America, South American lowland, and South American highland regions. While the highland population displayed lower overall immunome-wide variability, specific innate (Natural killer cell complex, Toll-like receptor) and adaptive (Major histocompatibility complex-class-II) immune genes crucial for adaptive responses showed promising diversity. Nonetheless, South American highland and Central American jaguars are severely threatened. Therefore, we propose re-evaluating evolutionary significant units to prioritize conservation efforts, preserving crucial genetic and adaptive diversity essential for the species resilience and long-term survival.

genomics↗

bioRxiv2023

The unexpected loss of the "hunger hormone" ghrelin in true passerines: A game changer in migration physiology

Migratory birds must accumulate large amounts of fat prior to migration to sustain long flights. In passerines, the small body size limits the amount of energy stores that can be transported and therefore birds undergo cycles of extreme fattening and rapid exhaustion of reserves. Research on these physiological adaptations was rattled by the discovery that birds have lost the main vertebrate regulator of fat deposition, leptin. Recent studies have thus focused on ghrelin, known as the "hunger hormone", a peptide secreted by the gastrointestinal tract to regulate food intake, body mass, and other important functions in vertebrates. Studies on domestic species showed that in birds ghrelin has effects opposite to those described in mammals, such as inhibiting instead of promoting food intake. Furthermore, a series of recent studies have shown that ghrelin administration influences migratory behaviour in passerine birds, suggesting an important role of this hormone in bird migration. However, using comparative genomic analyses we show that ghrelin has been lost in the largest avian taxon Eupasseres, after the basic split from Acanthisitti about 50 million years ago. Eupasserines, also known as True passerines, include all but two of the ca. 10,000 known passerine species. We further found that the ghrelin receptor (growth hormone secretagogue receptor, GHS-R) is still conserved in passerine birds, as indicated by sites under purifying selection and in line with the effects of ghrelin administration. Thus, ghrelin adds to a list of hormones highly conserved in vertebrates that have lost their main functions in specific taxa. The maintenance of a functional receptor system, however, suggests that in eupasserine birds another ligand has replaced ghrelin, perhaps to bypass the feedback system that would hinder large pre-migratory accumulation of subcutaneous fat.

evolutionary biology↗