Comparative Cytogenetic and Sequence Analysis of <i>U Small Nuclear RNA</i> Genes in Three <i>Ancistrus</i> Species (Siluriformes: Loricariidae)

Schott, Stephane Carolenn Quadros; Glugoski, Larissa; Azambuja, Matheus; Moreira‐Filho, Orlando; Vicari, Marcelo Ricardo; Nogaroto, Viviane

doi:10.1089/zeb.2022.0040

Cited by 7 publications

(18 citation statements)

References 67 publications

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“…The U snRNA genes represent another group of tandem repeat sequences used in comparative chromosomal analyses in fish [ 25 , 27 , 29 ]. Unlike other genes that express non-coding RNAs, U snRNA gene families exhibit remarkable similarity in base sequences when copies obtained from different groups of organisms are compared [ 25 , 27 , 29 ].…”

Section: Discussionmentioning

confidence: 99%

“…In Loricariidae, a syntenic and single-site organization between the 18S and 5S rDNA genes represents a plesiomorphic condition [ 11 ], while the synteny break and occurrence of multiple sites of these genes is frequent in Ancistrini, showing mechanisms of chromosomal differentiation involving this group of sequences [ 9 , 13 , 26 ]. However, information about the chromosomal organization of U snDNA sequences is limited to a few species of Loricariidae [ 26 , 28 , 29 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

“…The U snDNA are genes that transcribe non-coding RNAs involved in the spliceosome arrangement, the structure responsible for the maturation of messenger RNA (mRNA) in eukaryotes [ 31 ]. Sequences of these genes are organized in tandem repeats and used in comparative cytogenetic analysis [ 21 , 22 , 25 , 27 , 29 , 32 ]. Comparative analyses of in situ localization and molecular characterization demonstrate that, unlike other groups of genes encoding non-coding RNAs, U snRNA genes show remarkable similarity with orthologous copies [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

“…Comparative analyses of in situ localization and molecular characterization demonstrate that, unlike other groups of genes encoding non-coding RNAs, U snRNA genes show remarkable similarity with orthologous copies [ 27 ]. These genes may present distinct chromosomal organizations in different groups of species, occurring in single, multiple sites or clusters formed by different gene families (e.g., snRNA and rRNA genes) [ 26 , 27 , 28 , 29 , 32 , 33 , 34 , 35 ]. Furthermore, genomic data demonstrate that pseudogenes and non-functional copies of U snDNA occur in fish genomes [ 27 , 29 ], indicating the participation of these repetitive sequences in chromosomal reorganization, including transposition events.…”

Section: Introductionmentioning

confidence: 99%

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Mechanisms of Karyotypic Diversification in Ancistrus (Siluriformes, Loricariidae): Inferences from Repetitive Sequence Analysis

Santos da Silva,

Glugoski,

Vicari

et al. 2023

IJMS

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Ancistrus is a highly diverse neotropical fish genus that exhibits extensive chromosomal variability, encompassing karyotypic morphology, diploid chromosome number (2n = 34–54), and the evolution of various types of sex chromosome systems. Robertsonian rearrangements related to unstable chromosomal sites are here described. Here, the karyotypes of two Ancistrus species were comparatively analyzed using classical cytogenetic techniques, in addition to isolation, cloning, sequencing, molecular characterization, and fluorescence in situ hybridization of repetitive sequences (i.e., 18S and 5S rDNA; U1, U2, and U5 snDNA; and telomere sequences). The species analyzed here have different karyotypes: Ancistrus sp. 1 (2n = 38, XX/XY) and Ancistrus cirrhosus (2n = 34, no heteromorphic sex chromosomes). Comparative mapping showed different organizations for the analyzed repetitive sequences: 18S and U1 sequences occurred in a single site in all populations of the analyzed species, while 5S and U2 sequences could occur in single or multiple sites. A sequencing analysis confirmed the identities of the U1, U2, and U5 snDNA sequences. Additionally, a syntenic condition for U2-U5 snDNA was found in Ancistrus. In a comparative analysis, the sequences of rDNA and U snDNA showed inter- and intraspecific chromosomal diversification. The occurrence of Robertsonian rearrangements and other dispersal mechanisms of repetitive sequences are discussed.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mechanisms of Karyotypic Diversification in Ancistrus (Siluriformes, Loricariidae): Inferences from Repetitive Sequence Analysis

Santos da Silva,

Glugoski,

Vicari

et al. 2023

IJMS

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“…TRs, in contrast, are found as tandem arrays or head-to-tail motifs from several to more than a hundred copies [Myers, 2007]. TRs include microsatellite, minisatellite, satellite DNA, and also ribosomal genes (minor 5S and major 45S), histone genes, and small nuclear RNA (snRNA), which are found as clusters on single chromosomal locus or multiple loci [Valente et al, 2011;Sember et al, 2020;Gazoni et al, 2021;Schott et al, 2022]. These loci often undergo concerted evolution [Elder and Turner, 1995;Liao, 1999] which causes paralogous repetitive elements within a species to be more similar to each other than to orthologous repetitive elements, even when the origin of repetitive elements precedes speciation [Liao, 1999].…”

Section: Introductionmentioning

confidence: 99%

Consequences of polyploidy and divergence as revealed by cytogenetic mapping of repetitive elements in African clawed frogs (Xenopus, Pipidae)

Fornaini

Bergelová

Gvoždík

et al. 2023

Preprint

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Repetitive elements have multiple copies in a genome and have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here we compared the numbers and positions of repetitive elements in diploid and tetraploid species of the genus Xenopus, specifically between the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus (both from Silurana subgenus), and also in more phylogenetically distant allotetraploids from the amieti, muelleri, and laevis species groups (all from subgenus Xenopus). Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events – one closely related to the diploid species and one that is more distant. We used fluorescence in situ hybridization (FISH) to map the U1 and U2 small nuclear RNA (snRNA), histone H3, and retroelement Rex3 repeat loci. Our results demonstrated that U1 and U2 snRNA loci were conserved in copy number and position in the Silurana genomes, with one copy of U1 and U2 snRNA in diploid genome and one copy in each subgenome of allotetraploid species in subgenus Silurana and the muelleri species group. However, snRNA content varied among allotetraploid species in the amieti and laevis species groups, with only one U1 and U2 snRNA copy present in the entire allotetraploid genome of three species. Probes interrogating repetitive H3 and Rex3 loci were present on all chromosomes in diploid and allotetraploid species in subgenus Silurana, and in the muelleri species group. In the amieti and laevis species groups, H3 and Rex3 repeats were present on about half of all chromosomes. Overall, the results indicated that variation in the position and copy number of repetitive elements increases with phylogenetic distance, with high conservation in diploid and tetraploid Silurana species but more variation between Xenopus subgenera and among species groups in the subgenus Xenopus. In general and as expected, the effect of allotetraploidization was to increase the copy number of repetitive elements relative to diploid species, with the exception of the amieti and laevis species groups.

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Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus, Pipidae)

et al. 2023

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Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events — one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.

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Comparative Cytogenetic and Sequence Analysis of U Small Nuclear RNA Genes in Three Ancistrus Species (Siluriformes: Loricariidae)

Cited by 7 publications

References 67 publications

Mechanisms of Karyotypic Diversification in Ancistrus (Siluriformes, Loricariidae): Inferences from Repetitive Sequence Analysis

Mechanisms of Karyotypic Diversification in Ancistrus (Siluriformes, Loricariidae): Inferences from Repetitive Sequence Analysis

Consequences of polyploidy and divergence as revealed by cytogenetic mapping of repetitive elements in African clawed frogs (Xenopus, Pipidae)

Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus, Pipidae)

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