scholarly journals Chromosome-level assembly of the common lizard (Zootoca vivipara) genome

2019 ◽  
Author(s):  
Andrey A. Yurchenko ◽  
Hans Recknagel ◽  
Kathryn R. Elmer
Keyword(s):  
Sequence Data ◽  
Multiple Paternity ◽  
Single Copy ◽  
High Quality ◽  
High Coverage ◽  
Squamate Reptiles ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common ◽  
Chromosome Level

ABSTRACTSquamate reptiles exhibit high variation in their traits and geographical distribution and are therefore fascinating taxa for evolutionary and ecological research. However, high-quality genomic recourses are very limited for this group of species, which inhibits some research efforts. To address this gap, we assembled a high-quality genome of the common lizard Zootoca vivipara (Lacertidae) using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequence data, with RNAseq data and genetic linkage maps. The 1.46 Gbp genome assembly has scaffold N50 of 11.52 Mbp with N50 contig size of 220.4 Kbp and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total 19,829 gene models were annotated in the genome using a combination of three ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

scholarly journals Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

2020 ◽  
Vol 12 (11) ◽  
pp. 1953-1960
Author(s):  
Andrey A Yurchenko ◽  
Hans Recknagel ◽  
Kathryn R Elmer
Keyword(s):  
Linkage Map ◽  
Single Copy ◽  
Phenotypic Traits ◽  
Sequencing Data ◽  
High Coverage ◽  
Squamate Reptiles ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common ◽  
Chromosome Level

Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

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 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.

scholarly journals Environmental variation mediates the prevalence and co-occurrence of parasites in the common lizard, Zootoca vivipara

BMC Ecology ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Qiang Wu ◽  
Murielle Richard ◽  
Alexis Rutschmann ◽  
Donald B. Miles ◽  
Jean Clobert
Keyword(s):  
Environmental Factors ◽  
Human Disturbance ◽  
Vegetation Cover ◽  
Structural Equation ◽  
Environmental Gradients ◽  
Parasite Load ◽  
Single Species ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common

Abstract Background Hosts and their parasites are under reciprocal selection, leading to coevolution. However, parasites depend not only on a host, but also on the host’s environment. In addition, a single host species is rarely infested by a single species of parasite and often supports multiple species (i.e., multi-infestation). Although the arms race between a parasite and its host has been well studied, few data are available on how environmental conditions may influence the process leading to multiple infestations. In this study, we examine whether: (1) environmental factors including altitude, temperature, vegetation cover, human disturbance, and grazing by livestock affect the prevalence of two types of ectoparasites, mites and ticks, on their host (the common lizard, Zootoca vivipara) and (2) competition is evident between mites and ticks. Results We found the probability of mite infestation increased with altitude and vegetation cover, but decreased with human disturbance and presence of livestock. In contrast, the probability of tick infestation was inversely associated with the same factors. Individuals with low body condition and males had higher mite loads. However, this pattern was not evident for tick loads. The results from a structural equation model revealed that mites and ticks indirectly and negatively affected each other’s infestation probability through an interaction involving the environmental context. We detected a direct negative association between mites and ticks only when considering estimates of parasite load. This suggests that both mites and ticks could attach to the same host, but once they start to accumulate, only one of them takes advantage. Conclusion The environment of hosts has a strong effect on infestation probabilities and parasite loads of mites and ticks. Autecological differences between mites and ticks, as indicated by their opposing patterns along environmental gradients, may explain the pattern of weak contemporary interspecific competition. Our findings emphasize the importance of including environmental factors and the natural history of each parasite species in studies of host–parasite coevolution.

scholarly journals Warmer temperatures attenuate the classic offspring number and reproductive investment trade-off in the common lizard, Zootoca vivipara

2016 ◽  
Vol 12 (6) ◽  
pp. 20160101 ◽  
Author(s):  
Alexis Rutschmann ◽  
Donald B. Miles ◽  
Jean Clobert ◽  
Murielle Richard
Keyword(s):  
Life History ◽  
Environmental Conditions ◽  
Life History Traits ◽  
Natural Populations ◽  
Trade Off ◽  
Offspring Number ◽  
Common Lizard ◽  
Trade Offs ◽  
Zootoca Vivipara ◽  
The Common

Life-history traits involved in trade-offs are known to vary with environmental conditions. Here, we evaluate the response of the trade-off between ‘offspring number’ versus ‘energy invested per offspring’ to ambient temperature in 11 natural populations of the common lizard, Zootoca vivipara . We provide evidence at both the intra- and interpopulation levels that the trade-off is reduced with an increase in air temperature. If this effect enhances current individual fitness, it may lead to an accelerated pace of life in warmer environments and could ultimately increase adult mortality. In the context of global warming, our results advocate the need for more studies in natural populations to explore interactions between life-history traits' trade-offs and environmental conditions.

scholarly journals Male Reproductive Cycle in a Population of the Common Lizard Zootoca vivipara (Squamata, Lacertidae) from Southeast of Western Siberia

2019 ◽  
Vol 19 (1/2) ◽  
pp. 56-67
Author(s):  
Vadim V. Yartsev ◽  
◽  
Valentina N. Kuranova ◽  
Ekaterina N. Absalyamova ◽  
◽  
...  
Keyword(s):  
Reproductive Cycle ◽  
Western Siberia ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common

scholarly journals Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Sven Winter ◽  
Stefan Prost ◽  
Jordi de Raad ◽  
Raphael T. F. Coimbra ◽  
Magnus Wolf ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Morphological Differentiation ◽  
Chromosome Length ◽  
Morphological Transformation ◽  
High Quality ◽  
The North ◽  
Repeat Content ◽  
The Common ◽  
Species Specific ◽  
Chromosome Level

Background The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the ‘benthic associated clade’ of the order Syngnathiformes. The ‘benthic associated clade’ so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in ‘long-snouted’ syngnatiformes such as seahorses and pipefishes. Findings Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies’ long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp and a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.7%. Conclusions The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

scholarly journals A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Carolina Peñaloza ◽  
Alejandro P Gutierrez ◽  
Lél Eöry ◽  
Shan Wang ◽  
Ximing Guo ◽  
...  
Keyword(s):  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Sequence Data ◽  
High Coverage ◽  
Protein Coding ◽  
Rolling Circle ◽  
Repeat Elements ◽  
Pacific Biosciences ◽  
The Pacific ◽  
Chromosome Level

Abstract Background The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. Findings High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. Conclusions This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.

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