Chromosome‐scale Genome Assembly and Population Genomics Provide Insights into the Adaptation, Domestication, and Flavonoid Metabolism of Chinese Plum

Abstract Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.

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A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Diversity ◽

10.3390/d11090144 ◽

2019 ◽

Vol 11 (9) ◽

pp. 144 ◽

Cited By ~ 4

Author(s):

Laís Coelho ◽

Lukas Musher ◽

Joel Cracraft

Keyword(s):

Genome Assembly ◽

High Throughput Sequencing ◽

Population Genomics ◽

De Novo ◽

Structural Difference ◽

Whole Genome ◽

Sequencing Technology ◽

A Genome ◽

Avian Genomes ◽

Chromosome Level

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2023801118 ◽

2021 ◽

Vol 118 (37) ◽

pp. e2023801118

Author(s):

Jae Young Choi ◽

Xiaoguang Dai ◽

Ornob Alam ◽

Julie Z. Peng ◽

Priyesh Rughani ◽

...

Keyword(s):

Genome Assembly ◽

Adaptive Radiation ◽

Evolutionary Biology ◽

Population Genomics ◽

Hawaiian Islands ◽

Divergent Selection ◽

Metrosideros Polymorpha ◽

Nucleotide Polymorphisms ◽

Founder Populations ◽

Adaptive Radiations

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.

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A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia Illucens L.)

10.1101/2020.11.13.381889 ◽

2020 ◽

Author(s):

Tomas N. Generalovic ◽

Shane A. McCarthy ◽

Ian A. Warren ◽

Jonathan M.D. Wood ◽

James Torrance ◽

...

Keyword(s):

Genome Assembly ◽

Population Genomics ◽

Animal Feed ◽

Repetitive Sequences ◽

Genomic Variation ◽

Reference Sequence ◽

Runs Of Homozygosity ◽

High Quality ◽

Black Soldier Fly ◽

Hermetia Illucens

AbstractBackgroundHermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important mass reared entomological resource for bioconversion of organic material into animal feed.ResultsWe generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudo-chromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 17,664 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and the identification of an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This revealed a plethora of inbreeding events including recent long runs of homozygosity on chromosome five.ConclusionsRelease of this novel chromosome-scale BSF genome assembly will provide an improved platform for further genomic studies and functional characterisation of candidate regions of artificial selection. This reference sequence will provide an essential tool for future genetic modifications, functional and population genomics.

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A draft genome assembly for the eastern fox squirrel, Sciurus niger

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab315 ◽

2021 ◽

Author(s):

Lin Kang ◽

Pawel Michalak ◽

Eric Hallerman ◽

Nancy D Moncrief

Keyword(s):

Genome Assembly ◽

Population Genomics ◽

Coat Color ◽

Genome Structure ◽

Draft Genome ◽

Predicted Amino Acid Sequence ◽

Sciurus Niger ◽

Sequence Alignments ◽

A Genome ◽

Fox Squirrel

Abstract The eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2.99 Gb, containing 32,830 scaffolds with an average size of 90.9 Kb and N50 of 183.8 Kb. Genome completeness was estimated to be 93.78%. A total of 24,443 protein-encoding genes were predicted from the assembly and 23,079 (94.42%) were annotated. Repeat elements comprised an estimated 38.49% of the genome, with the majority being LINEs (13.92%), SINEs (6.04%), and LTR elements. The topology of the species tree reconstructed using maximum-likelihood phylogenetic analysis was congruent with those of previous studies. This genome assembly can prove useful for comparative studies of genome structure and function in this rapidly diversifying lineage of mammals, for studies of population genomics and adaptation, and for biomedical research. Predicted amino acid sequence alignments for genes affecting heme biosynthesis, color vision, and hibernation showed point mutations and indels that may affect protein function and ecological adaptation.

