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16 pages, 9134 KiB

Open AccessArticle

Comprehensive Comparative Analysis Sheds Light on the Patterns of Microsatellite Distribution across Birds Based on the Chromosome-Level Genomes

by Kaize Feng, Chuang Zhou, Lei Wang, Chunhui Zhang, Zhixiong Yang, Zhengrui Hu, Bisong Yue and Yongjie Wu

Animals 2023, 13(4), 655; https://doi.org/10.3390/ani13040655 - 13 Feb 2023

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Abstract

Microsatellites (SSRs) are widely distributed in the genomes of organisms and are an important genetic basis for genome evolution and phenotypic adaptation. Although the distribution patterns of microsatellites have been investigated in many phylogenetic lineages, they remain unclear within the morphologically and physiologically [...] Read more.

Microsatellites (SSRs) are widely distributed in the genomes of organisms and are an important genetic basis for genome evolution and phenotypic adaptation. Although the distribution patterns of microsatellites have been investigated in many phylogenetic lineages, they remain unclear within the morphologically and physiologically diverse avian clades. Here, based on high-quality chromosome-level genomes, we examined the microsatellite distribution patterns for 53 birds from 16 orders. The results demonstrated that each type of SSR had the same ratio between taxa. For example, the frequency of imperfect SSRs (I-SSRs) was 69.90–84.61%, while perfect SSRs (P-SSRs) were 14.86–28.13% and compound SSRs (C-SSRs) were 0.39–2.24%. Mononucleotide SSRs were dominant for perfect SSRs (32.66–76.48%) in most bird species (98.11%), and A(n) was the most abundant repeat motifs of P-SSRs in all birds (5.42–68.22%). Our study further confirmed that the abundance and diversity of microsatellites were less effected by evolutionary history but its length. The number of P-SSRs decreased with increasing repeat times, and longer P-SSRs motifs had a higher variability coefficient of the repeat copy number and lower diversity, indicating that longer motifs tended to have more stable preferences in avian genomes. We also found that P-SSRs were mainly distributed at the gene ends, and the functional annotation for these genes demonstrated that they were related to signal transduction and cellular process. In conclusion, our research provided avian SSR distribution patterns, which will help to explore the genetic basis for phenotypic diversity in birds. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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13 pages, 2850 KiB

Open AccessArticle

Exploring the Relationship between Spontaneous Sister Chromatid Exchange and Genome Instability in Two Cryptic Species of Non-Human Primates

by Mariela Nieves, Fiona Puntieri, Susan M. Bailey, Marta D. Mudry and David G. Maranon

Animals 2023, 13(3), 510; https://doi.org/10.3390/ani13030510 - 01 Feb 2023

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Abstract

There are extensive studies on chromosome morphology and karyotype diversity in primates, yet we still lack insight into genomic instability as a key factor underlying the enormous interspecies chromosomal variability and its potential contribution to evolutionary dynamics. In this sense, the assessment of [...] Read more.

There are extensive studies on chromosome morphology and karyotype diversity in primates, yet we still lack insight into genomic instability as a key factor underlying the enormous interspecies chromosomal variability and its potential contribution to evolutionary dynamics. In this sense, the assessment of spontaneous sister chromatid exchange (SCE) frequencies represents a powerful tool for evaluating genome stability. Here, we employed G-banding, fluorescence plus Giemsa (FPG), and chromosome orientation fluorescence in situ hybridization (CO-FISH) methodologies to characterize both chromosome-specific frequencies of spontaneously occurring SCE throughout the genome (G-SCE) and telomere-specific SCE (T-SCE). We analyzed primary fibroblast cultures from two male species of Ateles living in captivity: Ateles paniscus (APA) and Ateles chamek (ACH). High frequencies of G-SCEs were observed in both species. Interestingly, G-SCEs clustered on evolutionary relevant chromosome pairs: ACH chromosomes 1, 2, 3, 4, and 7, and APA chromosomes 1, 2, 3, 4/12, 7, and 10. Furthermore, a statistically significant difference between the observed and expected G-SCE frequencies, not correlated with chromosome size, was also detected. CO-FISH analyses revealed the presence of telomere-specific recombination events in both species, which included T-SCE, as well as interstitial telomere signals and telomere duplications, with APA chromosomes displaying higher frequencies, compared to ACH. Our analyses support the hypothesis that regions of Ateles chromosomes susceptible to recombination events are fragile sites and evolutionary hot spots. Thus, we propose SCE analyses as a valuable indicator of genome instability in non-human primates. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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9 pages, 846 KiB

