scholarly journals Tandem Repeats Contribute to Coding Sequence Variation in Bumblebees (Hymenoptera: Apidae)

2018 ◽  
Vol 10 (12) ◽  
pp. 3176-3187 ◽  
Author(s):  
Xiaomeng Zhao ◽  
Long Su ◽  
Sarah Schaack ◽  
Ben M Sadd ◽  
Cheng Sun
Keyword(s):  
Sequence Variation ◽  
Tandem Repeats ◽  
Coding Sequence

scholarly journals Tandem repeats contribute to coding sequence variation in bumblebees (Hymenoptera: Apidae)

2017 ◽  
Author(s):  
Xiaomeng Zhao ◽  
Long Su ◽  
Sarah Schaack ◽  
Ben M. Sadd ◽  
Cheng Sun
Keyword(s):  
Genetic Variation ◽  
Sequence Variation ◽  
Molecular Mechanisms ◽  
Tandem Repeats ◽  
Sequence Length ◽  
Length Variation ◽  
Coding Sequence ◽  
Bumblebee Species ◽  
Coding Regions ◽  
Wide Range

AbstractTandem repeats (TRs) are highly dynamic regions of the genome. Mutations at these loci represent a significant source of genetic variation and can facilitate rapid adaptation. Bumblebees are important pollinating insects occupying a wide range of habitats. However, to date, molecular mechanisms underlying the potential adaptation of bumblebees to diverse habitats are largely unknown. In the present study, we investigate how TRs contribute to genetic variation in bumblebees, thus potentially facilitating adaptation. We identified 26,595 TRs in the buff-tailed bumblebee (Bombus terrestris) genome, 66.7% of which reside in genic regions. We also compared TRs found in B. terrestris with those present in the whole genome sequence of a congener, B. impatiens. We found that a total of 1,137 TRs were variable in length between the two sequenced bumblebee species, and further analysis reveals that 101 of them are located within coding regions. The 101 TRs were responsible for coding sequence variation and corresponded to protein sequence length variation between the two bumblebee species. The variability of identified TRs in coding regions between bumblebees was confirmed by PCR amplification of a subset of loci. Functional classification of bumblebee genes where coding sequences include variable-length TRs suggests that a majority of these genes are related to transcriptional regulation. Our results show that TRs contribute to coding sequence variation in bumblebees and TRs may facilitate the adaptation of bumblebees through diversifying proteins involved in controlling gene expression.

scholarly journals Amino Acid Repeats Cause Extraordinary Coding Sequence Variation in the Social Amoeba Dictyostelium discoideum

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e46150 ◽  
Author(s):  
Clea Scala ◽  
Xiangjun Tian ◽  
Natasha J. Mehdiabadi ◽  
Margaret H. Smith ◽  
Gerda Saxer ◽  
...  
Keyword(s):  
Amino Acid ◽  
Dictyostelium Discoideum ◽  
Sequence Variation ◽  
Social Amoeba ◽  
Coding Sequence ◽  
Amino Acid Repeats ◽  
The Social

scholarly journals Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 352 ◽  
Author(s):  
Karen H. Miga
Keyword(s):  
Human Genome ◽  
Satellite Dna ◽  
Human Population ◽  
Sequence Variation ◽  
Tandem Repeats ◽  
Association Studies ◽  
Unmet Need ◽  
Satellite Dnas ◽  
Dna Variation ◽  
Medical Genomics

The central goal of medical genomics is to understand the inherited basis of sequence variation that underlies human physiology, evolution, and disease. Functional association studies currently ignore millions of bases that span each centromeric region and acrocentric short arm. These regions are enriched in long arrays of tandem repeats, or satellite DNAs, that are known to vary extensively in copy number and repeat structure in the human population. Satellite sequence variation in the human genome is often so large that it is detected cytogenetically, yet due to the lack of a reference assembly and informatics tools to measure this variability, contemporary high-resolution disease association studies are unable to detect causal variants in these regions. Nevertheless, recently uncovered associations between satellite DNA variation and human disease support that these regions present a substantial and biologically important fraction of human sequence variation. Therefore, there is a pressing and unmet need to detect and incorporate this uncharacterized sequence variation into broad studies of human evolution and medical genomics. Here I discuss the current knowledge of satellite DNA variation in the human genome, focusing on centromeric satellites and their potential implications for disease.

