13 results on '"Van der Zwan, Henriëtte"'
Search Results
2. Convergent evolution of parrot plumage coloration
- Author
-
Ke, Fushi, primary, van der Zwan, Henriëtte, additional, Poon, Emily Shui Kei, additional, Cloutier, Alison, additional, Van den Abeele, Dirk, additional, van der Sluis, Rencia, additional, and Sin, Simon Yung Wa, additional
- Published
- 2024
- Full Text
- View/download PDF
3. Dense sampling of bird diversity increases power of comparative genomics
- Author
-
25621572 - Van der Zwan, Henriëtte, 21224919 - Van der Sluis, Rencia, Feng, Shaohong, Van der Zwan, Henriëtte, Van der Sluis, Rencia, Stiller, Josefin, 25621572 - Van der Zwan, Henriëtte, 21224919 - Van der Sluis, Rencia, Feng, Shaohong, Van der Zwan, Henriëtte, Van der Sluis, Rencia, and Stiller, Josefin
- Abstract
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species
- Published
- 2020
4. Polly Wants a Genome: The Lack of Genetic Testing for Pet Parrot Species
- Author
-
van der Zwan, Henriëtte, primary and van der Sluis, Rencia, additional
- Published
- 2021
- Full Text
- View/download PDF
5. De novo sequencing, assembly and annotation of the Agapornis roseicollis genome to identify variants for the development of genetic screening tests
- Author
-
Van der Zwan, Henriëtte, Van der Sluis, Rencia, Visser, Carina, and 21224919 - Van der Sluis, Rencia (Supervisor)
- Abstract
PhD (Biochemistry), North-West University, Potchefstroom Campus, 2019 The genus Agapornis consists of nine small African parrots that are commonly called lovebirds. These birds are found in their natural habitat across Africa (eight species) and Madagascar (one species), but also house as domesticated pet birds across the globe. Eight of these species have been domesticated of which five are commonly found in breeding systems. Wild populations are placed under strain due to poaching and illegal export to sell birds to the pet market. Trade has subsequently been restricted in some countries due to declining numbers. Poaching, trapping and illegal export are however still a problem for some populations. The main selection criterion breeders use to select birds is plumage colour variations. There are 30 known colour variations found amongst these species, many of which can be combined. Very little research has been conducted on the molecular genetic mechanisms that control parrot plumage pigmentation. This group of birds have a unique pigment, psittacofulvin, that is only found amongst parrots. It is believed to be genetically controlled and not under dietary control. The inheritance pattern of these variations have been determined by breeders via test matings, and most are inherited as Mendelian traits. Despite the inheritance patterns being known, the genes and polymorphisms linked to these traits have not yet been identified. This has caused breeders to use pedigree data to predict the colour genotypes of an offspring with wildtype colouration. Notwithstanding this practice, there is no molecular parentage verification panel available for lovebirds. The avian parentage verification panels that are available were developed for an array of bird species and are all microsatellite marker based. Microsatellite markers are becoming redundant in animal breeding systems and replaced with Single Nucleotide Polymorphism (SNPs). One of the limitations of developing a parentage verification panel for this genus, is the lack of a reference genome from where SNPs could be identified. The de novo genome of A. roseicollis were subsequently sequenced, assembled and annotated for this purpose. Sequencing was performed at 100x coverage using the Illumina HiSeq 2000 platform. Three shotgun sequencing libraries of insert sizes 300 bp, 550 bp and 750 bp, respectively, as well as two long jumping distance pairedend libraries of sizes 3 kbp and 8kbp were constructed. The de novo assembly was performed using the SOAPdenovo v2.04 assembler and a k-mer length of 69 was applied. The genome was found to be 1.1 Gbp in size, with contig and scaffold N50 lengths of 5 45 bp and 108 514 bp, respectively, and the G/C content 43%. During the genome annotation phase 15 045 coding gene sequences and 999 non-coding gene sequences were identified. The genome assembly compared well with previously assembled avian genomes such as the budgerigar (Melopsittacus undulates), scarlet macaw (Ara macao) and Puerto Rican parrot (Amazona vittata) in terms of genome size, number of genes annotated and scaffold and contig N50 lengths. The number of eukaryotic core genes detected in the lovebird assembly outperformed those identified in the budgerigar, Puerto Rican parrot and scarlet macaw assemblies, indicating that the assembly was accurate and complete. The genomes of both of the parents of the reference genome individual were sequenced and the sequencing data used to identify SNPs throughout the genome that could be included in a parentage verification panel. Sequencing was performed at 30x coverage using the Illumina HiSeq 2000 platform. Two shotgun sequencing libraries of insert sizes 300 kb and 550 kb, respectively, were constructed. These reads were mapped against the reference genome of