Karyotype Evolution and Genomic Organization of Repetitive DNAs in the Saffron Finch, Sicalis flaveola (Passeriformes, Aves)

The Saffron finch (Sicalis flaveola), a semi-domestic species, is tolerant of human proximity and nesting in roof spaces. Considering the importance of cytogenomic approaches in revealing different aspects of genomic organization and evolution, we provide detailed cytogenetic data for S. flaveola, including the standard Giemsa karyotype, C- and G-banding, repetitive DNA mapping, and bacterial artificial chromosome (BAC) FISH. We also compared our results with the sister groups, Passeriformes and Psittaciformes, bringing new insights into the chromosome and genome evolution of birds. The results revealed contrasting rates of intrachromosomal changes, highlighting the role of SSR (simple short repetition probes) accumulation in the karyotype reorganization. The SSRs showed scattered hybridization, but brighter signals were observed in the microchromosomes and the short arms of Z chromosome in S. flaveola. BACs probes showed conservation of ancestral syntenies of macrochromosomes (except GGA1), as well as the tested microchromosomes. The comparison of our results with previous studies indicates that the great biological diversity observed in Passeriformes was not likely accompanied by interchromosomal changes. In addition, although repetitive sequences often act as hotspots of genome rearrangements, Passeriformes species showed a higher number of signals when compared with the sister group Psittaciformes, indicating that these sequences were not involved in the extensive karyotype reorganization seen in the latter.

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Comparative mapping of a new repetitive DNA sequence and chromosome region-specific probes unveiling rearrangements in an Amazonian frog complex

Genome ◽

10.1139/gen-2020-0199 ◽

2021 ◽

pp. 1-12

Author(s):

Kaleb Pretto Gatto ◽

Lucas H.B. Souza ◽

Juliana Nascimento ◽

Pablo Suárez ◽

Luciana Bolsoni Lourenço

Keyword(s):

Repetitive Dna ◽

Sex Chromosomes ◽

Chromosome Region ◽

Taxonomic Status ◽

Sister Group ◽

Z Chromosome ◽

Genetic Lineage ◽

New Family ◽

Heteromorphic Sex Chromosomes

The frog species Physalaemus ephippifer exists in the Amazonian region and harbors heteromorphic Z and W chromosomes. A genetic lineage closely related to this species was recognized based on its mitochondrial DNA and RADseq-style markers, but its taxonomic status is still unclear and has been referred to as Lineage 1 of “P. cuvieri”. The heteromorphic sex chromosomes found in P. ephippifer are not present in this lineage and which of its chromosome pairs is homologous to the sex chromosomes of P. ephippifer remain to be elucidated as well as the role of such a karyotypic divergence in the evolution of these frogs. Here, we described a new family of repetitive DNA and used its chromosomal sites along with the markers detected by a probe constructed from the microdissected segment of the Z chromosome of P. ephippifer to infer chromosomal homology. We also analyzed an unnamed species that is considered to be the sister group of the clade composed of Lineage 1 of “P. cuvieri” and P. ephippifer. Our results suggest that complex rearrangements involving the chromosomes that were inferred to be homeologous to the sex chromosomes of P. ephippifer have occurred during the divergence of this group of frogs.

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Repeat Sequence Mapping Shows Different W Chromosome Evolutionary Pathways in Two Caprimulgiformes Families

Birds ◽

10.3390/birds1010004 ◽

2020 ◽

Vol 1 (1) ◽

pp. 19-34

Author(s):

Marcelo Santos de Souza ◽

Rafael Kretschmer ◽

Suziane Alves Barcellos ◽

Alice Lemos Costa ◽

Marcelo de Bello Cioffi ◽

...

Keyword(s):

Genomic Organization ◽

Constitutive Heterochromatin ◽

Repetitive Sequences ◽

Repeat Sequence ◽

Z Chromosome ◽

W Chromosome ◽

Variation Data ◽

Extra Step ◽

The Common ◽

Consequent Increase

Although birds belonging to order Caprimulgiformes show extensive karyotype variation, data concerning their genomic organization is still scarce, as most studies have presented only results obtained from conventional staining analyses. Nevertheless, some interesting findings have been observed, such as the W chromosome of the Common Potoo, Nyctibius griseus (2n = 86), which has the same morphology and size of the Z chromosome, a rare feature in Neognathae birds. Hence, we aimed to investigate the process by which the W chromosome of this species was enlarged. For that, we analyzed comparatively the chromosome organization of the Common Potoo and the Scissor-tailed Nightjar, Hydropsalis torquata (2n = 74), which presents the regular differentiated sex chromosomes, by applying C-banding, G-banding and mapping of repetitive DNAs (microsatellite repeats and 18S rDNA). Our results showed an accumulation of constitutive heterochromatin in the W chromosome of both species. However, 9 out of 11 microsatellite sequences hybridized in the large W chromosome in the Common Potoo, while none of them hybridized in the W chromosome of the Scissor-tailed Nightjar. Therefore, we can conclude that the accumulation of microsatellite sequences, and consequent increase in constitutive heterochromatin, was responsible for the enlargement of the W chromosome in the Common Potoo. Based on these results, we conclude that even though these two species belong to the same order, their W chromosomes have gone through different evolutionary histories, with an extra step of accumulation of repetitive sequences in the Common Potoo.

