Genome assembly. chromosomal organization and comparative genomics of multiple bird species: beyond "catalogues of genes"
Lead Research Organisation:
University of Kent
Department Name: Sch of Biosciences
Abstract
Imagine trying to navigate through a town with only the index from your A-Z to guide you and not the street map. In essence, this is what happens when the genome of a new species is sequenced. Old fashioned technology used to "sketch the outline of the streets" first before filling in the gaps with the gene sequence. The new technology (so called "Next Generation Sequencing") is much cheaper and quicker but is quite poor at sorting out where the genes are in relation to one another. Essentially, Next Generation Sequencing assemblies are little more than catalogues of genes with little structure of the overall genome apparent. Fortunately this problem can be rectified using a technique called "FISH" that can take the data from next generation sequencing projects and visualise directly the genes as they appear in their rightful place in the genome. In this project we intend to do this with 25-30 recently completed genome sequences from birds. Birds are among the most diverse animals with around 10,000 living species. Many are models for human disease and development and are critical to agriculture (both meat and eggs). Others are threatened or endangered and, with impending global warming, molecular tools for the study of ecology and conservation of birds are essential. It is also possible to compare the overall structure of one genome with another, somewhat like comparing the maps of towns with similar layouts. We have developed online tools that can directly visualize the similarities and differences between the genomes of several birds at a time. Of course the differences between these bird genomes came about through changes that happened during evolution. One of the main aims of this project is to find out how and why this occurred. We have a number of ideas such as we think there may be different "gene signatures" at the places in the genome where evolutionary rearrangements are more or less likely to occur. We think that the whole process may be related to the mechanisms by which our genes recombine in our germ cells. We also think there may be a role for small pieces of DNA that "float around" these bird genomes. Finally, we have received overwhelming support from numerous laboratories all over the world, all of whom are interested in bird genomics and who would wish to use our online resource to ask biological questions of their own. For this reason we feel that this project not only will help us understand evolution in birds but also establish the UK as a central international hub for work of this kind.
Technical Summary
Every genome sequence needs a good map however modern next generation sequencing (NGS) technologies struggle fully to assemble whole genomes de-novo. This is disappointing as mapping information on a chromosomal basis brings the opportunity to address many fundamental biological questions of genome evolution. Modern genomic research generally focuses on the role of individual genes but the role of chromosomes and homologous synteny blocks (HSBs) is often disregarded. This is despite the ubiquity of HSBs and the phenotypic consequences/evolutionary implications of chromosome rearrangement. In mammals, there are sufficient assembled reference genomes to make assembly by comparative analysis. For birds however only three such reference genomes exist and chromosomal assembly needs to be achieved by other means. Classical approaches involving karyotyping and FISH coupled with comparative genomics browser technology provide a straightforward solution for the many avian genomes that are assembled to the point of 100+ large scaffolds. The aim of the project will thus be to generate a freely available comparative genomic resource that can be used to compare the genome structures of 25-30 bird species. HSBs and Evolutionary Breakpoint Regions (EBRs) will be displayed using the "Evolution Highway" browser. We will anchor each of the scaffolds physically to chromosomes by FISH. We will address at least four fundamental questions pertaining to genome evolution: We will test the hypotheses that HSB lengths are non-randomly distributed in birds, that there are specific gene ontology signatures of HSBs and EBRs, that EBRs coincide with recombination hotspots in birds (but not in mammals) and that transposable element density in increased in EBRs. The extensive letters of support from potential users indicate that this will be a widely used resource addressing a myriad of further biological questions in this most diverse and biologically important group of vertebrates.
Planned Impact
Exploitation and Application.
Technology Transfer activity at both Universities is administered by Enterprise offices. Collaborative agreement already exist with Digital Scientific and CytoCell. These separately capture exploitation and collaborative output issues going forward. Cytocell, Aviagen and Digital Scientific UK see benefit to this project either through the identification of commercially important traits or through the sales of products and have thus offered generous in kind support. A specific strategic advisory board has been established to identify potential impact issues from this and other projects.
Communications and engagement with the identified beneficiaries.