Open AccessArticle

Microchromosome BAC-FISH Reveals Different Patterns of Genome Organization in Three Charadriiformes Species

by Marcelo Santos de Souza, Suziane Alves Barcellos, Michelly da Silva dos Santos, Ricardo José Gunski, Analía del Valle Garnero, Edivaldo Herculano Corrêa de Oliveira, Rebecca E. O’Connor, Darren K. Griffin and Rafael Kretschmer

Animals 2022, 12(21), 3052; https://doi.org/10.3390/ani12213052 - 06 Nov 2022

Cited by 3 | Viewed by 1728

Abstract

Microchromosomes, once considered unimportant elements of the genome, represent fundamental building blocks of bird karyotypes. Shorebirds (Charadriiformes) comprise a wide variety of approximately 390 species and are considered a valuable model group for biological studies. Despite this variety, cytogenetic analysis is still very [...] Read more.

Microchromosomes, once considered unimportant elements of the genome, represent fundamental building blocks of bird karyotypes. Shorebirds (Charadriiformes) comprise a wide variety of approximately 390 species and are considered a valuable model group for biological studies. Despite this variety, cytogenetic analysis is still very scarce in this bird order. Thus, the aim of this study was to provide insight into the Charadriiformes karyotype, with emphasis on microchromosome evolution in three species of shorebirds—Calidris canutus, Jacana jacana, and Vanellus chilensis—combining classical and molecular approaches. Cross-species FISH mapping applied two BAC probes for each microchromosome, GGA10–28 (except GGA16). The experiments revealed different patterns of microchromosome organization in the species investigated. Hence, while in C. canutus, we found two microchromosomes involved in chromosome fusions, they were present as single pairs in V. chilensis. We also described a new chromosome number for C. canutus (2n = 92). Hence, this study contributed to the understanding of genome organization and evolution of three shorebird species. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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11 pages, 2252 KiB

Open AccessArticle

Chromosomal Diversification in Pseudacanthicus Species (Loricariidae, Hypostominae) Revealed by Comparative Mapping of Repetitive Sequences

by Kevin Santos da Silva, Augusto César Paes de Souza, Luís Reginaldo Ribeiro Rodrigues, Julio Cesar Pieczarka and Cleusa Yoshiko Nagamachi

Animals 2022, 12(19), 2612; https://doi.org/10.3390/ani12192612 - 29 Sep 2022

Cited by 2 | Viewed by 1255

Abstract

Pseudacanthicus is a genus of Neotropical fish with eight valid species, in addition to numerous lineages not formally identified. It occurs along the Amazon and Tocantins River basins, in Suriname and in the Guiana shield. There are no karyotypic data in the literature [...] Read more.

Pseudacanthicus is a genus of Neotropical fish with eight valid species, in addition to numerous lineages not formally identified. It occurs along the Amazon and Tocantins River basins, in Suriname and in the Guiana shield. There are no karyotypic data in the literature for species of this genus. Here, the karyotypes of three Pseudacanthicus species (P. spinosus, P. leopardus and Pseudacanthicus sp.) were comparatively analyzed by classical cytogenetics and fluorescence in situ hybridization using 18S and 5S rDNA probes, U2 snDNA and telomeric sequences. The analyzed species presented 52 chromosomes and KF = 18 m + 34 sm. Constitutive heterochromatin occurred in blocks on a few chromosomes. The 18S rDNA occurred in a single pair; interestingly, P. leopardus presented only one locus of this sequence in its diploid genome. The 5S rDNA sequence occurred in only one pair in P. leopardus, and in multiple sites in Pseudacanthicus sp. and P. spinosus. The snDNA U2 occurred in only one pair in all analyzed species. Telomeric sequences did not show interstitial sites. Although Pseudacanthicus species share the same 2n and KF, repetitive sequence analysis revealed karyotypic diversity among these species. The occurrence of DNA double-strand breaks related to fragile sites, unequal crossing over and transpositions is proposed as the mechanism of karyotypic diversification, suggesting that the conservation of the karyotypic macrostructure is only apparent in this group of fish. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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15 pages, 2328 KiB