their chick and variants were discovered using the variant caller Genome Analysis Toolkit (GATK). Over 2 million raw variants were discovered for the mother while 1,60 million raw variants were discovered for the father. The parents' genotypes were combined to identify SNPs that were shared by the two birds. Unwanted variants such as insertions and deletions (indels) were discarded which resulted in a callset of 1,66 million SNPs. These SNPs were filtered based on parameters as recommended by GATK resulting in 103 287 SNPs that passed the criterion that were set. Two of the parameters applied were QUAL (a Phred-based prediction of a false positive variant) and QD (normalization of the QUAL score for sequencing depth). True variants are found in the QD range of 11.5 to 12.5 and a higher QUAL score indicate a true variant. Therefore, all SNPs within this QD range, subsequently ranked by their QUAL scores were included. One SNP per scaffold was selected from this set and the top 480 SNPs were included in the final parentage verification panel. A population of 960 lovebirds from seven different species were genotyped at these 480 SNPs using the QuantStudio 12 K Flex platform. These birds included the reference genome individual and its father. A panel of 262 SNPs were constructed where the father’s genotype amplified and were used as a reference. This panel was further reduced to include SNPs with minor allele frequencies (MAF) and observed heterozygosity (HO) values greater than 0.1. This resulted in a panel of 195 SNPs. The third panel was filtered based on the same parameters but included SNPs with MAF and HO values greater than 0.3 and amounted to 40 SNPs. The three panels were all assessed for their exclusion power in 43 lovebird families with known pedigrees. It was found that the 195-SNP panel was the panel with the greatest exclusion power applying the least number of SNPs and was proposed as the lovebird parentage verification panel National Research Foundation (NRF) Human Resources for Industry Programme (THRIP) Technology Innovation Agency (TIA) Doctoral
- Published
- 2019
6. Plumage colour variations in the Agapornis genus: a review
- Author
-
van der Zwan, Henriëtte, primary, Visser, Carina, additional, and van der Sluis, Rencia, additional
- Published
- 2019
- Full Text
- View/download PDF
7. Draft De Novo Genome Sequence ofAgapornis roseicollisfor Application in Avian Breeding
- Author
-
van der Zwan, Henriëtte, primary, van der Westhuizen, Francois, additional, Visser, Carina, additional, and van der Sluis, Rencia, additional
- Published
- 2017
- Full Text
- View/download PDF
8. Draft De Novo Genome Sequence of Agapornis roseicollis for Application in Avian Breeding.
- Author
-
van der Zwan, Henriëtte, van der Westhuizen, Francois, Visser, Carina, and van der Sluis, Rencia
- Subjects
- *
AVICULTURE , *LOVEBIRDS , *BUDGERIGAR , *COLOR of birds , *AVIARIES - Abstract
In aviculture, lovebirds are considered one of the most popular birds to keep. This African parakeet is known for its range of plumage colors and ease to tame. Plumage variation is the most important price-determining trait of these birds, and also the main selection criterion for breeders. Currently, no genetic screening tests for traits of economic importance or to confirm pedigree data are available for any of the nine lovebird species. As a starting point to develop these tests, the de novo genome of Agapornis roseicollis (rosy-faced lovebird) was sequenced, assembled, and annotated. Sequencing was done on the Illumina HiSeq 2000 platform and the assembly was performed using SOAPdenovo v2.04. The genome was found to be 1.1 Gb in size and 16,044 genes were identified and annotated. This compared well with other previously sequenced avian genomes, such as the chicken, zebra finch, and budgerigar. To assess genome completeness, the number of benchmarking universal single-copy orthologs were identified in the genome. This was compared to other previously assembled avian genomes and the results indicated that the genome will be useful in the development of genetic screening tests to aid lovebird breeders in selecting breeding pairs. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
9. Canine multi-drug resistance-1 mutation prevalence: A South African perspective
- Author
-
Le Roux-Pullen, Lérica, primary and Van der Zwan, Henriëtte, additional
- Published
- 2014
- Full Text
- View/download PDF
10. Canine multi-drug resistance-1 mutation prevalence: A South African perspective
- Author
-
Roux-Pullen, Lérica le and van der Zwan, Henriëtte
- Abstract
The multi-drug resistance (mdr-1) gene mutation is a phenomenon well known to current veterinary practitioners. The mutation causes a predisposition for, amongst other phenomena, macrocyclic lactone-induced neurotoxicosis in affected canines, a condition that can be fatal. Various herding dog breeds can be heterozygous or homozygous for the mutation, and prevalence differs only slightly in dog populations between geographical regions. This report provides prevalence data of the canine mdr-1 mutation in 306 South African dogs. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