Macronuclear structure of the G surface antigen gene of Paramecium primaurelia and direct expression of its repeated epitopes in Escherichia coli

1985 ◽  
Vol 5 (9) ◽  
pp. 2414-2422
Author(s):  
E Meyer ◽  
F Caron ◽  
A Baroin
Keyword(s):  
Escherichia Coli ◽  
Surface Antigen ◽  
Tandem Repeats ◽  
Direct Proof ◽  
Antigenic Determinants ◽  
Gene Encoding ◽  
Coding Sequence ◽  
Genomic Environment ◽  
Cloned Gene

The gene encoding the G surface antigen of Paramecium primaurelia was cloned from a macronuclear DNA library by a screening procedure involving differential hybridization with cDNA probes synthesized from polyadenylated RNAs of cells expressing one of two alternate antigens. S1 mapping experiments and sequencing of the cloned DNA and the mRNA showed that the cloned gene corresponded to the high-molecular-weight mRNA that had been indirectly identified as that of the G surface antigen. Because the genetic code of Paramecium spp. is different from the "universal" code, this mRNA cannot be correctly translated in vitro; direct proof that it encoded the antigenic determinants of this protein was therefore obtained through expression of fragments of the coding sequence in Escherichia coli by using the expression vector lambda gt11. Studies on the structure of this gene revealed that the central part of the coding sequence contained at least five tandem repeats of 222 base pairs, encoding immunogenic domains of the protein. We also showed that, like other surface antigen genes of trypanosomes and paramecia, this gene lay next to a chromosome end and that no rearrangement of its immediate genomic environment was associated with its expression.

Worldwide haplotype diversity and coding sequence variation at human bitter taste receptor loci

2005 ◽  
Vol 26 (3) ◽  
pp. 199-204 ◽  
Author(s):  
Unkyung Kim ◽  
Stephen Wooding ◽  
Dante Ricci ◽  
Lynn B. Jorde ◽  
Dennis Drayna
Keyword(s):  
Sequence Variation ◽  
Bitter Taste ◽  
Taste Receptor ◽  
Haplotype Diversity ◽  
Bitter Taste Receptor ◽  
Coding Sequence

scholarly journals Functional interpretation of non‐coding sequence variation: Concepts and challenges

BioEssays ◽  
2013 ◽  
Vol 36 (2) ◽  
pp. 191-199 ◽  
Author(s):  
Dirk S. Paul ◽  
Nicole Soranzo ◽  
Stephan Beck
Keyword(s):  
Sequence Variation ◽  
Functional Interpretation ◽  
Coding Sequence

Sequence variation at three X chromosomal short tandem repeats in Caucasian and African populations

2008 ◽  
Vol 1 (1) ◽  
pp. 147-149 ◽  
Author(s):  
Iva Gomes ◽  
Mechthild Prinz ◽  
Rui Pereira ◽  
Erik Bieschke ◽  
António Amorim ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Sequence Variation ◽  
Tandem Repeats ◽  
African Populations ◽  
Short Tandem

Sub-Saharan African coding sequence variation and haplotype diversity at theNAT2gene

2006 ◽  
Vol 27 (7) ◽  
pp. 720-720 ◽  
Author(s):  
Etienne Patin ◽  
Christine Harmant ◽  
Ken K. Kidd ◽  
Judith Kidd ◽  
Alain Froment ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Haplotype Diversity ◽  
Coding Sequence ◽  
Sub Saharan

scholarly journals Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Maria N. Timofeeva ◽  
Ben Kinnersley ◽  
Susan M. Farrington ◽  
Nicola Whiffin ◽  
Claire Palles ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Genetic Architecture ◽  
Sequence Variation ◽  
Coding Sequence
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