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A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing

10.1101/499954 ◽

2018 ◽

Author(s):

Sarah B. Kingan ◽

Haynes Heaton ◽

Juliana Cudini ◽

Christine C. Lambert ◽

Primo Baybayan ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Population Genomics ◽

De Novo ◽

Anopheles Coluzzii ◽

High Quality ◽

De Novo Genome Assembly ◽

Core Technology ◽

Conserved Genes ◽

Diploid Individual

AbstractA high-quality reference genome is a fundamental resource for functional genetics, comparative genomics, and population genomics, and is increasingly important for conservation biology. PacBio Single Molecule, Real-Time (SMRT) sequencing generates long reads with uniform coverage and high consensus accuracy, making it a powerful technology for de novo genome assembly. Improvements in throughput and concomitant reductions in cost have made PacBio an attractive core technology for many large genome initiatives, however, relatively high DNA input requirements (∼5 µg for standard library protocol) have placed PacBio out of reach for many projects on small organisms that have lower DNA content, or on projects with limited input DNA for other reasons. Here we present a high-quality de novo genome assembly from a single Anopheles coluzzii mosquito. A modified SMRTbell library construction protocol without DNA shearing and size selection was used to generate a SMRTbell library from just 100 ng of starting genomic DNA. The sample was run on the Sequel System with chemistry 3.0 and software v6.0, generating, on average, 25 Gb of sequence per SMRT Cell with 20 hour movies, followed by diploid de novo genome assembly with FALCON-Unzip. The resulting curated assembly had high contiguity (contig N50 3.5 Mb) and completeness (more than 98% of conserved genes are present and full-length). In addition, this single-insect assembly now places 667 (>90%) of formerly unplaced genes into their appropriate chromosomal contexts in the AgamP4 PEST reference. We were also able to resolve maternal and paternal haplotypes for over 1/3 of the genome. By sequencing and assembling material from a single diploid individual, only two haplotypes are present, simplifying the assembly process compared to samples from multiple pooled individuals. The method presented here can be applied to samples with starting DNA amounts as low as 100 ng per 1 Gb genome size. This new low-input approach puts PacBio-based assemblies in reach for small highly heterozygous organisms that comprise much of the diversity of life.

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Population genomics of North American northern pike: variation and sex-specific signals from a chromosome-level, long read genome assembly

10.1101/2020.06.18.157701 ◽

2020 ◽

Author(s):

Hollie A Johnson ◽

Eric B Rondeau ◽

David R Minkley ◽

Jong S Leong ◽

Joanne Whitehead ◽

...

Keyword(s):

Genome Assembly ◽

North American ◽

Population Genomics ◽

Northern Pike ◽

Ice Age ◽

River Drainage ◽

Yukon River ◽

Long Read ◽

Tajima’S D ◽

Chromosome Level

AbstractWe present a chromosome-level, long-read genome assembly as a reference for northern pike (Esox lucius) where 97.5% of the genome is chromosome-anchored and N50 falls at 37.5 Mb. Whole-genome resequencing was genotyped using this assembly for 47 northern pike representing six North American populations from Alaska to New Jersey. We discovered that a disproportionate frequency of genetic polymorphism exists among populations east and west of the North American Continental Divide (NACD), indicating reproductive isolation across this barrier. Genome-wide analysis of heterozygous SNP density revealed a remarkable lack of genetic variation with 1 polymorphic site every 6.3kb in the Yukon River drainage and one every 16.5kb east of the NACD. Observed heterozygosity (Ho), nucleotide diversity (π), and Tajima’s D are depressed in populations east of the NACD (east vs. west: Ho: 0.092 vs 0.31; π: 0.092 vs 0.28; Tajima’s D: -1.61 vs -0.47). We confirm the presence of the master sex determining (MSD) gene, amhby, in the Yukon River drainage and in an invasive population in British Columbia and confirm its absence in populations east of the NACD. We also describe an Alaskan population where amhby is present but not associated with male gender determination. Our results support that northern pike originally colonized North America through Beringia, that Alaska provided an unglaciated refugium for northern pike during the last ice age, and southeast of the NACD was colonized by a small founding population(s) that lost amhby.

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A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

Genes ◽

10.3390/genes10010062 ◽

2019 ◽

Vol 10 (1) ◽

pp. 62 ◽

Cited By ~ 49

Author(s):

Sarah Kingan ◽

Haynes Heaton ◽

Juliana Cudini ◽

Christine Lambert ◽

Primo Baybayan ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Population Genomics ◽