The main beneficiaries of this grant will be the avian genomics community in industry, third sector and academia. In 2002 the Kent lab was set up as a resource centre for avian molecular cytogenetics (FARMACRHOM). Through these activities we developed a mature and functioning collaborative network with most of the major players in avian genomics and biology many of whom have attached letters of support. Evolution Highway the "industry standard" for browser comparative genomics in the mammalian chromosome world with over ~50 regular users 16,000 hits from academia, industry and third sector in the last year. Inherently used for collaborative research it is, in itself, a tool to facilitate communication and engagement. Another beneficiary is the poultry breeding industry through which the Kent lab is, and has been, supported and funded through BBSRC grants and PhD CASE studentships. In the past we have provided genome maps for the species of interest (turkey and duck). A local zoo (Wingham Wildlife Park) was engaged as another and benefitted by subsequent broadcast media coverage and by provision of a display on the collaborative work performed (this is currently on display to the general public). We will participate in company-managed events and community activities with specialist audiences and the general public to disseminate findings and will develop as a CPD module for delivery to outside engagers. We will contribute to the Bioscience KTN newsletter, to "BBSRC business," newsletters published by individual companies and by the Departments/Universities and to media coverage as well as online activities. Bioscience KTN provide further help and advice on collaboration and their website has >3,000 registered members working in industry and academia The PI's have a healthy relationship with the University press offices and are regular contributor to public engagement activities including "Café Scientifique," Science Fairs and public lectures. Thus far, this work has led to several press releases in addition to appearances in the national and local broadcast media (BBC's "Big Questions," "The World Tonight", Radio 2 Simon Mayo show" BBC radio Kent etc.). Both Universities have active outreach programmes to which the PIs will contribute.
Capacity and Involvement
The two PIs will be the primary participants in impact activities aided by by PhD students and post-doctoral researchers. Professor Griffin has extensive training and experience in communication activities and commercial exploitation of research. The communications and development office in both Universities provide technical expertise and help in writing publications, web pages and user-friendly interfaces and it is expected that post-docs and PhD students will be provided with significant training in both dissemination and exploitation activities through Departmental, University and Bioscience KTN related activities. In conclusion therefore, this project has a range of expertise and ambitious, but achievable plans for impact at local, regional national and international levels.
See complete impact plan (attached) for further details
Technology Transfer activity at both Universities is administered by Enterprise offices. Collaborative agreement already exist with Digital Scientific and CytoCell. These separately capture exploitation and collaborative output issues going forward. Cytocell, Aviagen and Digital Scientific UK see benefit to this project either through the identification of commercially important traits or through the sales of products and have thus offered generous in kind support. A specific strategic advisory board has been established to identify potential impact issues from this and other projects.
Communications and engagement with the identified beneficiaries.
The main beneficiaries of this grant will be the avian genomics community in industry, third sector and academia. In 2002 the Kent lab was set up as a resource centre for avian molecular cytogenetics (FARMACRHOM). Through these activities we developed a mature and functioning collaborative network with most of the major players in avian genomics and biology many of whom have attached letters of support. Evolution Highway the "industry standard" for browser comparative genomics in the mammalian chromosome world with over ~50 regular users 16,000 hits from academia, industry and third sector in the last year. Inherently used for collaborative research it is, in itself, a tool to facilitate communication and engagement. Another beneficiary is the poultry breeding industry through which the Kent lab is, and has been, supported and funded through BBSRC grants and PhD CASE studentships. In the past we have provided genome maps for the species of interest (turkey and duck). A local zoo (Wingham Wildlife Park) was engaged as another and benefitted by subsequent broadcast media coverage and by provision of a display on the collaborative work performed (this is currently on display to the general public). We will participate in company-managed events and community activities with specialist audiences and the general public to disseminate findings and will develop as a CPD module for delivery to outside engagers. We will contribute to the Bioscience KTN newsletter, to "BBSRC business," newsletters published by individual companies and by the Departments/Universities and to media coverage as well as online activities. Bioscience KTN provide further help and advice on collaboration and their website has >3,000 registered members working in industry and academia The PI's have a healthy relationship with the University press offices and are regular contributor to public engagement activities including "Café Scientifique," Science Fairs and public lectures. Thus far, this work has led to several press releases in addition to appearances in the national and local broadcast media (BBC's "Big Questions," "The World Tonight", Radio 2 Simon Mayo show" BBC radio Kent etc.). Both Universities have active outreach programmes to which the PIs will contribute.
Capacity and Involvement
The two PIs will be the primary participants in impact activities aided by by PhD students and post-doctoral researchers. Professor Griffin has extensive training and experience in communication activities and commercial exploitation of research. The communications and development office in both Universities provide technical expertise and help in writing publications, web pages and user-friendly interfaces and it is expected that post-docs and PhD students will be provided with significant training in both dissemination and exploitation activities through Departmental, University and Bioscience KTN related activities. In conclusion therefore, this project has a range of expertise and ambitious, but achievable plans for impact at local, regional national and international levels.