Open AccessArticle

Genomic Organization of Microsatellites and LINE-1-like Retrotransposons: Evolutionary Implications for Ctenomys minutus (Rodentia: Ctenomyidae) Cytotypes

by Thays Duarte de Oliveira, Natasha Avila Bertocchi, Rafael Kretschmer, Edivaldo H. C. de Oliveira, Marcelo de Bello Cioffi, Thomas Liehr and Thales R. O. de Freitas

Animals 2022, 12(16), 2091; https://doi.org/10.3390/ani12162091 - 16 Aug 2022

Cited by 1 | Viewed by 2055

Abstract

The Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae) comprise about 65 species, which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). Among them, C. minutus stands out with 45 different cytotypes already identified, among [...] Read more.

The Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae) comprise about 65 species, which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). Among them, C. minutus stands out with 45 different cytotypes already identified, among which, seven parental ones, named A to G, are parapatrically distributed in the coastal plains of Southern Brazil. Looking for possible causes that led to such extensive karyotype diversification, we performed chromosomal mapping of different repetitive DNAs, including microsatellites and long interspersed element-1 (LINE-1) retrotransposons in the seven parental cytotypes. Although microsatellites were found mainly in the centromeric and telomeric regions of the chromosomes, different patterns occur for each cytotype, thus revealing specific features. Likewise, the LINE-1-like retrotransposons also showed a differential distribution for each cytotype, which may be linked to stochastic loss of LINE-1 in some populations. Here, microsatellite motifs (A)₃₀, (C)₃₀, (CA)₁₅, (CAC)₁₀, (CAG)₁₀, (CGG)₁₀, (GA)₁₅, and (GAG)₁₀ could be mapped to fusion of chromosomes 20/17, fission and inversion in the short arm of chromosome 2, fusion of chromosomes 23/19, and different combinations of centric and tandem fusions of chromosomes 22/24/16. These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoints and highlight their direct impact in promoting chromosomal rearrangements. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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11 pages, 2042 KiB

Open AccessArticle

A Perspective of Molecular Cytogenomics, Toxicology, and Epigenetics for the Increase of Heterochromatic Regions and Retrotransposable Elements in Tambaqui (Colossoma macropomum) Exposed to the Parasiticide Trichlorfon

by Maria dos Santos Costa, Hallana Cristina Menezes da Silva, Simone Cardoso Soares, Ramon Marin Favarato, Eliana Feldberg, Ana Lúcia Silva Gomes, Roberto Ferreira Artoni and Daniele Aparecida Matoso

Animals 2022, 12(15), 1945; https://doi.org/10.3390/ani12151945 - 31 Jul 2022

Cited by 2 | Viewed by 1486

Abstract

Rex retroelements are the best-known transposable elements class and are broadly distributed through fish and also individual genomes, playing an important role in their evolutionary dynamics. Several agents can stress these elements; among them, there are some parasitic compounds such as the organochlorophosphate [...] Read more.

Rex retroelements are the best-known transposable elements class and are broadly distributed through fish and also individual genomes, playing an important role in their evolutionary dynamics. Several agents can stress these elements; among them, there are some parasitic compounds such as the organochlorophosphate Trichlorfon. Consequently, knowing that the organochlorophosphate Trichlorfon is indiscriminately used as an antiparasitic in aquaculture, the current study aimed to analyze the effects of this compound on the activation of the Transposable Elements (TEs) Rex1, Rex3, and Rex6 and the structure of heterochromatin in the mitotic chromosomes of the tambaqui (Colossoma macropomum). For this, two concentrations of the pesticide were used: 30% (0.261 mg/L) and 50% (0.435 mg/L) of the recommended LC_{50–96 h} concentration (0.87 mg/L) for this fish species. The results revealed a dispersed distribution for Rex1 and Rex6 retroelements. Rex3 showed an increase in both marking intensity and distribution, as well as enhanced chromosomal heterochromatinization. This probably happened by the mediation of epigenetic adaptive mechanisms, causing the retroelement mobilization to be repressed. However, this behavior was most evident when Trichlorfon concentrations and exposure times were the greatest, reflecting the genetic flexibility necessary for this species to successfully adapt to environmental changes. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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10 pages, 3284 KiB

