Berard, S. | Search bioRxiv

bioRxiv2018

A bird’s white-eye shot: looking down on a new avian sex chromosome evolution

AO_SCPCAPBSTRACTC_SCPCAPChromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we took advantage of this unusual event to study the early stages of sex chromosome evolution. To do so, we sequenced a female (ZW) of two Sylvioidea species, a Zosterops borbonicus and a Z. pallidus. Then, we organized the Z. borbonicus scaffolds along chromosomes and annotated genes. Molecular phylogenetic dating under various methods and calibration sets confidently confirmed the recent diversification of the genus Zosterops (1-3.5 million years ago), thus representing one of the most exceptional rates of diversification among vertebrates. We then combined genomic coverage comparisons of five males and seven females, and homology with the zebra finch genome (Taeniopygia guttata) to identify sex chromosome scaffolds, as well as the candidate chromosome breakpoints for the two translocation events. We observed reduced levels of within-species diversity in both translocated regions and, as expected, even more so on the neoW chromosome. In order to compare the rates of molecular evolution in genomic regions of the autosomal-to-sex transitions, we then estimated the ratios of non-synonymous to synonymous polymorphisms ({pi}N/{pi}S) and substitutions (dN/dS). Based on both ratios, no or little contrast between autosomal and Z genes was observed, thus representing a very different outcome than the higher ratios observed at the neoW genes. In addition, we report significant changes in base composition content for translocated regions on the W and Z chromosomes and a large accumulation of transposable elements (TE) on the newly W region. Our results revealed contrasted signals of molecular evolution changes associated to these autosome-to-sex transitions, with congruent signals of a W chromosome degeneration yet a surprisingly weak support for a fast-Z effect.

evolutionary biology↗

bioRxiv2018

Leveraging evolutionary relationships to improve Anopheles genome assemblies

While new sequencing technologies have lowered financial barriers to whole genome sequencing, resulting assemblies are often fragmented and far from finished. Subsequent improvements towards chromosomal-level status can be achieved by both experimental and computational approaches. Requiring only annotated assemblies and gene orthology data, comparative genomics approaches that aim to capture evolutionary signals to predict scaffold neighbours (adjacencies) offer potentially substantive improvements without the costs associated with experimental scaffolding or re-sequencing. We leverage the combined detection power of three such gene synteny-based methods applied to 21 Anopheles mosquito assemblies with variable contiguity levels to produce consensus sets of scaffold adjacency predictions. Three complementary validations were performed on subsets of assemblies with additional supporting data: six with physical mapping data; 13 with paired-end RNA sequencing (RNAseq) data; and three with new assemblies based on re-scaffolding or incorporating Pacific Biosciences (PacBio) sequencing data. Improved assemblies were built by integrating the consensus adjacency predictions with supporting experimental data, resulting in 20 new reference assemblies with improved contiguities. Combined with physical mapping data for six anophelines, chromosomal positioning of scaffolds improved assembly anchoring by 47% for A. funestus and 38% A. stephensi. Reconciling an A. funestus PacBio assembly with synteny-based and RNAseq-based adjacencies and physical mapping data resulted in a new 81.5% chromosomally mapped reference assembly and cytogenetic photomap. While complementary experimental data are clearly key to achieving high-quality chromosomal-level assemblies, our assessments and validations of gene synteny-based computational methods highlight the utility of applying comparative genomics approaches to improve community genomic resources.

genomics↗