See complete impact plan (attached) for further details
Organisations
- University of Kent (Lead Research Organisation)
- Natural Environment Research Council (Co-funder)
- Digital Scientific UK (Collaboration)
- Central Veterinary Research Laboratory (Collaboration, Project Partner)
- Aviagen (United Kingdom) (Project Partner)
- Cytocell Ltd (Project Partner)
- Digital Scientific (United Kingdom) (Project Partner)
People |
ORCID iD |
| Darren Griffin (Principal Investigator) |
Publications
Nishida C
(2013)
Karyotype reorganization with conserved genomic compartmentalization in dot-shaped microchromosomes in the Japanese mountain hawk-eagle (Nisaetus nipalensis orientalis, Accipitridae).
in Cytogenetic and genome research
Huang Y
(2013)
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.
in Nature genetics
Ishishita S
(2014)
Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric repetitive sequences in New World quails
in Chromosome Research
Skinner BM
(2014)
Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization.
in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Lithgow PE
(2014)
Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes.
in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Griffin DK
(2015)
20th International Chromosome Conference (ICCXX) : 50th Anniversary, University of Kent, Canterbury, 1st-4th September 2014.
in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Schmid M
(2015)
Third Report on Chicken Genes and Chromosomes 2015
in Cytogenetic and Genome Research
Farré M
(2016)
Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles.
in Genome biology and evolution
Damas J
(2017)
Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.
in Genome research
O'Connor RE
(2018)
Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes.
in Genome biology
O'Connor RE
(2018)
Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs.
in Nature communications
Damas J
(2018)
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes.
in Genome biology
O'Connor RE
(2019)
Patterns of microchromosome organization remain highly conserved throughout avian evolution.
in Chromosoma
Singchat W
(2020)
Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes.
in Frontiers in genetics
Furo IO
(2020)
Chromosomal Evolution in the Phylogenetic Context: A Remarkable Karyotype Reorganization in Neotropical Parrot Myiopsitta monachus (Psittacidae).
in Frontiers in genetics
Griffin DK
(2020)
Time lapse: A glimpse into prehistoric genomics.
in European journal of medical genetics
Singchat W
(2020)
Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome.
in Cells
Singchat W
(2020)
Do sex chromosomes of snakes, monitor lizards, and iguanian lizards result from multiple fission of an "ancestral amniote super-sex chromosome"?
in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Kretschmer R
(2020)
A Comprehensive Cytogenetic Analysis of Several Members of the Family Columbidae (Aves, Columbiformes).
in Genes
Carvalho CA
(2021)
Comparative chromosome painting in Spizaetus tyrannus and Gallus gallus with the use of macro- and microchromosome probes.
in PloS one
Kretschmer R
(2021)
Karyotype Evolution and Genomic Organization of Repetitive DNAs in the Saffron Finch, Sicalis flaveola (Passeriformes, Aves).
in Animals : an open access journal from MDPI
Ribas TFA
(2021)
Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype.
in BMC ecology and evolution
Kretschmer R
(2021)
Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes).
in Cells
Furo IO
(2021)
Cytotaxonomy of Gallinula melanops (Gruiformes, Rallidae): Karyotype evolution and phylogenetic inference.
in Genetics and molecular biology
Smith J
(2022)
Fourth Report on Chicken Genes and Chromosomes 2022
in Cytogenetic and Genome Research
Griffin D
(2022)
Dinosaurs: Comparative Cytogenomics of Their Reptile Cousins and Avian Descendants
in Animals
| Title | Additional file 1 of Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype |
| Description | Addtional file 1. Phylogenetic relationship among chicken, zebra finch, the Eurasian Stone Curlew and the Wedge-Billed Woodcreeper. The phylogeny is based in Prum et al. [48]. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2021 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_1_of_Analysis_of_multiple_chromo... |
| Title | Additional file 1 of Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype |
| Description | Addtional file 1. Phylogenetic relationship among chicken, zebra finch, the Eurasian Stone Curlew and the Wedge-Billed Woodcreeper. The phylogeny is based in Prum et al. [48]. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2021 |
| URL | https://springernature.figshare.com/articles/figure/Additional_file_1_of_Analysis_of_multiple_chromo... |
| Title | Additional file 1: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent "a hypothetical ancestral super-sex chromosome" or random distribution? |
| Description | Figure S1. Chromosomal locations of microsatellite repeat motifs in the Siamese cobra (Naja kaouthia). Hybridization patterns of FITC-labeled (CA)15 (a), (AT)15 (b), (GC)15 (c), (CAT)10 (d), and (AAT)10 (e) on DAPI-stained chromosomes. Scale bar represents 10 µm. (JPG 175 kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Chromosome_map_of_the_Siamese_cobr... |
| Title | Additional file 1: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent "a hypothetical ancestral super-sex chromosome" or random distribution? |
