scholarly journals Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 362 ◽  
Author(s):  
Lucas G. Kiazim ◽  
Rebecca E. O’Connor ◽  
Denis M. Larkin ◽  
Michael N. Romanov ◽  
Valery G. Narushin ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Karyotype Evolution ◽  
Chromosome Rearrangement ◽  
Bird Species ◽  
Artificial Chromosome ◽  
Houbara Bustard ◽  
Mathematical Analyses ◽  
Genome Assemblies ◽  
Probe Set ◽  
Common Blackbird

Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.

scholarly journals Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 124
Author(s):  
Alessio Iannucci ◽  
Alexey I. Makunin ◽  
Artem P. Lisachov ◽  
Claudio Ciofi ◽  
Roscoe Stanyon ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Karyotype Evolution ◽  
Genomic Data ◽  
Anolis Carolinensis ◽  
Vertebrate Genome ◽  
Single Chromosome ◽  
Sequencing Technologies ◽  
Novel Approaches ◽  
Genome Assemblies ◽  
Generation Sequencing

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

scholarly journals Donkey genome and insight into the imprinting of fast karyotype evolution

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jinlong Huang ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Wunierfu Shiraigol ◽  
Bei Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Karyotype Evolution ◽  
De Novo ◽  
Cycle Phase ◽  
Satellite Sequences ◽  
Chromatid Segregation ◽  
Karyotypic Instability ◽  
Wild Ass ◽  
Genome Assemblies ◽  
Insight Into

Abstract The donkey, like the horse, is a promising model for exploring karyotypic instability. We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. Our results reflect the distinct characteristics of donkeys, including more effective energy metabolism and better immunity than horses. The donkey shows a steady demographic trajectory. We detected abundant satellite sequences in some inactive centromere regions but not in neocentromere regions, while ribosomal RNAs frequently emerged in neocentromere regions but not in the obsolete centromere regions. Expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution. APC/C, controlling sister chromatid segregation, cytokinesis and the establishment of the G1 cell cycle phase were identified by analysis of miRNA targets and rapidly evolving genes.

scholarly journals Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 259 ◽  
Author(s):  
Karolina Susek ◽  
Wojciech Bielski ◽  
Katarzyna B. Czyż ◽  
Robert Hasterok ◽  
Scott A. Jackson ◽  
...  
Keyword(s):  
Karyotype Evolution ◽  
Chromosomal Rearrangements ◽  
Chromosome Mapping ◽  
Artificial Chromosome ◽  
Basic Chromosome Number ◽  
Plant Genome ◽  
Old World ◽  
Whole Genome Duplications ◽  
Genome Duplications

Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.

Karyotype evolution and phylogenetic relationships of hamsters (Cricetidae, Muroidea, Rodentia) inferred from chromosomal painting and banding comparison

2007 ◽  
Author(s):  
Svetlana A. Romanenko ◽  
Vitaly T. Volobouev ◽  
Polina L. Perelman ◽  
Vladimir S. Lebedev ◽  
Natalya A. Serdukova ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Karyotype Evolution ◽  
Chromosomal Painting

scholarly journals Muntjac chromosome evolution and architecture

2019 ◽  
Author(s):  
Austin B. Mudd ◽  
Jessen V. Bredeson ◽  
Rachel Baum ◽  
Dirk Hockemeyer ◽  
Daniel S. Rokhsar
Keyword(s):  
Chromosome Evolution ◽  
Common Ancestor ◽  
Karyotype Evolution ◽  
Karyotype Analysis ◽  
Rapid Evolution ◽  
Unique Case ◽  
Show Evidence ◽  
Genome Assemblies ◽  
Muntiacus Muntjak ◽  
Muntiacus Reevesi

AbstractDespite their recent divergence, muntjac deer show striking karyotype differences. Here we describe new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyze their evolution and architecture. We identified six fusion events shared by both species relative to the cervid ancestor and therefore present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and twenty-six fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reverses an earlier fission in the cervid lineage. Although comparative Hi-C analysis revealed differences in long-range genome contacts and A/B compartment structures, we discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. A small number of genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype. Analysis of muntjac genomes reveals new insights into this unique case of rapid karyotype evolution and the resulting biological variation.

scholarly journals Vineyards, but not cities, are associated with lower presence of a generalist bird, the Common Blackbird (Turdus merula), in Western France

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bertille Mohring ◽  
François Brischoux ◽  
Frédéric Angelier
Keyword(s):  
Urban Areas ◽  
Bird Species ◽  
Common Species ◽  
Fine Scale ◽  
Generalist Species ◽  
Landscape Characteristics ◽  
Turdus Merula ◽  
The Common ◽  
Positive Effect ◽  
Common Blackbird

