scholarly journals Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Giulia I. M. Pasquesi ◽  
Richard H. Adams ◽  
Daren C. Card ◽  
Drew R. Schield ◽  
Andrew B. Corbin ◽  
...  
Keyword(s):  
Repeat Element ◽  
Squamate Reptiles ◽  
Genomic Repeat ◽  
Element Evolution

scholarly journals Genomic Repeat Element Analyzer for Mammals (GREAM)

2014 ◽  
Author(s):  
Darshan S Chandrashekar ◽  
Poulami Dey ◽  
Kshitish K Acharya
Keyword(s):  
Transcriptional Regulation ◽  
Gene Expression Regulation ◽  
Mammalian Species ◽  
Query Sequence ◽  
Repeat Element ◽  
Transcription Control ◽  
Element Analysis ◽  
Repeat Elements ◽  
Specific Distribution ◽  
Genomic Repeat

Background: Understanding the mechanism behind the transcriptional regulation of genes is still a challenge. Recent findings indicate that the genomic repeat elements (such as LINES, SINES and LTRs) could play an important role in the transcription control. Hence, it is important to further explore the role of genomic repeat elements in the gene expression regulation, and perhaps in other molecular processes. Although many computational tools exists for repeat element analysis, almost all of them simply identify and/or classifying the genomic repeat elements within query sequence(s); none of them facilitate identification of repeat elements that are likely to have a functional significance, particularly in the context of transcriptional regulation. Result: We developed the 'Genomic Repeat Element Analyzer for Mammals' (GREAM) to allow gene-centric analysis of genomic repeat elements in 17 mammalian species, and validated it by comparing with some of the existing experimental data. The output provides a categorized list of the specific type of transposons, retro-transposons and other genome-wide repeat elements that are statistically over-represented across specific neighborhood regions of query genes. The position and frequency of these elements, within the specified regions, are displayed as well. The tool also offers queries for position-specific distribution of repeat elements within chromosomes. In addition, GREAM facilitates the analysis of repeat element distribution across the neighborhood of orthologous genes. Conclusion: GREAM allows researchers to short-list the potentially important repeat elements, from the genomic neighborhood of genes, for further experimental analysis. GREAM is free and available for all at http://resource.ibab.ac.in/GREAM/

scholarly journals Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1341-1351 ◽  
Author(s):  
I King Jordan ◽  
John F McDonald
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Negative Selection ◽  
Sequence Variation ◽  
Size Variation ◽  
Sequence Comparisons ◽  
Ty Elements ◽  
Ty Element ◽  
Amino Acid Sequence Variation ◽  
Element Evolution ◽  
High Level

Abstract The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.

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.

Porcine Repeat Element DNA: In Situ Detection of Xenotransplanted Cells

1995 ◽  
Vol 4 (2) ◽  
pp. 253-256 ◽  
Author(s):  
Henry F. Oettinger ◽  
Amelie Rodrigue-Way ◽  
Joyce J. Bousquet ◽  
Albert S.B. Edge
Keyword(s):  
Southern Blotting ◽  
Host Tissue ◽  
Repeat Element ◽  
Tissue Analysis ◽  
Specific Staining ◽  
Tetrazolium Chloride ◽  
Tissue Sections ◽  
Blue Tetrazolium Chloride ◽  
In Situ Detection

Using a digoxygenin-labelled DNA probe derived from the porcine repeat element PRE-1, we have developed a protocol for the detection of transplanted porcine islets and hepatocytes against a background of murine host tissue. Analysis of this probe by Southern blotting indicated that PRE-1 hybridizes to pig genomic DNA but not to human or mouse DNA. On tissue sections, hybridizing probe was detected using alkaline phosphatase-conjugated anti-digoxygenin antibody visualized with 5-bromo-4-chloro-3-indolyl-phosphate/4-nitro-blue tetrazolium chloride (BCIP/ NBT) substrate. We have demonstrated sensitive and highly specific staining of porcine nuclei in fixed, paraffin embedded tissue sections, and have applied the technique to detect porcine pancreatic islets and hepatocytes transplanted into murine kidney and spleen. Applications of this technique include detection of transplanted cells or organs across a variety of xenogeneic barriers.

scholarly journals The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

2017 ◽  
Vol 4 (8) ◽  
pp. 170685 ◽  
Author(s):  
Alessandro Palci ◽  
Mark N. Hutchinson ◽  
Michael W. Caldwell ◽  
Michael S. Y. Lee
Keyword(s):  
Geometric Morphometrics ◽  
Inner Ear ◽  
Phylogenetic Signal ◽  
Three Dimensional ◽  
Lizard Species ◽  
Squamate Reptiles ◽  
Strong Affinity ◽  
Ear Morphology

The inner ear morphology of 80 snake and lizard species, representative of a range of ecologies, is here analysed and compared to that of the fossil stem snake Dinilysia patagonica , using three-dimensional geometric morphometrics. Inner ear morphology is linked to phylogeny (we find here a strong phylogenetic signal in the data that can complicate ecological correlations), but also correlated with ecology, with Dinilysia resembling certain semi-fossorial forms ( Xenopeltis and Cylindrophis ), consistent with previous reports. We here also find striking resemblances between Dinilysia and some semi-aquatic snakes, such as Myron (Caenophidia, Homalopsidae). Therefore, the inner ear morphology of Dinilysia is consistent with semi-aquatic as well as semi-fossorial habits: the most similar forms are either semi-fossorial burrowers with a strong affinity to water ( Xenopeltis and Cylindrophis ) or amphibious, intertidal forms which shelter in burrows ( Myron). Notably, Dinilysia does not cluster as closely with snakes with exclusively terrestrial or obligate burrowing habits (e.g. scolecophidians and uropeltids). Moreover, despite the above similarities, Dinilysia also occupies a totally unique morphospace, raising issues with linking it with any particular ecological category.

scholarly journals Late Pleistocene echimyid rodents (Rodentia, Hystricognathi) from northern Brazil

2016 ◽  
Vol 88 (2) ◽  
pp. 829-845 ◽  
Author(s):  
THAIS M.F. FERREIRA ◽  
ADRIANA ITATI OLIVARES ◽  
LEONARDO KERBER ◽  
RODRIGO P. DUTRA ◽  
LEONARDO S. AVILLA
Keyword(s):  
South America ◽  
Tropical Forests ◽  
Late Pleistocene ◽  
Fossil Record ◽  
South American ◽  
Squamate Reptiles ◽  
Northern Brazil ◽  
Northern South America ◽  
First Time

ABSTRACT Echimyidae (spiny rats, tree rats and the coypu) is the most diverse family of extant South American hystricognath rodents (caviomorphs). Today, they live in tropical forests (Amazonian, coastal and Andean forests), occasionally in more open xeric habitats in the Cerrado and Caatinga of northern South America, and open areas across the southern portion of the continent (Myocastor). The Quaternary fossil record of this family remains poorly studied. Here, we describe the fossil echimyids found in karst deposits from southern Tocantins, northern Brazil. The analyzed specimens are assigned to Thrichomys sp., Makalata cf. didelphoides and Proechimys sp. This is the first time that a fossil of Makalata is reported. The Pleistocene record of echimyids from this area is represented by fragmentary remains, which hinders their determination at specific levels. The data reported here contributes to the understanding of the ancient diversity of rodents of this region, evidenced until now in other groups, such as the artiodactyls, cingulates, carnivores, marsupials, and squamate reptiles.

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