| Description | Figure S1. Chromosomal locations of microsatellite repeat motifs in the Siamese cobra (Naja kaouthia). Hybridization patterns of FITC-labeled (CA)15 (a), (AT)15 (b), (GC)15 (c), (CAT)10 (d), and (AAT)10 (e) on DAPI-stained chromosomes. Scale bar represents 10 µm. (JPG 175 kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Chromosome_map_of_the_Siamese_cobr... |
| Title | Additional file 2: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution? |
| Description | Figure S2. Cytogenetic map of the Siamese cobra (Naja kaouthia), which shows chromosome homologies with chicken and zebra finch. This map was constructed with 25 chicken and zebra finch BACs mapped on the Siamese cobra macrochromosomes. Locations of BACs are shown to the right of the Siamese cobra chromosomes. The chromosome numbers show the chromosomes of the chicken (Gallus gallus, GGA) and zebra finch (Taeniopygia guttata, TGU), which show homologies with the Siamese cobra chromosomes. (JPG 118 kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Chromosome_map_of_the_Siamese_cobr... |
| Title | Additional file 2: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution? |
| Description | Figure S2. Cytogenetic map of the Siamese cobra (Naja kaouthia), which shows chromosome homologies with chicken and zebra finch. This map was constructed with 25 chicken and zebra finch BACs mapped on the Siamese cobra macrochromosomes. Locations of BACs are shown to the right of the Siamese cobra chromosomes. The chromosome numbers show the chromosomes of the chicken (Gallus gallus, GGA) and zebra finch (Taeniopygia guttata, TGU), which show homologies with the Siamese cobra chromosomes. (JPG 118 kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Chromosome_map_of_the_Siamese_cobr... |
| Description | Throughout the course of this project, we have make substantial progress with numerous publications. We have mapped the genomes of several species as well as provided insight into the genomes of dinosaurs |
| Exploitation Route | The project is ongoing and we have numerous collaborators |
| Sectors | Agriculture Food and Drink Education |
| URL | http://www.bbsrc.ac.uk/news/fundamental-bioscience/2017/170105-pr-complete-animal-genomes-become-easier-to-map/ |
| Description | I continue to get several invitations to give public and academic lectures based around the work. We have worked with a company Cytocell in order to develop screening devices for infertility and comparative genomics in the agricultural industry. We now market these devices and are spinning off a company to progress this further |
| First Year Of Impact | 2017 |
| Sector | Agriculture, Food and Drink,Education |
| Impact Types | Cultural |
| Description | Rapid reconstruction of reference chromosome-level mammalian genome assemblies and insight into the mechanisms of gross genomic rearrangement |
| Amount | £292,975 (GBP) |
| Funding ID | BB/P020054/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2021 |
| Title | Additional file 1: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| Description | Intrachromosomal rearrangements: BAC IDs and chromosomal orientation of clones (with start and stop coordinates from the chicken genome). The order of clones from the top to the bottom represents the order in which that appears on the chromosomes of the species of interest. Text in red indicates the p- (short) arm of the chromosome (where it is discernable). Data is listed in supplementary tables as follows: Table S1. Ostrich genome; Table S2. Budgerigar genome; Table S3. Saker falcon genome. (ZIP 58 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Chromosome-level_assembly_reveals_... |
| Title | Additional file 1: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| Description | Intrachromosomal rearrangements: BAC IDs and chromosomal orientation of clones (with start and stop coordinates from the chicken genome). The order of clones from the top to the bottom represents the order in which that appears on the chromosomes of the species of interest. Text in red indicates the p- (short) arm of the chromosome (where it is discernable). Data is listed in supplementary tables as follows: Table S1. Ostrich genome; Table S2. Budgerigar genome; Table S3. Saker falcon genome. (ZIP 58 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Chromosome-level_assembly_reveals_... |
| Title | Additional file 2: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| Description | Chromosomal coordinates and orientation of mapped scaffolds and PCFs are listed by chromosome for each species. Data is listed in supplementary tables as follows: Table S4. Ostrich genome; Table S5. Budgerigar genome; Table S6. Saker falcon genome. (ZIP 87 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Chromosome-level_assembly_reveals_... |
| Title | Additional file 2: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| Description | Chromosomal coordinates and orientation of mapped scaffolds and PCFs are listed by chromosome for each species. Data is listed in supplementary tables as follows: Table S4. Ostrich genome; Table S5. Budgerigar genome; Table S6. Saker falcon genome. (ZIP 87 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Chromosome-level_assembly_reveals_... |