Abstract Background Land-use change is one of the main drivers of the global erosion of biodiversity. In that context, it is crucial to understand how landscape characteristics drive the presence of rare endangered species. Nevertheless, it is also important to study common species in multiple habitats, because they represent a large proportion of biodiversity and are essential to maintain ecological functions. Interestingly, some habitats, as farmlands with permanent crops (e.g. vineyards), have been overlooked in the literature. Methods In this study, we investigated the distribution of a widespread and common bird species, the Common Blackbird (Turdus merula), within and between the three main habitats of our study area (rural Western France). We specifically focused on (1) woodlands, (2) farmlands with a high vineyard coverage, and (3) moderately urbanized areas. Specifically, we aimed to assess the beneficial and detrimental effects of these habitats and their fine-scale composition on the presence of a common bird species, relying on a survey by point counts (nearly 100 locations). We studied the effects of habitats and gradients of fine-scale habitat composition on blackbird presence using logistic regression analyses. Results Blackbirds were present in all studied habitats. However, their presence varied between habitats, being lower in vineyards than in woodlands and cities. In woodlands and cities, fine-scale analyses did not reveal any component driving the species’ presence. However, we found that shrub and tree vegetation cover had a significant positive effect on blackbird presence in vineyards. Conclusions Our results are in agreement with the definition of a generalist species. Interestingly, species distribution varied between habitats. The high presence of blackbirds in urban areas suggests that medium-sized cities, despite their artificialization, do not constrain the settlement of this former forest specialist and that green spaces may allow blackbirds to thrive in medium-sized cities. On the contrary, we found an impoverished presence of blackbirds in vineyards and a positive effect of vegetation on their presence in these landscapes. This suggests that permanent crops, and more generally farmlands, may impose important constraints to common species. Future studies should examine how to enhance biodiversity through agricultural management policies, especially in vineyards.

scholarly journals A target enrichment probe set for resolving the flagellate plant tree of life

2020 ◽  
Author(s):  
Jesse W. Breinholt ◽  
Sarah B. Carey ◽  
George P. Tiley ◽  
E. Christine Davis ◽  
Lorena Endara ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Sequence Data ◽  
Low Cost ◽  
Tree Of Life ◽  
Target Enrichment ◽  
Sequencing Technologies ◽  
Flanking Regions ◽  
Probe Set

ABSTRACTPremise of the studyNew sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and gymnosperms.Methods and ResultsWe leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding flanking regions across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate plants and demonstrate the potential of the data to resolve relationships among both ancient and closely related taxa.ConclusionsA target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate plants.

Identification and molecular characterization of a sex chromosome rearrangement causing a soft and pliable (spli) larval body phenotype in the silkworm, Bombyx mori

Genome ◽  
2010 ◽  
Vol 53 (1) ◽  
pp. 45-54 ◽  
Author(s):  
Tsuguru Fujii ◽  
Seigo Kuwazaki ◽  
Kimiko Yamamoto ◽  
Hiroaki Abe ◽  
Akio Ohnuma ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Sex Chromosome ◽  
Chromosome Rearrangement ◽  
Artificial Chromosome ◽  
Chromosome Breakage ◽  
Z Chromosome ◽  
Larval Body ◽  
Cytogenetic Analyses ◽  
Eye Pigmentation ◽  
Silkworm Bombyx Mori

We carried out genetic and cytogenetic analyses of X-ray-induced deleterious Z chromosomes that result in a soft and pliable (spli) phenotype in the silkworm, Bombyx mori . In a B. mori strain with a spli phenotype, we found the Z chromosome broken between the sch (1–21.5) and od (1–49.6) loci. We also found a chromosomal fragment bearing a fifth-chromosome locus for egg and eye pigmentation fused to a Z chromosome fragment. By means of fluorescence in situ hybridization using bacterial artificial chromosome clones as probes, we confirmed that the fused chromosome is composed of a fragment of chromosome 5 and a fragment of the Z chromosome. Moreover, a predicted gene, GA002017, the Bombyx ortholog of the Drosophila gene acj6 (Bmacj6), was completely deleted by the Z chromosome breakage event. The relationship between Bmacj6 and the spli phenotype is discussed.

scholarly journals Genomic architecture and introgression shape a butterfly radiation

Science ◽  
2019 ◽  
Vol 366 (6465) ◽  
pp. 594-599 ◽  
Author(s):  
Nathaniel B. Edelman ◽  
Paul B. Frandsen ◽  
Michael Miyagi ◽  
Bernardo Clavijo ◽  
John Davey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Color Pattern ◽  
Lineage Sorting ◽  
Genome Sequences ◽  
Genomic Architecture ◽  
Genome Assemblies

We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome. Introgressed loci are underrepresented in low-recombination and gene-rich regions, consistent with the purging of foreign alleles more tightly linked to incompatibility loci. Here, we identify a hitherto unknown inversion that traps a color pattern switch locus. We infer that this inversion was transferred between lineages by introgression and is convergent with a similar rearrangement in another part of the genus. These multiple de novo genome sequences enable improved understanding of the importance of introgression and selective processes in adaptive radiation.

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