Open AccessArticle

Establishment of the Primary Avian Gonadal Somatic Cell Lines for Cytogenetic Studies

by Inna E. Pristyazhnyuk, Lyubov P. Malinovskaya and Pavel M. Borodin

Animals 2022, 12(13), 1724; https://doi.org/10.3390/ani12131724 - 04 Jul 2022

Viewed by 1717

Abstract

The last decade was marked by a steep rise in avian studies at genomic and cellular levels. Cell lines are important tools for in vitro studies in cell biology and cytogenetics. We developed a simple method of primary somatic cell culture establishment from [...] Read more.

The last decade was marked by a steep rise in avian studies at genomic and cellular levels. Cell lines are important tools for in vitro studies in cell biology and cytogenetics. We developed a simple method of primary somatic cell culture establishment from the ovaries of the great tits (Parus major) and testes of ten Passerine species, characterized the cellular composition of the ovary-derived lines using RT-PCR and immunolocalization of the tissue-specific markers and tested the efficiency of two methods of genetic transformation of the ovary-derived cell line. We found that the ovary-derived cell cultures of the great tit were composed of fibroblasts mainly, but also contained interstitial and granulosa cells. They were cultivated until the 10th passage without any noticeable decrease in their proliferative activity. The testis-derived cell cultures had lower proliferative potential. However, both ovary- and testis-derived cell cultures provided enough material for high quality mitotic metaphase chromosome preparations. The efficiency of its transduction with lentivirus containing a GFP reporter was very low, while electroporation with episomal vectors expressing GFP resulted in a high yield of GFP-positive cells. The proposed method could be used for the generation of high quality material for various cytogenetic and genomic studies. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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Review

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19 pages, 2013 KiB

Open AccessReview

B Chromosomes in Psalidodon scabripinnis (Characiformes, Characidae) Species Complex

by Duílio M. Z. A. Silva, Jonathan P. Castro, Caio A. G. Goes, Ricardo Utsunomia, Mateus R. Vidal, Cristiano N. Nascimento, Lucas F. Lasmar, Fabilene G. Paim, Letícia B. Soares, Claudio Oliveira, Fábio Porto-Foresti, Roberto F. Artoni and Fausto Foresti

Animals 2022, 12(17), 2174; https://doi.org/10.3390/ani12172174 - 25 Aug 2022

Cited by 2 | Viewed by 2084

Abstract

B chromosomes are extra-genomic components of cells found in individuals and in populations of some eukaryotic organisms. They have been described since the first observations of chromosomes, but several aspects of their biology remain enigmatic. Despite being present in hundreds of fungi, plants, [...] Read more.

B chromosomes are extra-genomic components of cells found in individuals and in populations of some eukaryotic organisms. They have been described since the first observations of chromosomes, but several aspects of their biology remain enigmatic. Despite being present in hundreds of fungi, plants, and animal species, only a small number of B chromosomes have been investigated through high-throughput analyses, revealing the remarkable mechanisms employed by these elements to ensure their maintenance. Populations of the Psalidodon scabripinnis species complex exhibit great B chromosome diversity, making them a useful material for various analyses. In recent years, important aspects of their biology have been revealed. Here, we review these studies presenting a comprehensive view of the B chromosomes in the P. scabripinnis complex and a new hypothesis regarding the role of the B chromosome in the speciation process. Full article

(This article belongs to the Special Issue Vertebrate Chromosome Organization and Evolution: From Conventional Staining to Chromosomics)

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