Publications by year
In Press
Hayward A, Baril T (In Press). A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience
Baril T, Imrie RM, Hayward A (In Press). Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline.
Abstract:
Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline
ABSTRACTBackgroundTransposable elements (TEs) are found in nearly all eukaryotic genomes and are implicated in a range of evolutionary processes. Despite considerable research attention on TEs, their annotation and characterisation remain challenging, particularly for non-specialists. Current methods of automated TE annotation are subject to several issues that can reduce their overall quality: (i) fragmented and overlapping TE annotations may lead to erroneous estimates of TE count and coverage; (ii) repeat models may represent small proportions of their total length, where 5’ and 3’ regions are poorly captured; (iii) resultant libraries may contain redundancy, with the same TE family represented more than once. Existing pipelines can also be challenging to install, run, and extract data from. To address these issues, we present Earl Grey: a fully automated transposable element annotation pipeline designed for the user-friendly curation and annotation of TEs in eukaryotic genome assemblies.ResultsUsing a simulated genome, three model genome assemblies, and three non-model genome assemblies, Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above by producing longer TE consensus sequences in non-redundant TE libraries, which are then used to produce less fragmented TE annotations without the presence of overlaps. Earl Grey scores highly in benchmarking for TE annotation (MCC: 0.99) and classification (97% correctly classified) in comparison to existing software.ConclusionsEarl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focussed on further quality control aspects and tailored analyses in future releases.
Abstract.
Baril T, Imrie RM, Hayward A (In Press). Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline.
Abstract:
Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline
Abstract
. Background
Transposable elements (TEs) are found in nearly all eukaryotic genomes and are implicated in a range of evolutionary processes. Despite considerable research attention on TEs, their annotation and characterisation remain challenging, particularly for non-specialists. Current methods of automated TE annotation are subject to several issues that can reduce their overall quality: (i) fragmented and overlapping TE annotations may lead to erroneous estimates of TE count and coverage; (ii) repeat models may represent small proportions of their total length, where 5’ and 3’ regions are poorly captured; (iii) resultant libraries may contain redundancy, with the same TE family represented more than once. Existing pipelines can also be challenging to install, run, and extract data from. To address these issues, we present Earl Grey: a fully automated transposable element annotation pipeline designed for the user-friendly curation and annotation of TEs in eukaryotic genome assemblies.
Results
Using a simulated genome, three model genome assemblies, and three non-model genome assemblies, Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above by producing longer TE consensus sequences in non-redundant TE libraries, which are then used to produce less fragmented TE annotations without the presence of overlaps. Earl Grey scores highly in benchmarking for TE annotation (MCC: 0.99) and classification (97% correctly classified) in comparison to existing software.
Conclusions
Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focussed on further quality control aspects and tailored analyses in future releases.
Abstract.
Baril T, Hayward A (In Press). Migrators Within Migrators: Exploring Transposable Element Dynamics in the Monarch Butterfly, <i>Danaus plexippus</i>.
Abstract:
Migrators Within Migrators: Exploring Transposable Element Dynamics in the Monarch Butterfly, Danaus plexippus
AbstractBackgroundLepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome.ResultsWe find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1- 2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes.ConclusionsWe provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.
Abstract.
Baril T, Hayward A (In Press). Migrators Within Migrators: Exploring Transposable Element Dynamics in the Monarch Butterfly, Danaus plexippus.
Mobile DNAAbstract:
Migrators Within Migrators: Exploring Transposable Element Dynamics in the Monarch Butterfly, Danaus plexippus
Background
Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome.
Results
We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1- 2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes.
Conclusions
We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.
Abstract.
Qu Z, Nong W, So WL, Barton-Owen T, Li Y, Li C, Leung TCN, Baril T, Wong AYP, Swale T, et al (In Press). Millipede genomes reveal unique adaptation of genes and microRNAs during myriapod evolution.
