A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

Nowell, Reuben W.; Elsworth, Benjamin; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher W.; Saastamoinen, Marjo; Saccheri, Ilik J.; Hof, Arjen E Van’t; Wasik, Bethany R.; Connahs, Heidi; Aslam, Muhammad; Kumar, Sujai; Challis, Richard; Monteiro, Antónia; Brakefield, Paul M.; Blaxter, Mark

doi:10.1093/gigascience/gix035

Cited by 58 publications

(59 citation statements)

References 46 publications

(42 reference statements)

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“…To investigate the Heliconius radiation, we aligned our highest quality de novo assemblies with representative Lepidoptera reference genomes 17,[24][25][26][27][28][29][30][31] (Supplementary Information Section 3). Previous work in Heliconius inferred a high level of phylogenetic discordance among genes, arguably a result of rampant introgression 6 , though this has been disputed 32 .…”

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confidence: 99%

Genomic architecture and introgression shape a butterfly radiation

Edelman

Frandsen

Miyagi

et al. 2018

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We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

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confidence: 99%

Genomic architecture and introgression shape a butterfly radiation

Edelman

Frandsen

Miyagi

et al. 2018

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“…BUSCO profile and N50 at the scaffold and contig level are overlaid. The high levels of duplication in the previous P. xylostella reference and the haplotype conserving assembly is apparent, as is the effect of merging haplotypes which produces a profile similar to previously sequenced Lepidoptera (11,30,(34)(35)(36)(37)(38)(39)(40). The erroneous collapse of real duplications would theoretically lead to a bimodal distribution for the deduplicated (green) genes, with one peak at approximately the same position as single copy genes (red) and an additional peak with two-fold higher coverage.…”

Section: Figure 4: Quality Comparison With Other Lepidopteran Genomesmentioning

confidence: 86%

Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)

Whiteford

Hof

Krishna

et al. 2019

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BackgroundRecent advances in genomics have addressed the challenge that divergent haplotypes pose to the reconstruction of haploid genomes. However for many organisms, the sequencing of either field-caught individuals or a pool of heterogeneous individuals is still the only practical option. Here we present methodological approaches to achieve three outcomes from pooled long read sequencing: the generation of a contiguous haploid reference sequence, the sequences of heterozygous haplotypes; and reconstructed genomic sequences of individuals related to the pooled material. Results PacBio long read sequencing, DovetailHi-C scaffolding and linkage map integration yielded a haploid chromosome-level assembly for the diamondback moth (Plutella xylostella), a global pest of Brassica crops, from a pool of related individuals. The final assembly consisted of 573 scaffolds, with a total assembly size of 343.6Mbp a scaffold N50 value of 11.3Mbp (limited by chromosome size) and a maximum scaffold size of 14.4Mbp. This assembly was then integrated with an existing RAD-seq linkage map, anchoring 95% of the assembled sequence to defined chromosomal positions. ConclusionsWe describe an approach to resolve divergent haplotype sequences and describe multiple validation approaches. We also reconstruct individual genomes from pooled long-reads, by applying a recently developed k-mer binning method.

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“…The 111 million retained read pairs were aligned to the most recent B. anynana genome assembly (v1.2)shiv with its corresponding annotation (Nowell et al 2017). This reference assembly is highly fragmented and composed of 10,800 scaffolds with an N50 of 638.3 Kb, a total assembly size of 475 Mb, and 22,642 annotated genes.…”

Section: Methodsmentioning

confidence: 99%

“…The current B. anynana reference assembly (Nowell et al , 2017) has an N50 of 638.3 kb and is composed of 10,800 unlinked scaffolds. To assess whether associated SNPs on separate B. anynana genome scaffolds could be part of the same block of association, we ordered the scaffolds of the B. anynana genome along the Heliconius melpomene v2 genome assembly (Davey et al 2016).…”

Section: Methodsmentioning

confidence: 99%

Multiple loci control eyespot number variation on the hindwings ofBicyclus anynanabutterflies

Rivera‐Colón

Westerman

Belleghem

et al. 2019

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27The underlying genetic changes that regulate the appearance and disappearance of 28 repeated traits, or serial homologs, remain poorly understood. One hypothesis is 29 that variation in genomic regions flanking master regulatory genes, also known as 30 input-output genes, controls variation in trait number, making the locus of 31 evolution almost predictable. Other hypotheses implicate genetic variation in up-32 stream or downstream loci of master control genes. Here, we use the butterfly 33Bicyclus anynana, a species which exhibits natural variation in eyespot number 34 on the dorsal hindwing, to test these two hypotheses. We first estimated the 35 heritability of dorsal hindwing eyespot number by breeding multiple butterfly 36 families differing in eyespot number, and regressing eyespot number of offspring 37 on mid-parent values. We then estimated the number and identity of independent 38 genetic loci contributing to eyespot number variation by performing a genome-39 wide association study with restriction site-associated DNA Sequencing (RAD-seq) 40 from multiple individuals varying in number of eyespots sampled across a freely 41 breeding lab population. We found that dorsal hindwing eyespot number has a 42 moderately high heritability of approximately 0.50. In addition, multiple loci near 43 previously identified genes involved in eyespot development display high 44 association with dorsal hindwing eyespot number, suggesting that homolog 45 number variation is likely determined by regulatory changes at multiple loci that 46 build the trait and not by variation at single master regulators or input-output 47 49 Body plans often evolve through changes in the number of repeated parts or serial 50 homologs by either addition or subtraction. For instance, the pelvic fins of 51 vertebrates are inferred to have originated by addition to a body plan displaying 52 only pectoral fins, perhaps via co-option of the pectoral or caudal fin 53 developmental programs to a novel location in the body (Ruvinsky and Gibson-54 Brown 2000; Larouche et al. 2017). In insects, the absence of limbs and wings in 55 the abdomen is inferred to be due to a process of subtraction, i.e. via the repression 56 or modification of limbs and wings in these segments by hox genes (Galant and 57 Carroll 2002; Ronshaugen et al. 2002; Tomoyasu et al. 2005; Ohde et al. 2013). 58 Regulatory targets of abdominal hox genes are likely to underlie loss of limb/wing 59 number in these body segments (Tomoyasu et al. 2005; Ohde et al. 2013), 60 although these mutations have not yet been identified. Thus, while serial homolog 61 number variation is a common feature in the evolution of organisms' body plans, 62 the underlying genetic changes that regulate the appearance and disappearance of 63 these repeated traits remain poorly understood. 64 65 Studies in Drosophila have contributed most to the identification of the genetic 66 basis underlying the evolution of serial homolog number. Larvae of different 67 species have different numbers of small hairs, or tr...

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A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

Cited by 58 publications

References 46 publications

Genomic architecture and introgression shape a butterfly radiation

Genomic architecture and introgression shape a butterfly radiation

Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)

Multiple loci control eyespot number variation on the hindwings ofBicyclus anynanabutterflies

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