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Genomic organization of the 260 kb surrounding the waxy locus in a Japonica rice

Genome ◽

10.1139/g99-068 ◽

1999 ◽

Vol 42 (6) ◽

pp. 1121-1126 ◽

Cited By ~ 4

Author(s):

Hironori Nagano ◽

Lihua Wu ◽

Shinji Kawasaki ◽

Yuji Kishima ◽

Yoshio Sano

Keyword(s):

Genomic Organization ◽

Physical Map ◽

Repetitive Sequences ◽

Bac Library ◽

Artificial Chromosome ◽

Molecular Organization ◽

Japonica Rice ◽

Class 1 ◽

Average Size ◽

Waxy Locus

The present study was carried out to characterize the molecular organization in the vicinity of the waxy locus in rice. To determine the structural organization of the region surrounding waxy, contiguous clones covering a total of 260 kb were constructed using a bacterial artificial chromosome (BAC) library from the Shimokita variety of Japonica rice. This map also contains 200 overlapping subclones, which allowed construction of a fine physical map with a total of 64 HindIII sites. During the course of constructing the map, we noticed the presence of some repeated regions which might be related to transposable elements. We divided the 260-kb region into 60 segments (average size of 5.7 kb) to use as probes to determine their genomic organization. Hybridization patterns obtained by probing with these segments were classified into four types: class 1, a single or a few bands without a smeared background; class 2, a single or a few bands with a smeared background; class 3, multiple discrete bands without a smeared background; and class 4, only a smeared background. These classes constituted 6.5%, 20.9%, 3.7%, and 68.9% of the 260-kb region, respectively. The distribution of each class revealed that repetitive sequences are a major component in this region, as expected, and that unique sequence regions were mostly no longer than 6 kb due to interruption by repetitive sequences. We discuss how the map constructed here might be a powerful tool for characterization and comparison of the genome structures and the genes around the waxy locus in the Oryza species.Key words: BAC library, genomic organization, physical map, rice (Oryza sativa), the waxy locus.

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Challenging the State: Devolutionary Tenure Transitions for Saving and Expanding Forests

Human Ecology ◽

10.1007/s10745-021-00231-2 ◽

2021 ◽

Author(s):

Liz Alden Wily

Keyword(s):

Rural Communities ◽

Property Rights ◽

Protected Areas ◽

Forest Cover ◽

Biological Diversity ◽

Convention On Biological Diversity ◽

Property Relations ◽

The Will ◽

Customary Land

AbstractI address a contentious element in forest property relations to illustrate the role of ownership in protecting and expanding of forest cover by examining the extent to which rural communities may legally own forests. The premise is that whilst state-owned protected areas have contributed enormously to forest survival, this has been insufficiently successful to justify the mass dispossession of customary land-owning communities this has entailed. Further, I argue that state co-option of community lands is unwarranted. Rural communities on all continents ably demonstrate the will and capacity to conserve forests – provided their customary ownership is legally recognized. I explore the property rights reforms now enabling this. The replication potential of community protected forestlands is great enough to deserve flagship status in global commitments to expand forest including in the upcoming new Convention on Biological Diversity (CBD).

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Chromosomal Analysis in Crotophaga ani (Aves, Cuculiformes) Reveals Extensive Genomic Reorganization and an Unusual Z-Autosome Robertsonian Translocation

Cells ◽

10.3390/cells10010004 ◽

2020 ◽

Vol 10 (1) ◽

pp. 4

Author(s):

Rafael Kretschmer ◽

Ricardo José Gunski ◽

Analía del Valle Garnero ◽

Thales Renato Ochotorena de Freitas ◽

Gustavo Akira Toma ◽

...

Keyword(s):

Robertsonian Translocation ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Rare Event ◽

Chromosome Morphology ◽

Z Chromosome ◽

Molecular Cytogenetic ◽

Intrachromosomal Rearrangements ◽

Genomic Reorganization

Although cytogenetics studies in cuckoos (Aves, Cuculiformes) have demonstrated an interesting karyotype variation, such as variations in the chromosome morphology and diploid number, their chromosome organization and evolution, and relation with other birds are poorly understood. Hence, we combined conventional and molecular cytogenetic approaches to investigate chromosome homologies between chicken and the smooth-billed ani (Crotophaga ani). Our results demonstrate extensive chromosome reorganization in C. ani, with interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were observed in some macrochromosomes, including the Z chromosome. The most evolutionary notable finding was a Robertsonian translocation between the microchromosome 17 and the Z chromosome, a rare event in birds. Additionally, the simple short repeats (SSRs) tested here were preferentially accumulated in the microchromosomes and in the Z and W chromosomes, showing no relationship with the constitutive heterochromatin regions, except in the W chromosome. Taken together, our results suggest that the avian sex chromosome is more complex than previously postulated and revealed the role of microchromosomes in the avian sex chromosome evolution, especially cuckoos.