De Novo ◽

Anopheles Coluzzii ◽

High Quality ◽

De Novo Genome Assembly ◽

Core Technology ◽

Conserved Genes ◽

Diploid Individual

A high-quality reference genome is a fundamental resource for functional genetics, comparative genomics, and population genomics, and is increasingly important for conservation biology. PacBio Single Molecule, Real-Time (SMRT) sequencing generates long reads with uniform coverage and high consensus accuracy, making it a powerful technology for de novo genome assembly. Improvements in throughput and concomitant reductions in cost have made PacBio an attractive core technology for many large genome initiatives, however, relatively high DNA input requirements (~5 µg for standard library protocol) have placed PacBio out of reach for many projects on small organisms that have lower DNA content, or on projects with limited input DNA for other reasons. Here we present a high-quality de novo genome assembly from a single Anopheles coluzzii mosquito. A modified SMRTbell library construction protocol without DNA shearing and size selection was used to generate a SMRTbell library from just 100 ng of starting genomic DNA. The sample was run on the Sequel System with chemistry 3.0 and software v6.0, generating, on average, 25 Gb of sequence per SMRT Cell with 20 h movies, followed by diploid de novo genome assembly with FALCON-Unzip. The resulting curated assembly had high contiguity (contig N50 3.5 Mb) and completeness (more than 98% of conserved genes were present and full-length). In addition, this single-insect assembly now places 667 (>90%) of formerly unplaced genes into their appropriate chromosomal contexts in the AgamP4 PEST reference. We were also able to resolve maternal and paternal haplotypes for over 1/3 of the genome. By sequencing and assembling material from a single diploid individual, only two haplotypes were present, simplifying the assembly process compared to samples from multiple pooled individuals. The method presented here can be applied to samples with starting DNA amounts as low as 100 ng per 1 Gb genome size. This new low-input approach puts PacBio-based assemblies in reach for small highly heterozygous organisms that comprise much of the diversity of life.

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A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum (Hausmann) (Hemiptera: Aphididae)

10.1101/2020.05.29.121947 ◽

2020 ◽

Author(s):

Roberto Biello ◽

Archana Singh ◽

Cindayniah J. Godfrey ◽

Felicidad Fernández Fernández ◽

Sam T. Mugford ◽

...

Keyword(s):

Genome Assembly ◽

Population Genomics ◽

Sister Group ◽

Single Copy ◽

Phylogenomic Analysis ◽

Plant Interactions ◽

Eriosoma Lanigerum ◽

Woolly Apple Aphid ◽

Chromosome Level

ABSTRACTWoolly apple aphid (WAA, Eriosoma lanigerum Hausmann) (Hemiptera: Aphididae), is a major pest of apple trees (Malus domestica, order Rosales) and is critical to the economics of the apple industry in most parts of the world. Here, we generated a chromosome-level genome assembly of WAA – representing the first genome sequence from the aphid subfamily Eriosomatinae – using a combination of 10X Genomics linked-reads and in vivo Hi-C data. The final genome assembly is 327 Mb, with 91% of the assembled sequences anchored into six chromosomes. The contig and scaffold N50 values are 158 kb and 71 Mb, respectively, and we predicted a total of 28,186 protein-coding genes. The assembly is highly complete, including 97% of conserved arthropod single-copy orthologues based on BUSCO analysis. Phylogenomic analysis of WAA and nine previously published aphid genomes, spanning four aphid tribes and three subfamilies, reveals that the tribe Eriosomatini (represented by WAA) is recovered as a sister group to Aphidini + Macrosiphini (subfamily Aphidinae). We identified syntenic blocks of genes between our WAA assembly and the genomes of other aphid species and find that two WAA chromosomes (El5 and El6) map to the conserved Macrosiphini and Aphidini X chromosome. Our high-quality WAA genome assembly and annotation provides a valuable resource for research in a broad range of areas such as comparative and population genomics, insect-plant interactions and pest resistance management.

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The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome

10.1101/2021.12.16.472906 ◽

2021 ◽

Author(s):

Alexander Mackintosh ◽

Dominik Laetsch ◽

Tobias Baril ◽

Robert Foster ◽

Vlad Dincă ◽

...

Keyword(s):

Chromosome Number ◽

Genome Assembly ◽

Chromosome Evolution ◽

Population Genomics ◽

The Other ◽

Z Chromosome ◽

Valuable Resource ◽

Male Individual ◽

Show Evidence ◽

Chromosome Level

The lesser marbled fritillary, Brenthis ino (Rottemburg, 1775), is a species of Palearctic butterfly. Male B. 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 B. ino, as well as gene and transposable element annotations. The assembly is 411.8 Mb in span with contig and scaffold N50s of 9.6 and 29.5 Mb respectively. 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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