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10 pages, 1389 KiB

Open AccessReview

A Brief Review of Meiotic Chromosomes in Early Spermatogenesis and Oogenesis and Mitotic Chromosomes in the Viviparous Lizard Zootoca vivipara (Squamata: Lacertidae) with Multiple Sex Chromosomes

by Larissa Kupriyanova and Larissa Safronova

Animals 2023, 13(1), 19; https://doi.org/10.3390/ani13010019 - 20 Dec 2022

Cited by 3 | Viewed by 2150

Abstract

This brief review is focused on the viviparous lizard Zootoca vivipara (Lichtenstein, 1823), of the family Lacertidae, which possesses female heterogamety and multiple sex chromosomes (male 2n = 36, Z₁Z₁Z₂Z₂/Z₁Z₂W, female 2n = 35, with variable W sex chromosome). Multiple sex chromosomes and their changes may influence meiosis and the female meiotic drive, and they may play a role in reproductive isolation. In two cryptic taxa of Z. vivipara with different W sex chromosomes, meiosis during early spermatogenesis and oogenesis proceeds normally, without any disturbances, with the formation of haploid spermatocytes, and in female meiosis with the formation of synaptonemal complexes (SCs) and the lampbrush chromosomes. In females, the SC number was constantly equal to 19 (according to the SC length, 16 SC autosomal bivalents plus three presumed SC sex chromosome elements). No variability in the chromosomes at the early stages of meiotic prophase I, and no significant disturbances in the chromosome segregation at the anaphase–telophase I stage, have been discovered, and haploid oocytes (n = 17) at the metaphase II stage have been revealed. There should be a factor/factors that maintain the multiple sex chromosomes, their equal transmission, and the course of meiosis in these cryptic forms of Z. vivipara. Full article

(This article belongs to the Special Issue Reptile Evolution and Genetics - Special Issue Dedicated to the Memory of Prof. Teresa Capriglione)

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11 pages, 1799 KiB

Open AccessArticle

Single-Cell DNA Methylation Analysis of Chicken Lampbrush Chromosomes

by Artem Nurislamov, Timofey Lagunov, Maria Gridina, Alla Krasikova and Veniamin Fishman

Int. J. Mol. Sci. 2022, 23(20), 12601; https://doi.org/10.3390/ijms232012601 - 20 Oct 2022

Cited by 5 | Viewed by 2660

Abstract

DNA methylation is an essential epigenetic regulation mechanism implicated in transcription and replication control, developmental reprogramming, retroelements silencing and other genomic processes. During mammalian development, a specific DNA methylation pattern should be established in germ cells to allow embryonic development. Less is known about germ cell DNA methylation in other species. To close this gap, we performed a single-cell methylome analysis of chicken diplotene oocytes. We comprehensively characterized methylation patterns in these cells, obtained methylation-based chicken genome segmentation and identified oocyte-specific methylated gene promoters. Our data show that despite the formation of specific transcriptionally hyperactive genome architecture in chicken diplotene oocytes, methylation patterns in these cells closely resemble genomic distribution observed in somatic tissues. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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12 pages, 1521 KiB

Open AccessArticle

Amplified Fragments of an Autosome-Borne Gene Constitute a Significant Component of the W Sex Chromosome of Eremias velox (Reptilia, Lacertidae)

by Artem Lisachov, Daria Andreyushkova, Guzel Davletshina, Dmitry Prokopov, Svetlana Romanenko, Svetlana Galkina, Alsu Saifitdinova, Evgeniy Simonov, Pavel Borodin and Vladimir Trifonov

Genes 2021, 12(5), 779; https://doi.org/10.3390/genes12050779 - 20 May 2021

Cited by 5 | Viewed by 3821

Abstract

Heteromorphic W and Y sex chromosomes often experience gene loss and heterochromatinization, which is frequently viewed as their “degeneration”. However, the evolutionary trajectories of the heterochromosomes are in fact more complex since they may not only lose but also acquire new sequences. Previously, we found that the heterochromatic W chromosome of a lizard Eremias velox (Lacertidae) is decondensed and thus transcriptionally active during the lampbrush stage. To determine possible sources of this transcription, we sequenced DNA from a microdissected W chromosome sample and a total female DNA sample and analyzed the results of reference-based and de novo assembly. We found a new repetitive sequence, consisting of fragments of an autosomal protein-coding gene ATF7IP2, several SINE elements, and sequences of unknown origin. This repetitive element is distributed across the whole length of the W chromosome, except the centromeric region. Since it retained only 3 out of 10 original ATF7IP2 exons, it remains unclear whether it is able to produce a protein product. Subsequent studies are required to test the presence of this element in other species of Lacertidae and possible functionality. Our results provide further evidence for the view of W and Y chromosomes as not just “degraded” copies of Z and X chromosomes but independent genomic segments in which novel genetic elements may arise. Full article

