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DNA, Volume 1, Issue 2 (December 2021) – 7 articles

Cover Story (view full-size image): Sex determination is one of the most fundamental traits in the animal kingdom, and yet, its mechanisms are highly variable and evolve rapidly. Variation in this mechanism has been observed among many lineages and even among closely related species or even populations. The oriental garden lizard Calotes versicolor is one such species in which multiple sex-determining modes have been observed. Here, we used genotyping-by-sequencing to show that C. versicolor comprises a complex of cryptic species whose members include female and male heterogamety as well as temperature-dependent modes of sex determination. Our results provide further evidence that frequent transitions between modes of sex determination have occurred among closely related species and within populations of Agamid lizards. View this paper.
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5 pages, 874 KiB  
Obituary
One for Sorrow
by Darren K. Griffin
DNA 2021, 1(2), 105-109; https://doi.org/10.3390/dna1020011 - 20 Dec 2021
Viewed by 2161
Abstract
“Did it work [...] Full article
(This article belongs to the Special Issue In Memoriam of Joy Dorothy Ann Delhanty)
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14 pages, 1557 KiB  
Hypothesis
Large Intra-Age Group Variation in Chromosome Abnormalities in Human Blastocysts
by Sarthak Sawarkar, Darren K. Griffin, Lia Ribustello and Santiago Munné
DNA 2021, 1(2), 91-104; https://doi.org/10.3390/dna1020010 - 6 Dec 2021
Cited by 2 | Viewed by 4074
Abstract
Research Question: Is maternal age only a gross predictor of chromosome abnormalities in human embryos? Design: Here, we evaluated the less-studied variation in chromosome abnormality rates in embryos of patients within the same age group. Patients undergoing IVF and PGD for chromosomal abnormalities [...] Read more.
Research Question: Is maternal age only a gross predictor of chromosome abnormalities in human embryos? Design: Here, we evaluated the less-studied variation in chromosome abnormality rates in embryos of patients within the same age group. Patients undergoing IVF and PGD for chromosomal abnormalities in ~127 different IVF clinics were included. PGT-A analysis was performed by a single reference laboratory using array CGH or NGS. To get an estimate of the range of abnormalities observed, the aCGH and NGS data were studied both independently and together. Results: The overall results showed the typical increase in aneuploidy rates with advancing maternal age (AMA) but extensive variability within each age group. Conclusions: Increasing aneuploidy with maternal age has been demonstrated in live births, unborn fetuses, IVF embryos and oocytes. In contrast, post-meiotic and other abnormalities that might lead to mosaicism, polyploidy and haploidy, are commonplace (around 30%), regardless of maternal age. Here we conclude that age is only a gross predictor of chromosome abnormalities in IVF embryos. In contrast to the existing standard of offering PGT-A to AMA patients, the high rate and extreme variation of chromosomal abnormalities in human embryos may warrant PGT-A for further IVF cycles even in younger age groups, especially if a history of increased levels of aneuploidy is evident. Furthermore, better indicators are needed to determine which patients are at a higher risk of producing increased levels of aneuploid embryos. Full article
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7 pages, 1933 KiB  
Commentary
Classification Problems of Repetitive DNA Sequences
by Eva Šatović-Vukšić and Miroslav Plohl
DNA 2021, 1(2), 84-90; https://doi.org/10.3390/dna1020009 - 2 Nov 2021
Cited by 3 | Viewed by 3616
Abstract
Repetitive DNA sequences, satellite DNAs (satDNAs) and transposable elements (TEs) are essential components of the genome landscape, with many different roles in genome function and evolution. Despite significant advances in sequencing technologies and bioinformatics tools, detection and classification of repetitive sequences can still [...] Read more.
