Transcript- and annotation-guided genome assembly of the European starling

Stuart, Katarina C.; Edwards, Richard J.; Cheng, Yuanyuan; Wc, Warren; Burt, David W.; Sherwin, William B.; Nr, Hofmeister; Sj, Werner; Ball, Gregory F.; Bateson, Melissa; Mc, Brandley; Kl, Buchanan; Cassey, Phillip; Df, Clayton; Td, Meyer; Sl, Meddle; Rollins, Lee A.

doi:10.1101/2021.04.07.438753

Cited by 14 publications

(32 citation statements)

References 72 publications

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“…Completeness was evaluated by BUSCO (BUSCO, RRID:SCR_015008) v3.0.2b [29], implementing BLAST+ v2.2.31 [30], Hmmer (Hmmer, RRID:SCR_005305) v3.2.1 [31], Augustus (Augustus, RRID:SCR_008417) v3.3.2 [32] and EMBOSS (EMBOSS, RRID:SCR_008493) v6.6.0 [33]) against the embryophyta_odb9 dataset (n = 1,440; Table S1). BUSCO results were collated using BUSCOMP (BUSCO Compilation and Comparison Tool; RRID:SCR_021233) v0.11.0 [34] to better evaluate the gains and losses in completeness between different assembly stages (Figure 3, Additional file 1).…”

Section: Assembly Completeness and Accuracymentioning

confidence: 99%

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

Rossetto

et al. 2021

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Background: Telopea speciosissima, the New South Wales waratah, is Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Findings: Here, we report the first chromosome-level reference genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 91.2 % of Embryophyta BUSCOs complete. We introduce a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering assembly scaffolds. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single copy orthologues and find that the assembly is 93.9 % of the estimated genome size. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. Our results indicate that the waratah genome is highly repetitive, with a repeat content of 62.3 %. Conclusions: The T. speciosissima genome (Tspe_v1) will accelerate waratah evolutionary genomics and facilitate marker assisted approaches for breeding. Broadly, it represents an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

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Section: Assembly Completeness and Accuracymentioning

confidence: 99%

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

Rossetto

et al. 2021

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“…We used the process_radtags function to clean the tags; discarding reads of low quality (-q), removing reads with uncalled bases (-c), and rescuing barcodes and radtags (-r). We used the Burrows-Wheeler aligner (BWA) v0.7.15 (Li & Durbin 2009) aln function to align the read data to the reference genome S. vulgaris vAU1.0 (Stuart et al 2021b). Using FastQC, we identified base sequence bias in the adapter region, and so the first five base sequences were trimmed (-B 5) during alignment.…”

Section: Sequencing and Genome Variant Callingmentioning

confidence: 99%

“…We analysed these five groups of SNPs for their functional roles and the nature of the mutation. We completed SNP analyses primarily using VARIANT EFFECT PREDICTOR (VEP) (McLaren et al 2016), using the genome annotation version released alongside the S. vulgaris vAU1.0 assembly (Stuart et al 2021b) to examine the functional consequences of the SNPs (processed to exclude multiple isoforms using AGAT agat_sp_keep_longest_isoform.pl (Dainat 2020)). We used BEDTOOLS and the AGAT function agat_sp_functional_statistics to extract genes and transcripts that overlapped the putative loci under selection, and extract gene ontology (GO) terms.…”

Section: Variant Analysis and Annotationmentioning

confidence: 99%

“…The sequencing failure rate of this study is comparable to another study using similarly aged museum skins (Ewart et al 2019), suggesting that future projects seeking to use museum samples might expect similar failure rates (30-40%) and adjust their sampling design accordingly. Finally, similar analyses may be conducted between the historic UK and the well-studied contemporary North American starlings (as this population has a similar introduction time, range size, and environmental variation: Bodt et al 2020;Hofmeister et al 2021b), and then further extended upon through comparisons to other invasive populations in New Zealand, South Africa, and South America.…”

Section: Future Directionsmentioning

confidence: 99%

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Using historical museum samples to examine divergent and parallel evolution in the invasive starling

Stuart

Sherwin

Austin

et al. 2021

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During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in north-western Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants (e.g. TCDD) and food carbohydrate content. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.

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“…For each snake, raw 10x linked-reads were assembled using Supernova v2.0.0 (10x Genomics) using default settings. Additional cleanup of the pseudohap2 output was performed as described in [24] to generate a non-redundant primary and alternative assembly for each species. In each case, the primary assembly contains the longest of each pair of phased haplotigs.…”

Section: Genome Assembly Of Terrestrial Elapidsmentioning

confidence: 99%

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

Edwards

et al. 2021

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Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they can be exapted as coding and regulatory elements, or can promote genetic rearrangement. In so doing TEs act as a source of genetic novelty, hence understanding TE evolution within lineages is key in understanding adaptation to their environment. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. The few broad scale studies in Squamata which have been conducted found both the diversity and total number of TEs differs significantly across the entire order. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if this pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~15-25 Mya and have since rapidly diversified into 6 amphibious, ~60 marine and ~100 terrestrial species which fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three transferred into the ancestral hydrophiine likely from marine species. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.

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Transcript- and annotation-guided genome assembly of the European starling

Cited by 14 publications

References 72 publications

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

Using historical museum samples to examine divergent and parallel evolution in the invasive starling

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

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