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

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.

scholarly journals Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds

Chromosoma ◽  
2021 ◽  
Vol 130 (1) ◽  
pp. 15-25
Author(s):  
Phuong T. N. Hoang ◽  
Jean-Marie Rouillard ◽  
Jiří Macas ◽  
Ivona Kubalová ◽  
Veit Schubert ◽  
...  
Keyword(s):  
Growth Rate ◽  
Chromosome Number ◽  
Chromosome Evolution ◽  
Sequence Similarity ◽  
Flowering Plants ◽  
The Other ◽  
Probe Design ◽  
Congeneric Species ◽  
Specific Design ◽  
Spirodela Polyrhiza

AbstractDuckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.

scholarly journals Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution

2019 ◽  
Vol 5 (6) ◽  
pp. eaau3648 ◽  
Author(s):  
Jason Hill ◽  
Pasi Rastas ◽  
Emily A. Hornett ◽  
Ramprasad Neethiraj ◽  
Nathan Clark ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Evolution ◽  
Chromosome Structure ◽  
Holocentric Chromosomes ◽  
Chromosome Counts ◽  
Pieris Napi ◽  
Haploid Chromosome Number ◽  
Genome Wide ◽  
The Face ◽  
Chromosome Level

Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.

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

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 144 ◽  
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.

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

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.

scholarly journals A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Fanghao Wan ◽  
Chuanlin Yin ◽  
Rui Tang ◽  
Maohua Chen ◽  
Qiang Wu ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Genome Assembly ◽  
Association Studies ◽  
Receptor Gene ◽  
Cydia Pomonella ◽  
Codling Moth ◽  
Invasive Pest ◽  
Z Chromosome ◽  
Genome Wide Association Studies ◽  
Chromosome Level

Abstract The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion.

scholarly journals Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology

2021 ◽  
Vol 13 (4) ◽  
Author(s):  
María Recuerda ◽  
Joel Vizueta ◽  
Cristian Cuevas-Caballé ◽  
Guillermo Blanco ◽  
Julio Rozas ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Evolutionary Biology ◽  
Sequence Data ◽  
Single Copy ◽  
Valuable Resource ◽  
Structural Annotation ◽  
Data Set ◽  
Fringilla Coelebs ◽  
The Common ◽  
Chromosome Level

Abstract The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa, and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87-Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian data set. Around 7.8% of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.

scholarly journals Telomere to telomere genome assembly of Fusarium musae F31, causal agent of crown rot disease of banana.

2021 ◽  
Author(s):  
Luca Degradi ◽  
Valeria Tava ◽  
Andrea Kunova ◽  
Paolo Cortesi ◽  
Marco Saracchi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Species Complex ◽  
Crown Rot ◽  
Fusarium Fujikuroi ◽  
Valuable Resource ◽  
High Quality ◽  
Long Reads ◽  
Fusarium Fujikuroi Species Complex ◽  
Rot Disease ◽  
Chromosome Level

Fusarium musae van Hove causes crown rot of banana and it is also associated to clinical fusariosis. A chromosome-level genome assembly of Fusarium musae F31 obtained combining Nanopore long reads and Illumina paired end reads resulted in 12 chromosomes plus one contig with overall N50 of 4.36 Mb, and is presented together with its mitochondrial genome (58072 bp). F31 genome includes telomeric regions for 11 of the 12 chromosomes representing the most complete genome available in the Fusarium fujikuroi species complex. The high-quality assembly of the F31 genome will be a valuable resource for studying the pathogenic interactions occurring between F. musae and banana. Moreover, it represents an important resource for understanding the genome evolution in the Fusarium fujikuroi species complex.

scholarly journals Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Huizhong Fan ◽  
Qi Wu ◽  
Fuwen Wei ◽  
Fengtang Yang ◽  
Bee Ling Ng ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Giant Panda ◽  
Chromosome Evolution ◽  
Chromosome Level

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

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.

scholarly journals Chromosome-level genome assembly of the common chaffinch (Aves: Fringilla coelebs): a valuable resource for evolutionary biology

2020 ◽  
Author(s):  
María Recuerda ◽  
Joel Vizueta ◽  
Cristian Cuevas-Caballé ◽  
Guillermo Blanco ◽  
Julio Rozas ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Evolutionary Biology ◽  
Sequence Data ◽  
Single Copy ◽  
Valuable Resource ◽  
Structural Annotation ◽  
Data Set ◽  
Fringilla Coelebs ◽  
The Common ◽  
Chromosome Level

AbstractThe common chaffinch, Fringilla coelebs, is one of the most common, widespread and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87 Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian dataset. Around 7.8 % of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian and vertebrate evolution.

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