Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant

2020 ◽  
Author(s):  
Chuan He ◽  
Lele Zhao ◽  
Lu Xiao ◽  
Ke Xu ◽  
Jinmei Ding ◽  
...  
Keyword(s):  
Gene Organization ◽  
Immune Gene ◽  
Common Pheasant ◽  
The Common ◽  
Chromosome Level

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.

The gene organization of the human β7 subunit, the common β subunit of the leukocyte integrins HML-1 and LPAM-1

1992 ◽  
Vol 4 (9) ◽  
pp. 1031-1040 ◽  
Author(s):  
Wei-Meng Jiang ◽  
David Jenkins ◽  
Qian Yuan ◽  
Euphemia Leung ◽  
K. H. Andy Choo ◽  
...  
Keyword(s):  
Gene Organization ◽  
Β Subunit ◽  
Leukocyte Integrins ◽  
The Common

scholarly journals Influence of Pre-Sampling Handling Duration on Selected Biochemical Indices in the Common Pheasant (Phasianus colchicus)

2009 ◽  
Vol 78 (1) ◽  
pp. 23-28 ◽  
Author(s):  
Petr Chloupek ◽  
Eva Voslářová ◽  
Pavel Suchý ◽  
Iveta Bedáňová ◽  
Vladimíra Pištěková ◽  
...  
Keyword(s):  
Czech Republic ◽  
Glucose Concentration ◽  
Plasma Concentrations ◽  
Plasma Corticosterone ◽  
Phasianus Colchicus ◽  
Blood Samples ◽  
Common Pheasant ◽  
The Common ◽  
Glucose Plasma ◽  
Biochemical Indices

The effects of varying periods of pre-sampling handling (1.5 min, 3 min, 4.5 min, 6 min) on selected biochemical indices were monitored in a group of 8–9-month-old common pheasants (Phasianus colchicus) kept at a pheasantry in Jinačovice, Czech Republic. The duration of pheasant handling (capture, restraint, and blood sampling) was positively correlated with plasma corticosterone (p < 0.001) and lactate (p < 0.05) levels. Negative correlations were found between the handling duration and glucose concentration (p < 0.01), and aspartate aminotransferase level (p < 0.05) in the blood plasma. A significant increase in corticosterone plasma concentrations and a decrease in glucose plasma concentrations were already found in blood samples taken after 3 min of capture in comparison to blood samples of pheasants taken within 1.5 min.

scholarly journals Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

GigaScience ◽  
2020 ◽  
Vol 9 (7) ◽  
Author(s):  
Morteza Roodgar ◽  
Afshin Babveyh ◽  
Lan H Nguyen ◽  
Wenyu Zhou ◽  
Rahul Sinha ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Innate Immune ◽  
Human Diseases ◽  
Macaca Nemestrina ◽  
Proximity Ligation Assay ◽  
Immune Gene ◽  
Proteomics Data ◽  
Macaque Species ◽  
Chromosome Level

Abstract Background Macaque species share &gt;93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. Results To close this gap and enhance functional genomics approaches, we used a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells derived from the same animal. Reconstruction of the evolutionary tree using whole-genome annotation and orthologous comparisons among 3 macaque species, human, and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. Conclusions These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.

Chromosome‐level assembly of wild Bactrian camel genome reveals organization of immune gene loci

2020 ◽  
Vol 20 (3) ◽  
pp. 770-780
Author(s):  
Liang Ming ◽  
Zhen Wang ◽  
Li Yi ◽  
Mijiddorj Batmunkh ◽  
Tao Liu ◽  
...  
Keyword(s):  
Bactrian Camel ◽  
Immune Gene ◽  
Chromosome Level

Multiple ornaments are positively related to male survival in the common pheasant

2003 ◽  
Vol 65 (1) ◽  
pp. 143-147 ◽  
Author(s):  
Anna Papeschi ◽  
Francesco Dessı̀-Fulgheri
Keyword(s):  
Multiple Ornaments ◽  
Common Pheasant ◽  
The Common

scholarly journals Regionally divergent drivers of historical diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

2019 ◽  
Author(s):  
Simin Liu ◽  
Yang Liu ◽  
Edouard Jelen ◽  
Mansour Alibadian ◽  
Cheng-Te Yao ◽  
...  
Keyword(s):  
Central Asia ◽  
Demographic History ◽  
Central China ◽  
Phylogeographic Structure ◽  
Phasianus Colchicus ◽  
Widespread Species ◽  
South Central ◽  
Common Pheasant ◽  
The Common ◽  
Spatio Temporal

ABSTRACTAimHistorical factors such as Pleistocene climate cycles and associated environmental changes have influenced the phylogeographic structure and demographic dynamics of many species. Resulting patterns not only depend on species’ life-history but also vary regionally. Consequently, different populations of species with large ranges over different biomes might have experienced divergent drivers of diversification and show different population histories. Such a representative species is the common pheasant Phasianus colchicus, an ecological generalist with a wide distribution in the Palearctic and at the edge of the Oriental region. We aimed at identifying distinct phylogeographic lineages of the common pheasant and investigating their evolutionary trajectories.Study locationAsiaMethodsWe used coalescent approaches to describe the phylogeographic structure and to reconstruct the spatio-temporal diversification and demographic history of the common pheasant based on a comprehensive geographic sampling of 265 individuals genotyped at seven nuclear and two mitochondrial loci.ResultsThe common pheasant diversified during the late Pleistocene into eight distinct evolutionary lineages which only partly correspond to traditional morphological groups. It originated at the edge of the Qinghai-Tibetan plateau and spread from there to East and Central Asia. Only the widely distributed genetically uniform lowland lineage of East Asia showed a recent range and population expansion, starting during last glacial. More phylogeographic structure was found elsewhere with lineages showing no signs of recent range expansions. One lineage of subtropical south-central China this is the result of long-term isolation in a climatically stable and topographically complex region. In others from arid Central Asia and China, demographic and range expansions were impeded by repeated population fragmentation during dry glacial and recent aridification. Given such a phylogeographic structure and demographic scenarios among lineages, we proposed split the range-wide common pheasant into three species.Main conclusionsSpatio-temporal phylogeographic frameworks of widespread species complexes such as the common pheasant provide valuable opportunities to identify regionally divergent drivers of diversification.

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.

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