Biology subjects

Leder, E. H.

Publications and source records attributed to Leder, E. H..

3 recordsLinked to original sources

bioRxiv2026

A haplotype-resolved bluethroat (Luscinia s. svecica) genome assembly uncovers the complex MHC region

We describe a chromosome-level, haplotype-resolved genome assembly from a female bluethroat (Luscinia s. svecica). The assembly comprises two pseudo-haplotypes of 1461 Mb and 1171 Mb, with 77.4% and 88.4% scaffolded into 40 autosomal chromosomes and the W and Z sex chromosomes (haplotype one). Assembly completeness is high (BUSCO 99.2% and 94.9%), with 22,462 and 18,769 annotated protein-coding genes for haplotypes one and two, respectively. The use of Oxford Nanopore Technologies sequencing enables resolution of genomic regions that are often fragmented in genome assemblies, including the hypervariable Major Histocompatibility Complex (MHC). We find that MHC loci include both the canonical organization of tandemly duplicated MHCII{beta} genes with a single MHCIIA, and a distinct arrangement in which MHCI and MHCII{beta} loci are interspersed in intermixed arrays, and that substantial structural differences between haplotypes are directly resolved in the assembly.

genomics↗

bioRxiv2024

Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mtDNA copy number in songbird blood and sperm cells

Mitochondrial DNA copy number varies across species, individuals and cell types. Two avian cell types carrying a relatively low number of mitochondria are the red blood cells and spermatozoa. While previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (qPCR), this method shows potential limitations when quantifying low abundant targets. To mitigate such issues, we investigated and compared the reliability and accuracy of qPCR, digital PCR (dPCR) and droplet digital PCR (ddPCR) to quantify high and low concentration DNA. Using synthetic DNA, we found that both dPCR and ddPCR displayed lower Limit of Detection and Limit of Quantification than qPCR. Using DNA extracted from blood and sperm cells of Eurasian Siskin, we found that qPCR, dPCR and ddPCR reliably quantified mitochondrial DNA in sperm samples, but showed significant differences when analyzing typically lower levels of mtDNA in blood. We found that ddPCR consistently showed lower variation among replicates. These analyses provide critical insights and recommendations for future studies aiming to quantify target mtDNA. Our study indicates that dPCR and ddPCR are the preferred methods when working with samples with low abundance of mtDNA.

molecular biology↗

bioRxiv2024

Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis

The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44kb) and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1 % of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation. SignificanceThe rough periwinkle, L. saxatilis has become a model to study adaptation, evolutionary innovation and speciation, including the role of chromosomal inversions in these processes. Chromosomal inversions have also been identified in other species of Littorina providing a valuable opportunity for investigating their origin and evolution. Here, we present a new chromosome-scale reference genome of L. saxatilis generated from long reads and HiC chromatin proximity mapping replacing an earlier highly fragmented genome. This will enable detailed investigations of how inversions contribute to adaptation and reproductive isolation in L. saxatilis and related taxa, including studies of the effects of individual loci within and outside inversions.

genomics↗