| Title | Additional file 3: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| Description | EBRs detected and genome position in relation to the chicken genome. Data is listed in supplementary tables as follows: Table S7. Ostrich genome; Table S8. Budgerigar genome; Table S9. Saker falcon genome. (ZIP 61 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_3_of_Chromosome-level_assembly_reveals_... |
| Title | Additional file 3: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| Description | EBRs detected and genome position in relation to the chicken genome. Data is listed in supplementary tables as follows: Table S7. Ostrich genome; Table S8. Budgerigar genome; Table S9. Saker falcon genome. (ZIP 61 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_3_of_Chromosome-level_assembly_reveals_... |
| Title | Cytotaxonomy of Gallinula melanops (Gruiformes, Rallidae): Karyotype evolution and phylogenetic inference |
| Description | Abstract Although Rallidae is the most diverse family within Gruiformes, there is little information concerning the karyotype of the species in this group. In fact, Gallinula melanops, a species of Rallidae found in Brazil, is among the few species studied cytogenetically, but only with conventional staining and repetitive DNA mapping, showing 2n=80. Thus, in order to understand the karyotypic evolution and phylogeny of this group, the present study aimed to analyze the karyotype of G. melanops by classical and molecular cytogenetics, comparing the results with other species of Gruiformes. The results show that G. melanops has the same chromosome rearrangements as described in Gallinula chloropus (Clade Fulica), including fission of ancestral chromosomes 4 and 5 of Gallus gallus (GGA), beyond the fusion between two of segments resultants of the GGA4/GGA5, also fusions between the chromosomes GGA6/GGA7. Thus, despite the fact that some authors have suggested the inclusion of G. melanops in genus Porphyriops, our molecular cytogenetic results confirm its place in the Gallinula genus. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://scielo.figshare.com/articles/dataset/Cytotaxonomy_of_Gallinula_melanops_Gruiformes_Rallidae_... |
| Title | Cytotaxonomy of Gallinula melanops (Gruiformes, Rallidae): Karyotype evolution and phylogenetic inference |
| Description | Abstract Although Rallidae is the most diverse family within Gruiformes, there is little information concerning the karyotype of the species in this group. In fact, Gallinula melanops, a species of Rallidae found in Brazil, is among the few species studied cytogenetically, but only with conventional staining and repetitive DNA mapping, showing 2n=80. Thus, in order to understand the karyotypic evolution and phylogeny of this group, the present study aimed to analyze the karyotype of G. melanops by classical and molecular cytogenetics, comparing the results with other species of Gruiformes. The results show that G. melanops has the same chromosome rearrangements as described in Gallinula chloropus (Clade Fulica), including fission of ancestral chromosomes 4 and 5 of Gallus gallus (GGA), beyond the fusion between two of segments resultants of the GGA4/GGA5, also fusions between the chromosomes GGA6/GGA7. Thus, despite the fact that some authors have suggested the inclusion of G. melanops in genus Porphyriops, our molecular cytogenetic results confirm its place in the Gallinula genus. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://scielo.figshare.com/articles/dataset/Cytotaxonomy_of_Gallinula_melanops_Gruiformes_Rallidae_... |
| Title | Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes |
| Description | The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.q70q40m |
| Title | Supplementary Material for: Fourth Report on Chicken Genes and Chromosomes 2022 |
| Description | none |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://karger.figshare.com/articles/dataset/Supplementary_Material_for_Fourth_Report_on_Chicken_Gen... |
| Title | Supplementary Material for: Fourth Report on Chicken Genes and Chromosomes 2022 |
| Description | none |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://karger.figshare.com/articles/dataset/Supplementary_Material_for_Fourth_Report_on_Chicken_Gen... |
| Description | List of collaborators |
| Organisation | Central Veterinary Research Laboratory |
| Country | United Arab Emirates |
| Sector | Public |
| PI Contribution | A number of collaborations formed part of this project (see list) |
| Start Year | 2006 |
| Description | List of collaborators |
| Organisation | Central Veterinary Research Laboratory |
| Country | United Arab Emirates |
| Sector | Public |
| PI Contribution | A number of collaborations formed part of this project (see list) |
| Start Year | 2006 |
| Description | List of collaborators |
| Organisation | Digital Scientific UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | A number of collaborations formed part of this project (see list) |
| Start Year | 2006 |
| Description | Multiple press coverage for work on avian genome evolution |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Our work led to the discovery of the likely dinosaur karyotype - this had extensive media coverage, including the BBC (see URL below) |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.bbc.co.uk/news/science-environment-44711974 |