Abstract:
Millipede genomes reveal unique adaptation of genes and microRNAs during myriapod evolution
AbstractThe Myriapoda including millipedes and centipedes is of major importance in terrestrial ecology and nutrient recycling. Here, we sequenced and assembled two chromosomal-scale genomes of millipedes Helicorthomorpha holstii (182 Mb, N50 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (449 Mb, N50 26.78 Mb mainly on 15 pseudomolecules). Unique defense systems, genomic features, and patterns of gene regulation in millipedes, not observed in other arthropods, are revealed. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules in centipedes. Sets of genes associated with anti-microbial activity are identified with proteomics, suggesting that the ozadene gland is not primarily an antipredator adaptation (at least in T. corallinus). Macro-synteny analyses revealed highly conserved genomic blocks between centipede and the two millipedes. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute proteins for loading small RNAs are duplicated in both millipedes, but unlike insects, an argonaute duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs, including species-specific microRNA arm switching that provide differential gene regulation is also obtained. Millipede genomes reveal a series of unique genomic adaptations and microRNA regulation mechanisms have occurred in this major lineage of arthropod diversity. Collectively, the two millipede genomes shed new light on this fascinating but poorly understood branch of life, with a highly unusual body plan and novel adaptations to their environment.
Abstract.
2022
Doyle T, Jimenez-Guri E, Hawkes WLS, Massy R, Mantica F, Permanyer J, Cozzuto L, Hermoso Pulido T, Baril T, Hayward A, et al (2022). Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration.
Mol EcolAbstract:
Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration.
Insects are capable of extraordinary feats of long-distance movement that have profound impacts on the function of terrestrial ecosystems. The ability to undertake these movements arose multiple times through the evolution of a suite of traits that make up the migratory syndrome, however the underlying genetic pathways involved remain poorly understood. Migratory hoverflies (Diptera: Syrphidae) are an emerging model group for studies of migration. They undertake seasonal movements in huge numbers across large parts of the globe and are important pollinators, biological control agents and decomposers. Here, we assembled a high-quality draft genome of the marmalade hoverfly (Episyrphus balteatus). We leveraged this genomic resource to undertake a genome-wide transcriptomic comparison of actively migrating Episyrphus, captured from a high mountain pass as they flew south to overwinter, with the transcriptomes of summer forms which were non-migratory. We identified 1543 genes with very strong evidence for differential expression. Interrogation of this gene set reveals a remarkable range of roles in metabolism, muscle structure and function, hormonal regulation, immunity, stress resistance, flight and feeding behaviour, longevity, reproductive diapause and sensory perception. These features of the migrant phenotype have arisen by the integration and modification of pathways such as insulin signalling for diapause and longevity, JAK/SAT for immunity, and those leading to octopamine production and fuelling to boost flight capabilities. Our results provide a powerful genomic resource for future research, and paint a comprehensive picture of global expression changes in an actively migrating insect, identifying key genomic components involved in this important life-history strategy.
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Author URL.
Mackintosh A, Laetsch DR, Baril T, Foster RG, Dincă V, Vila R, Hayward A, Lohse K (2022). The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome.
G3 (Bethesda),
12(6).
Abstract:
The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome.
The lesser marbled fritillary, Brenthis ino (Rottemburg, 1775), is a species of Palearctic butterfly. Male Brenthis ino individuals have been reported to have between 12 and 14 pairs of chromosomes, a much-reduced chromosome number than is typical in butterflies. Here, we present a chromosome-level genome assembly for Brenthis ino, as well as gene and transposable element annotations. The assembly is 411.8 Mb in length with a contig N50 of 9.6 Mb and a scaffold N50 of 29.5 Mb. We also show evidence that the male individual from which we generated HiC data was heterozygous for a neo-Z chromosome, consistent with inheriting 14 chromosomes from one parent and 13 from the other. This genome assembly will be a valuable resource for studying chromosome evolution in Lepidoptera, as well as for comparative and population genomics more generally.
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Author URL.
Mackintosh A, Laetsch DR, Baril T, Ebdon S, Jay P, Vila R, Hayward A, Lohse K (2022). The genome sequence of the scarce swallowtail, Iphiclides podalirius.
G3 (Bethesda)Abstract:
The genome sequence of the scarce swallowtail, Iphiclides podalirius.