11. LOVEBIRDS COMPENDIUM—GENUS AGAPORNIS.
- Author
-
van der Zwan, Henriëtte
- Published
- 2017
12. Development of an <scp>SNP</scp> ‐based parentage verification panel for lovebirds
- Author
-
M Schoonen, Carina Visser, H van der Zwan, R van der Sluis, 21224919 - Van der Sluis, Rencia, 20574495 - Schoonen, Maryke, and 25621572 - Van der Zwan, Henriëtte
- Subjects
Male ,0301 basic medicine ,Population ,Single-nucleotide polymorphism ,Breeding ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Agapornis ,Loss of heterozygosity ,03 medical and health sciences ,Genetics ,Animals ,SNP ,education ,Selection (genetic algorithm) ,Parrot breeding ,education.field_of_study ,Pigmentation ,0402 animal and dairy science ,Pedigree confirmation ,04 agricultural and veterinary sciences ,General Medicine ,Feathers ,040201 dairy & animal science ,Pedigree ,Minor allele frequency ,Whole‐genome resequencing ,030104 developmental biology ,Female ,Animal Science and Zoology ,Reference genome - Abstract
The genus Agapornis, or lovebirds, are popular pet parrots worldwide. Currently, breeders are dependent on pedigree records as a selection tool as no molecular parentage verification test is available for any of the nine species. The A. roseicollis reference genome was recently assembled. This was followed by the sequencing of the whole genomes of the parents of the reference genome individual at 30× coverage. The parents' reads were mapped against the reference genome to identify SNPs. Over 1.6 million SNPs, shared between the parents, were discovered using the Genome Analysis Toolkit pipeline. SNPs were filtered to a panel of 480 SNPs based on Genome Analysis Toolkit parameters. The panel of 480 SNPs was genotyped in a population of 960 lovebirds across seven species. A panel of 262 SNPs was compiled that included SNPs successfully amplified across all species. The 262-SNP panel was reduced based on the observed heterozygosity (HO ) and minor allele frequency (MAF) values per SNP to include the lowest number of SNPs with the highest exclusion power for parentage verification. Two smaller panels consisting of 195 SNPs with MAF and HO values >0.1 and 40 SNPs with MAF and HO values >0.3, were constructed. The panels were verified using 43 families from different species with known relationships to evaluate the exclusion power of each panel. The 195 SNP panel with an average exclusion probability of 99.9% and MAF and HO values >0.1 was proposed as the routine Agapornis parentage verification panel.