Repetitive DNA sequences, satellite DNAs (satDNAs) and transposable elements (TEs) are essential components of the genome landscape, with many different roles in genome function and evolution. Despite significant advances in sequencing technologies and bioinformatics tools, detection and classification of repetitive sequences can still be an obstacle to the analysis of genomic repeats. Here, we summarize how specificities in repetitive DNA organizational patterns can lead to an inability to classify (and study) a significant fraction of bivalve mollusk repetitive sequences. We suggest that the main reasons for this inability are: the predominant association of satDNA arrays with Helitron/Helentron TEs; the existence of many complex loci; and the unusual, highly scattered organization of short satDNA arrays or single monomers across the whole genome. The specificities of bivalve genomes confirm the need for introducing diverse organisms as models in order to understand all aspects of repetitive DNA biology. It is expected that further development of sequencing techniques and synergy among different bioinformatics tools and databases will enable quick and unambiguous characterization and classification of repetitive DNA sequences in assembled genomes. Full article
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7 pages, 1063 KiB  
Article
Karyotype Organization of the Endangered Species Yellow Cardinal (Gubernatrix cristata)
by Sandra Eloisa Bülau, Rafael Kretschmer, Ivanete de Oliveira Furo, Edivaldo Herculano Correa de Oliveira and Thales Renato Ochotorena de Freitas
DNA 2021, 1(2), 77-83; https://doi.org/10.3390/dna1020008 - 27 Oct 2021
Cited by 3 | Viewed by 3240
Abstract
Karyotypic analyses have several applications in studies of chromosome organization, evolution, and cytotaxonomy. They are also essential to genome assembly projects. Here, we present for the first time the karyotype description of the endangered species yellow cardinal, Gubernatrix cristata (Passeriformes, Thraupidae), using conventional [...] Read more.
Karyotypic analyses have several applications in studies of chromosome organization, evolution, and cytotaxonomy. They are also essential to genome assembly projects. Here, we present for the first time the karyotype description of the endangered species yellow cardinal, Gubernatrix cristata (Passeriformes, Thraupidae), using conventional staining with Giemsa and 18S rDNA probes. This species has 78 chromosomes, with 12 pairs of macrochromosomes and 27 microchromosome pairs. The 18S rDNA clusters were found in four microchromosomes. Our results revealed that G. cristata has a typical avian karyotype (approximately 80 chromosomes). However, G. cristata has an apomorphic state in relation to the 18S rDNA distribution since the ancestral condition corresponds to only two microchromosomes with these sequences. Probably, duplications and translocations were responsible for increasing the number of 18S rDNA clusters in G. cristata. The results were compared and discussed with respect to other Thraupidae and Passeriformes members. Considering the globally threatened status of G. cristata, we believe that its karyotype description could be a starting point for future cytogenetics and sequencing projects. Full article
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9 pages, 540 KiB  
Article
Incidence, Reproductive Outcome, and Economic Impact of Reciprocal Translocations in the Domestic Pig
by Nicole M. Lewis, Claudia C. Rathje, Carla Canedo-Ribeiro, Lisa M. Bosman, Lucas G. Kiazim, Rebecca L. Jennings, Rebecca E. O’Connor, Giuseppe Silvestri and Darren K. Griffin
DNA 2021, 1(2), 68-76; https://doi.org/10.3390/dna1020007 - 9 Oct 2021
Cited by 2 | Viewed by 3351
Abstract
Pigs (Sus scrofa) have vast economic importance, with pork accounting for over 30% of the global meat consumption. Chromosomal abnormalities, and in particular reciprocal translocations (RTs), are an important cause of hypoprolificacy (litter size reduction) in pigs. However, these do not [...] Read more.