The scarce swallowtail, Iphiclides podalirius (Linnaeus, 1758), is a species of butterfly in the family Papilionidae. Here we present a chromosome-level genome assembly for I. podalirius as well as gene and transposable element annotations. We investigate how the density of genomic features differ between the 30 I. podalirius chromosomes. We find that shorter chromosomes have higher heterozygosity at fourfold-degenerate sites and a greater density of transposable elements. While the first result is an expected consequence of differences in recombination rate, the second suggests a counter-intuitive relationship between recombination and transposable element evolution. This high quality genome assembly, the first for any species in the tribe Leptocircini, will be a valuable resource for population genomics in the genus Iphiclides and comparative genomics more generally.
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Author URL.
2021
Dupeyron M, Baril T, Hayward A (2021). Broadscale evolutionary analysis of eukaryotic DDE transposons.
Nong W, Qu Z, Li Y, Barton-Owen T, Wong AYP, Yip HY, Lee HT, Narayana S, Baril T, Swale T, et al (2021). Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication.
Commun Biol,
4(1).
Abstract:
Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication.
Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.
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Author URL.
Hayward A, Vila R, Laetsch DR, Lohse K, Baril T (2021). The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775).
Wellcome Open Research,
6, 304-304.
Abstract:
The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775)
We present a genome assembly from an individual female Melitaea athalia (also known as Mellicta athalia; the heath fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 610 megabases in span. In total, 99.98% of the assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 12,824 protein coding genes.
Abstract.
Mackintosh A, Laetsch DR, Baril T, Foster R, Dincă V, Vila R, Hayward A, Lohse K (2021). The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome.
2020
Nong W, Law STS, Wong AYP, Baril T, Swale T, Chu LM, Hayward A, Lau DTW, Hui JHL (2020). Chromosomal-level reference genome of the incense tree Aquilaria sinensis.
Nong W, Law STS, Wong AYP, Baril T, Swale T, Chu LM, Hayward A, Lau DTW, Hui JHL (2020). Chromosomal‐level reference genome of the incense tree. <i>Aquilaria sinensis</i>. Molecular Ecology Resources, 20(4), 971-979.
Qu Z, Nong W, Yu Y, Baril T, Yip HY, Hayward A, Hui JHL (2020). Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae).
BMC Genomics,
21(1).
Abstract:
Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)
Background: Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae. Results: We sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07–10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs. Conclusions: the four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish.
Abstract.
Qu Z, Nong W, So WL, Barton-Owen T, Li Y, Leung TCN, Li C, Baril T, Wong AYP, Swale T, et al (2020). Millipede genomes reveal unique adaptations during myriapod evolution.
PLoS Biol,
18(9).
Abstract:
Millipede genomes reveal unique adaptations during myriapod evolution.
The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs-including species-specific microRNA arm switching-providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes-and in particular the reconstruction of the myriapod ancestral situation-for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely.
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Author URL.
Dupeyron M, Baril T, Bass C, Hayward A (2020). Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements.
Mob DNA,
11Abstract:
Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements.
BACKGROUND: Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the Tc1/mariner superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on Tc1/mariner elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of Tc1/mariner TEs by performing analyses that consider elements that originate from across host diversity. RESULTS: We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. A total of 5158 Tc1/mariner elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of Tc1/mariner elements. In particular, we identify a new family of plant-genome restricted Tc1/mariner elements, which we call PlantMar. We also show that the pogo family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily. CONCLUSIONS: Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. Tc1/mariner TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for Tc1/mariner elements (except the PlantMar family). Meanwhile, the pogo family, which is by far the largest Tc1/mariner family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of pogo elements in vertebrates, including humans, in addition to the well-known example of CENP-B. Collectively, our findings provide a considerable advancement in understanding of Tc1/mariner elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.
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Author URL.
Li Y, Nong W, Baril T, Yip HY, Swale T, Hayward A, Ferrier DEK, Hui JHL (2020). Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome.
BMC Genomics,
21(1).
Abstract:
Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome
Background: Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. Results: Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~ 758 Mb, scaffold N50 = 72.3 Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al. (Mol Ecol Resources, 2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. Conclusions: the analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.
Abstract.