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 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 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 A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem

2020 ◽  
Vol 10 (10) ◽  
pp. 3549-3555
Author(s):  
Like Fokkens ◽  
Li Guo ◽  
Susanne Dora ◽  
Bo Wang ◽  
Kai Ye ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Large Scale ◽  
Plant Pathogens ◽  
Single Copy ◽  
Model Systems ◽  
Fungal Genome ◽  
Suitable Model ◽  
Sequencing Data ◽  
High Coverage ◽  
Phylogenomic Analyses

Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step toward the establishment of a highly promising pathosystem.

Reproduction and Morphology of the Common Lizard (Zootoca vivipara) from Montane Populations in Slovakia

2013 ◽  
Vol 30 (2) ◽  
pp. 92-98 ◽  
Author(s):  
Terézia Horváthová ◽  
Michal Baláž ◽  
David Jandzik
Keyword(s):  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common

Isolation and Characterization of Interspersed Repeated Sequences in the Common Lizard, Zootoca vivipara, and Their Conservation in Squamata

2019 ◽  
Vol 157 (1-2) ◽  
pp. 65-76 ◽  
Author(s):  
Agnese Petraccioli ◽  
Fabio M. Guarino ◽  
Larissa Kupriyanova ◽  
Marcello Mezzasalma ◽  
Gaetano Odierna ◽  
...  
Keyword(s):  
Sex Chromosome ◽  
Pcr Amplification ◽  
Active Role ◽  
Disjunct Distribution ◽  
Significant Similarity ◽  
Isolation And Characterization ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common ◽  
Almost All

The common lizard (Zootoca vivipara) displays characteristic cytogenetic, reproductive, molecular, and biogeographic variability. This species comprises oviparous and viviparous populations with disjunct distribution and sex chromosome polymorphisms, from simple ZZ/ZW to complex Z1Z1Z2Z2/Z1Z2W systems with different morphologies of the W chromosome. In this study, we used the primers SINE A and SINE B and a newly designed primer pair to (1) obtain information on the presence and distribution of transposable elements (TEs) in 8 squamate families and (2) assess the chromosomal location of SINE Squam elements in Z. vivipara. PCR amplification with SINE A and SINE B produced single or multiple products in different Z. vivipara populations, subsequently used to design the SINE-Zv primers. Using the newly designed SINE-Zv primers, we identified 2 sequences of about 700 and 300 bp (SINE-Zv 700 and SINE-Zv 300) in all the investigated populations of Z. vivipara. Fluorescence in situ hybridizations showed a preferential localization of SINE-Zv sequences in the peritelomeric regions of almost all chromosomes, with the exception of the W. Both sequences contained a distinct segment of SINE Squam2. SINE-Zv 700 appeared to be restricted to Z. vivipara, while SINE-Zv 300 contained a partial Gypsy sequence that is highly conserved among Squamata and showed high identity values (72-93%) with several transcripts from different species. Using the same primers, we also highlighted the presence of another highly conserved Gypsy-like fragment in snakes which displayed significant similarity with the stomatin-like protein 2 of colubrids. Our results suggest that SINEs and the Gypsy-like elements are widely distributed among squamates and may have played an active role in their genomic evolution and differentiation.

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