Pigs (Sus scrofa) have vast economic importance, with pork accounting for over 30% of the global meat consumption. Chromosomal abnormalities, and in particular reciprocal translocations (RTs), are an important cause of hypoprolificacy (litter size reduction) in pigs. However, these do not necessarily present with a recognizable phenotype and may cause significant economic losses for breeders when undetected. Here, we present a reappraisal of the incidence of RTs across several European pig herds, using contemporary methodology, as well as an analysis modelling the economic impact of these abnormalities. Molecular cytogenetic investigation was completed by karyotyping and/or multiprobe FISH (fluorescence in situ hybridisation) between 2016–2021, testing 2673 animals. We identified 19 types of chromosome abnormalities, the prevalence of these errors in the database was 9.1%, and the estimated incidence of de novo errors was 0.90%. Financial modelling across different scenarios revealed the potential economic impact of an undetected RT, ranging from £69,802 for an individual affected terminal boar in a commercial farm selling weaned pigs, to £51,215,378 for a genetics company with an undetected RT in a dam line boar used in a nucleus farm. Moreover, the added benefits of screening by FISH instead of karyotyping were estimated, providing a strong case for proactive screening by this approach. Full article
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19 pages, 2218 KiB  
Article
Sex-Determination Mechanisms among Populations within Cryptic Species Complex of Calotes (Squamata: Agamidae: Draconinae)
by Shayer Mahmood Ibney Alam, Tulyawat Prasongmaneerut, Dianne Gleeson, Arthur Georges, Stephen D. Sarre, Kornsorn Srikulnath and Tariq Ezaz
DNA 2021, 1(2), 49-67; https://doi.org/10.3390/dna1020006 - 6 Oct 2021
Viewed by 10744
Abstract
Sex-determination mechanisms and sex chromosomes are known to vary among reptile species and, in a few celebrated examples, within populations of the same species. The oriental garden lizard, Calotes versicolor, is one of the most intriguing species in this regard, exhibiting evidence [...] Read more.
Sex-determination mechanisms and sex chromosomes are known to vary among reptile species and, in a few celebrated examples, within populations of the same species. The oriental garden lizard, Calotes versicolor, is one of the most intriguing species in this regard, exhibiting evidence of multiple sex-determination modes within a single species. One possible explanation for this unusual distribution is that in C. versicolor, different modes of sex determination are confined to a particular population or a species within a cryptic species complex. Here, we report on a population genetic analysis using SNP data from a methylation-sensitive DArT sequencing analysis and mitochondrial DNA data obtained from samples collected from six locations: three from Bangladesh and three from Thailand. Our aim was to determine whether C. versicolor is best described as a single species with multiple lineages or as multiple species, as well as if its sex-determination mechanisms vary within or between species. We present evidence that the latter possibility is the case and that C. versicolor comprises a complex of cryptic species. We also identify sex-linked markers within these species and use them to identify modes of sex determination. Overall, our results suggest that different sex-determination modes have evolved among closely related species and within populations of Agamid lizards. Full article
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12 pages, 11240 KiB  
Review
Small RNAs Worm Up Transgenerational Epigenetics Research
by Alla Grishok
DNA 2021, 1(2), 37-48; https://doi.org/10.3390/dna1020005 - 29 Sep 2021
Cited by 4 | Viewed by 3888
Abstract
DNA is central to the propagation and evolution of most living organisms due to the essential process of its self-replication. Yet it also encodes factors that permit epigenetic (not included in DNA sequence) flow of information from parents to their offspring and beyond. [...] Read more.
DNA is central to the propagation and evolution of most living organisms due to the essential process of its self-replication. Yet it also encodes factors that permit epigenetic (not included in DNA sequence) flow of information from parents to their offspring and beyond. The known mechanisms of epigenetic inheritance include chemical modifications of DNA and chromatin, as well as regulatory RNAs. All these factors can modulate gene expression programs in the ensuing generations. The nematode Caenorhabditis elegans is recognized as a pioneer organism in transgenerational epigenetic inheritance research. Recent advances in C. elegans epigenetics include the discoveries of control mechanisms that limit the duration of RNA-based epigenetic inheritance, periodic DNA motifs that counteract epigenetic silencing establishment, new mechanistic insights into epigenetic inheritance carried by sperm, and the tantalizing examples of inheritance of sensory experiences. This review aims to highlight new findings in epigenetics research in C. elegans with the main focus on transgenerational epigenetic phenomena dependent on small RNAs. Full article
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