Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

Abstract

University 28 29 Correspondence 30 31 V.P. (valentina.peona@ebc.uu.se), A.S. (alexander.suh@ebc.uu.se) 32 33 Abstract 38 39 Genome assemblies are currently being produced at an impressive rate by consortia and individual 40 laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a 41 whole new world of genomic biodiversity. Although these technologies generate high-quality genome 42assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich 43 regions (genomic "dark matter"). In this study, we compare the efficiency of currently used 44 a non-model organism (paradise crow) for which only suboptimal samples are available. Our 51 approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and 52 several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most 53 organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for 54 downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness 55 of both the coding and non-coding parts of the genomes. 56 57 2005). It is key now for the genomics field to overcome these limitations and investigate this dark 70 matter. 71 72Repetitive elements represent an important and prevalent part of the genomic dark matter of many 73 genomes, given that their abundance and repetitive nature makes it difficult to fully and confidently 74 assemble their sequences. This is particularly problematic when the read length is significantly shorter 75 than the repetitive element, in which case it is impossible to anchor the reads to unique genomic 76 regions. To what extent repeats can hamper genome assemblies depends on whether they are 77 interspersed or arranged in tandem. Highly similar interspersed repeats, like for example transposable 78

Genome Report:De novogenome assembly and annotation for the Taita white-eye (Zosterops silvanus)

“…High BUSCO gene completeness has been found in most bird genomes (Peñalba et al 2019) even though noticeable variation can be apparent among different assembly techniques and sequencing technologies (Peñalba et al 2019, Peona et al 2019. We therefore expect our BUSCO values to further improve in future assembly versions.…”

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

“…We assume this phenomenon to reflect that the non-recombining region of the W, no matter how big or small, constantly accumulates large quantities of new TEs. It is important to note that, given the difficulties in assembling SLCs even with long-read sequencing technologies [8,23,24,33], the W chromosome models are likely to be less complete than the other chromosomes. We thus consider our W repeat annotations as well as indexes to be conservative estimates for the true repeat content.…”

“…For paradise crow, we used one 10X Genomics Chromium linked-read library of DNA from a pectoral muscle sample of a female from [23]. We also newly generated such data for three females and one male using the same methods [23] and generated RNA-seq library from female pectoral muscle (preserved in RNAlater).…”

“…For paradise crow, we used one 10X Genomics Chromium linked-read library of DNA from a pectoral muscle sample of a female from [23]. We also newly generated such data for three females and one male using the same methods [23] and generated RNA-seq library from female pectoral muscle (preserved in RNAlater). RNA was extracted with phenol-based phase separation using the TRIzol reagent (ThermoFisher Scientific) following the standard protocol recommended by the supplier, followed by DNase treatment for 30 min using the DNA-free DNA Removal kit (ThermoFisher Scientific).…”

“…Here we provide the first evidence that the avian W chromosome is not merely a graveyard of repetitive elements but a refugium of potentially active TEs that likely have sex-specific implications. Bird genomes are known to be repeat-poor with a mean TE content of <10% [19], but the first female assemblies based on short [20] or long reads [21][22][23] showed that the non-recombining W chromosome is >50% repetitive and especially rich in endogenous retroviruses (ERVs). By analysing reference-quality genomes of six species spanning the avian Tree of Life from both Paleognathae (emu with homomorphic sex chromosomes) and Neognathae (chicken, Anna's hummingbird, kakapo, paradise crow, zebra finch with heteromorphic sex chromosomes), we demonstrate that the avian W has generally accumulated ERVs and likely contains active ERVs as indicated by signatures of transcription and translation of W-linked ERVs.…”