The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773)

Boyes, Douglas; Crowley, Liam M.; Lab, Wytham Woods Genome Acquisition

doi:10.12688/wellcomeopenres.17349.1

Cited by 10 publications

(8 citation statements)

References 17 publications

(5 reference statements)

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“…To evaluate Verkko on a highly heterozygous sample, we chose the Darwin Tree of Life insect genome Harmonia axyridis 40 (Data availability). Since Verkko outputs phased unitigs, we compared its output to fully phased equivalents from other assemblers.…”

Section: Resultsmentioning

confidence: 99%

Verkko: telomere-to-telomere assembly of diploid chromosomes

Rautiainen

Nurk

Walenz

et al. 2022

Preprint

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The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high-resolution assembly graph built from long, accurate PacBio HiFi reads. We have improved and automated this strategy in Verkko, an iterative, graph-based pipeline for assembling complete, diploid genomes. Verkko begins with a multiplex de Bruijn graph built from long, accurate reads and progressively simplifies this graph via the integration of ultra-long reads and haplotype-specific markers. The result is a phased, diploid assembly of both haplotypes, with many chromosomes automatically assembled from telomere to telomere. Running Verkko on the HG002 human genome resulted in 20 of 46 diploid chromosomes assembled without gaps at 99.9997% accuracy. The complete assembly of diploid genomes is a critical step towards the construction of comprehensive pangenome databases and chromosome-scale comparative genomics.

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Section: Resultsmentioning

confidence: 99%

Verkko: telomere-to-telomere assembly of diploid chromosomes

Rautiainen

Nurk

Walenz

et al. 2022

Preprint

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“…Our PSMC analyses of historical variation in effective population sizes using high quality H. axyridis whole genomes, one being representative of its native range in China [ 43 ] and another its non-native range in Europe [ 44 ], indicated (1) signatures of a large progressive, historical bottleneck in the common ancestors of both populations, (2) commensurating in similar bottlenecked populations around 10,000 ybp, (3) smaller effective sizes of the non-native population through time (~ 50,000; 100,000 ybp) compared to the native population (~ 75,000; 100,000 ybp), and (4) more “recent” coalescence of the European H. axyridis genome compared to the Chinese H. axyridis genome (Fig. 4 c).…”

Section: Resultsmentioning

confidence: 99%

“…Another supposition is that there was a gene exchange between ladybird populations from which our samples were collected and those introduced populations. Comparative analyses of historical effective population sizes using two whole genomes [ 43 , 44 ] also indicate a large historical bottleneck event in the pre-establishment past of both native and non-native H. axyridis , along the timelines of the last glacial maximum (100,000 ybp–10,000 ybp). Similar declines with glacial recession have been reported in other insects, such as the scarce heath, Coenonympha hero [ 51 ], and the darkling beetle, Nyctelia confusa [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

“…We inferred historical variation in effective population sizes of H. axyridis in its native range China versus in its non-native range Europe using two published resequenced whole genomes (Accession ID: SRR1348220, Beijing Academy of Agriculture and Forestry Sciences; Accession ID: ERR6054990, Wytham Woods, Oxfordshire, UK) [ 43 , 44 ]. Briefly, we utilized the consensus reference genome to construct whole genome alignments using Bwa-mem2 v.2.0 [ 43 , 101 ] and then sorted and constructed a consensus sequence using Samtools v.1.16.1 [ 88 ].…”

Section: Methodsmentioning

confidence: 99%

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Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird

Yan

Wang

et al. 2023

BMC Biol

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Background The harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae), native to Asia, has been introduced to other major continents where it has caused serious negative impacts on local biodiversity. Though notable advances to understand its invasion success have been made during the past decade, especially with then newer molecular tools, the conclusions reached remain to be confirmed with more advanced genomic analyses and especially using more samples from larger geographical regions across the native range. Furthermore, although H. axyridis is one of the best studied invasive insect species with respect to life history traits (often comparing invasive and native populations), the traits responsible for its colonization success in non-native areas warrant more research. Results Our analyses of genome-wide nuclear population structure indicated that an eastern Chinese population could be the source of all non-native populations and revealed several putatively adaptive candidate genomic loci involved in body color variation, visual perception, and hemolymph synthesis. Our estimates of evolutionary history indicate (1) asymmetric migration with varying population sizes across its native and non-native range, (2) a recent admixture between eastern Chinese and American populations in Europe, (3) signatures of a large progressive, historical bottleneck in the common ancestors of both populations and smaller effective sizes of the non-native population, and (4) the southwest origin and subsequent dispersal routes within its native range in China. In addition, we found that while two mitochondrial haplotypes-Hap1 and Hap2 were dominant in the native range, Hap1 was the only dominant haplotype in the non-native range. Our laboratory observations in both China and USA found statistical yet slight differences between Hap1 and Hap2 in some of life history traits. Conclusions Our study on H. axyridis provides new insights into its invasion processes into other major continents from its native Asian range, reconstructs a geographic range evolution across its native region China, and tentatively suggests that its invasiveness may differ between mitochondrial haplotypes.

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“…We selected genomes of 11 ladybird beetle (Coccinellidae) species ( Adalia bipunctata (Wellcome Sanger Institute Tree of Life programme, et al 2022), Coccinella septempunctata (Crowley, et al 2021), Cryptolaemus montrouzieri (Li, Huang, et al 2021), Cynegetis impunctata (our unpublished data, NCBI accession: GCA_030704885.1), Halyzia sedecimguttata (Crowley, et al 2023), Harmonia axyridis (Boyes, et al 2021), Henosepilachna vigintioctomaculata (Zhu, et al 2023), Henosepilachna vigintioctopunctata (our unpublished data, NCBI accession: GCA_030704895.1), Micraspis discolor (our unpublished data, NCBI accession: GCA_030674115.1), Novius pumilus (Tang, et al 2022) and Propylea japonica (Zhang, et al 2020)), and one Coccinelloidea outgroup Dastarcus helophoroides (Zhang, et al 2023), as reference species (Table S1). The genomes were downloaded from the NCBI Genome database.…”

Section: Methodsmentioning

confidence: 99%

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

Huang,

Sun,

et al. 2024

Preprint

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The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, traditional methods typically involve intricate and time-consuming procedures prior to core analyses. These procedures encompass assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive datasets. In this study, we present PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as reference for phylogenetic and evolutionary analyses. Through testing with both simulated and authentic datasets, PhyloAln demonstrates consistently robust performance in terms of alignment completeness and identity when compared to other reference-based tools. Additionally, we validate the tool's adeptness in managing foreign and cross-contamination issues prevalent in sequencing data, which are often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments and reconstructing phylogenies from transcriptomes of ladybird beetles, plastid genes of peppers, and ultraconserved elements of turtles. These results underscore the versatility of our tool. Leveraging these advantages, PhyloAln stands poised to expedite phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.

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The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773)

Cited by 10 publications

References 17 publications

Verkko: telomere-to-telomere assembly of diploid chromosomes

Verkko: telomere-to-telomere assembly of diploid chromosomes

Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

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