(This article belongs to the Special Issue Chromosome-Centric View of the Genome Organization and Evolution)

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16 pages, 3269 KiB

Open AccessArticle

Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches (Cobitis) and Their Clonal Hybrids

by Anatolie Marta, Dmitry Dedukh, Oldřich Bartoš, Zuzana Majtánová and Karel Janko

Genes 2020, 11(6), 617; https://doi.org/10.3390/genes11060617 - 4 Jun 2020

Cited by 14 | Viewed by 3914

Abstract

Interspecific hybridization is a powerful evolutionary force. However, the investigation of hybrids requires the application of methodologies that provide efficient and indubitable identification of both parental subgenomes in hybrid individuals. Repetitive DNA, and especially the satellite DNA sequences (satDNA), can rapidly diverge even between closely related species, hence providing a useful tool for cytogenetic investigations of hybrids. Recent progress in whole-genome sequencing (WGS) offers unprecedented possibilities for the development of new tools for species determination, including identification of species-specific satDNA markers. In this study, we focused on spined loaches (Cobitis, Teleostei), a group of fishes with frequent interspecific hybridization. Using the WGS of one species, C. elongatoides, we identified seven satDNA markers, which were mapped by fluorescence in situ hybridization on mitotic and lampbrush chromosomes of C. elongatoides, C. taenia and their triploid hybrids (C. elongatoides × 2C. taenia). Two of these markers were chromosome-specific in both species, one had centromeric localization in multiple chromosomes and four had variable patterns between tested species. Our study provided a novel set of cytogenetic markers for Cobitis species and demonstrated that NGS-based development of satDNA cytogenetic markers may provide a very efficient and easy tool for the investigation of hybrid genomes, cell ploidy, and karyotype evolution. Full article

(This article belongs to the Special Issue Vertebrate Karyotype Evolution: How Far Have We Come, and Where Are We Going?)

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8 pages, 1001 KiB

Open AccessReview

Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes

by Alla Krasikova and Tatiana Kulikova

Non-Coding RNA 2020, 6(1), 1; https://doi.org/10.3390/ncrna6010001 - 25 Dec 2019

Cited by 5 | Viewed by 4891

Abstract

In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs. Full article

(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)

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14 pages, 1342 KiB

Open AccessReview

Amphibian and Avian Karyotype Evolution: Insights from Lampbrush Chromosome Studies

by Anna Zlotina, Dmitry Dedukh and Alla Krasikova

Genes 2017, 8(11), 311; https://doi.org/10.3390/genes8110311 - 8 Nov 2017

Cited by 12 | Viewed by 7377

Abstract

Amphibian and bird karyotypes typically have a complex organization, which makes them difficult for standard cytogenetic analysis. That is, amphibian chromosomes are generally large, enriched with repetitive elements, and characterized by the absence of informative banding patterns. The majority of avian karyotypes comprise a small number of relatively large macrochromosomes and numerous tiny morphologically undistinguishable microchromosomes. A good progress in investigation of amphibian and avian chromosome evolution became possible with the usage of giant lampbrush chromosomes typical for growing oocytes. Due to the giant size, peculiarities of organization and enrichment with cytological markers, lampbrush chromosomes can serve as an opportune model for comprehensive high-resolution cytogenetic and cytological investigations. Here, we review the main findings on chromosome evolution in amphibians and birds that were obtained using lampbrush chromosomes. In particular, we discuss the data on evolutionary chromosomal rearrangements, accumulation of polymorphisms, evolution of sex chromosomes as well as chromosomal changes during clonal reproduction of interspecies hybrids. Full article

(This article belongs to the Special Issue Chromosomal Evolution)

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