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Big hitting collectors make massive and disproportionate contribution to the discovery of plant species

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.2439 ◽

2012 ◽

Vol 279 (1736) ◽

pp. 2269-2274 ◽

Cited By ~ 21

Author(s):

Daniel P. Bebber ◽

Mark A. Carine ◽

Gerrit Davidse ◽

David J. Harris ◽

Elspeth M. Haston ◽

...

Keyword(s):

Plant Species ◽

Biological Diversity ◽

High Rate ◽

Type Specimens ◽

Fundamental Goal ◽

The World ◽

Plant Families ◽

The Right ◽

Geographical Locations

Discovering biological diversity is a fundamental goal—made urgent by the alarmingly high rate of extinction. We have compiled information from more than 100 000 type specimens to quantify the role of collectors in the discovery of plant diversity. Our results show that more than half of all type specimens were collected by less than 2 per cent of collectors. This highly skewed pattern has persisted through time. We demonstrate that a number of attributes are associated with prolific plant collectors: a long career with increasing productivity and experience in several countries and plant families. These results imply that funding a small number of expert plant collectors in the right geographical locations should be an important element in any effective strategy to find undiscovered plant species and complete the inventory of the world flora.

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THE ROLE OF EDGE ECOTONES FOR CONSERVATION BIOLOGICAL DIVERSITY

Сурский вестник ◽

10.36461/2619-1202_2021_04_001 ◽

2021 ◽

pp. 3-7

Author(s):

A.A. Volodkin ◽

O.A. Volodkina

Keyword(s):

Biological Diversity

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Breakpoint junctions of chromosome 9p deletions in two human glioma cell lines

Molecular and Cellular Biology ◽

10.1128/mcb.14.11.7604-7610.1994 ◽

1994 ◽

Vol 14 (11) ◽

pp. 7604-7610

Author(s):

H M Pomykala ◽

S K Bohlander ◽

P L Broeker ◽

O I Olopade ◽

M O Díaz

Keyword(s):

Cell Line ◽

Cell Lines ◽

Lymphoblastic Leukemia ◽

Repetitive Sequences ◽

Leukemia Cell ◽

Chromosome 9 ◽

Breakpoint Junction ◽

Leukemia Cell Lines ◽

Long Interspersed Nuclear Elements

Interstitial deletions of the short arm of chromosome 9 are associated with glioma, acute lymphoblastic leukemia, melanoma, mesothelioma, lung cancer, and bladder cancer. The distal breakpoints of the deletions (in relation to the centromere) in 14 glioma and leukemia cell lines have been mapped within the 400 kb IFN gene cluster located at band 9p21. To obtain information about the mechanism of these deletions, we have isolated and analyzed the nucleotide sequences at the breakpoint junctions in two glioma-derived cell lines. The A1235 cell line has a complex rearrangement of chromosome 9, including a deletion and an inversion that results in two breakpoint junctions. Both breakpoints of the distal inversion junction occurred within AT-rich regions. In the A172 cell line, a tandem heptamer repeat was found on either side of the deletion breakpoint junction. The distal breakpoint occurred 5' of IFNA2; the 256 bp sequenced from the proximal side of the breakpoint revealed 95% homology to long interspersed nuclear elements. One- and two-base-pair overlaps were observed at these junctions. The possible role of sequence overlaps, and repetitive sequences, in the rearrangement is discussed.

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Chromatin Diminution in Cyclops kolensis Lill. (Copepoda, Crustacea) as a Radical Way to Inactivate Redundant Genome in Somatic Cells

Cytogenetic and Genome Research ◽

10.1159/000494157 ◽

2018 ◽

Vol 156 (3) ◽

pp. 165-172 ◽

Cited By ~ 2

Author(s):

Andrey K. Grishanin ◽

Maxim V. Zagoskin

Keyword(s):

Chromosome Number ◽

Repetitive Sequences ◽

Early Embryogenesis ◽

Chromosome Size ◽

Chromatin Diminution ◽

Elimination Process ◽

Dna Elimination ◽

Molecular Studies ◽

Cyclops Kolensis

Chromatin diminution (CD) is a phenomenon of programmed DNA elimination which takes place in early embryogenesis in some eukaryotes. The mechanism and biological role of CD remain largely unknown. During CD in the freshwater copepod Cyclops kolensis, the genome of cells of the somatic lineage is reorganized and reduced in size by more than 90% without affecting the genome of germline cells. Although the diploid chromosome number is unchanged, chromosome size is dramatically reduced by CD. The eliminated DNA consists primarily of repetitive sequences and localizes within granules during the elimination process. In this review, we provide an overview of CD in C. kolensis including both cytological and molecular studies.

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