- Published
- 2019
13. Dense sampling of bird diversity increases power of comparative genomics
- Author
-
Rencia van der Sluis, Nadine Thiele, Borja Milá, Araxi O. Urrutia, Josefin Stiller, Joel Cracraft, Zongji Wang, Qiye Li, Barney A. Schlinger, Guojie Zhang, Ana Tereza Ribeiro de Vasconcelos, Oliver A. Ryder, Rebecca B. Dikow, Thomas L. Parchman, Emily Cavill, John G. Blake, Libby C. Megna, Andrew G. Clark, Christopher C. Witt, Ángela M. Parody-Merino, Jason T. Weir, Wanjun Chen, Jason T. Howard, T. Brandt Ryder, Michael G. Campana, Jon Fjeldså, Robb T. Brumfield, M. Thomas P. Gilbert, Alexandre Aleixo, Gerald Borgia, Qi Fang, Phil F. Battley, Ellen D. Ketterson, Matthew I. M. Louder, Scott A. Taylor, Glaucia Del-Rio, Scott V. Edwards, Sergio Andreu-Sánchez, Fumin Lei, Irby J. Lovette, Neil J. Gemmell, Mikkel-Holger S. Sinding, Carole A. Parent, Huanming Yang, André E. R. Soares, David W. Burt, Guanliang Meng, André Corvelo, Nicolas Dussex, Jimmy A. McGuire, Kira E. Delmore, Marc P. Hoeppner, Julio Rozas, Ângela M. Ribeiro, Les Christidis, Haw Chuan Lim, Guillermo Friis, Guangji Chen, Martin Stervander, Mads F. Bertelsen, Siavash Mirarab, Biao Wang, Hanna Sigeman, Lara Puetz, Qi Zhou, Marta Riutort, Knud A. Jønsson, Christopher N. Balakrishnan, Alexander Suh, Edward L. Braun, Nicholas Costa Barroso Lima, Jeffrey M. DaCosta, Reed Bowman, Yang Liu, Kim Rutherford, Ashot Margaryan, Peter Njoroge, Beth Shapiro, Benedict Paten, Shaohong Feng, Adam M. Fudickar, Jacob González-Solís, Bent O. Petersen, Subir B. Shakya, Henrik Mouritsen, Glauco Camenisch, Maude W. Baldwin, Andrew Hart Reeve, Bruce C. Robertson, Morgan Wirthlin, Shannon J. Hackett, Chunxue Guo, Bengt Hansson, Peter G. Ryan, Miriam Liedvogel, Alain Vignal, Saul J. Cowen, Matthew J. Fuxjager, Robert C. Fleischer, Dustin J. Foote, Joel Armstrong, Joann Mudge, Nancy F. Chen, Santiago Claramunt, Joan Ferrer-Obiol, John W. Fitzpatrick, Leopold Eckhart, Mark E. Hauber, Michael Bunce, Carsten Rahbek, George Pacheco, Dieter Thomas Tietze, Gang Song, Jérôme Fuchs, John P. Dumbacher, Henriette van der Zwan, Love Dalén, Michael J. Braun, Lukas F. Keller, Yuan Deng, Jian Wang, Thomas Sicheritz-Pontén, Tamás Székely, Erich D. Jarvis, Alison Cloutier, David Haussler, Matthew D. Carling, Carina Visser, Paul B. Frandsen, Anna Tigano, Andre Franke, Suvi Ponnikas, Claudio V. Mello, Vicki L. Friesen, Timothy B. Sackton, Rute R. da Fonseca, Frederick H. Sheldon, Duo Xie, Brant C. Faircloth, Bette A. Loiselle, Gary R. Graves, Ian G. Jamieson, Mark Diekhans, Lainy B. Day, Peter A. Hosner, Murray P. Cox, Oliver Krone, Andrew E. Fidler, Peter Houde, Francisco Prosdocimi, Zoology, Chinese Academy of Sciences, Carlsberg Foundation, Velux Foundation, National Natural Science Foundation of China, Howard Hughes Medical Institute, National Institutes of Health (US), China National GeneBank, Kunming Institute of Zoology, Chinese Academy of Sciences [Beijing] (CAS), Beijing Genomics Institute [Shenzhen] (BGI), University of Copenhagen = Københavns Universitet (KU), University of California [Santa Cruz] (UCSC), University of California, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of Chinese Academy of Sciences [Beijing] (UCAS), Louisiana State University (LSU), Museum of Natural Science, IT University of Copenhagen, AIMST University, Zhejiang University, University of Vienna [Vienna], Zhejiang University School of Medicine [China], Institute of Molecular Biology of the National Academy of Sciences of Armenia (IMB NAS RA), National Academy of Sciences of the Republic of Armenia [Yerevan] (NAS RA), Novogene, Duke University Medical Center, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), United States Department of Health & Human Services, National Institutes of Health (NIH) - USA, NIH National Human Genome Research Institute (NHGRI) (U54 HG007990, T32 HG008345, R01 HG010053), NIH National Heart Lung & Blood Institute (NHLBI) (U01 HL137183), 25621572 - Van der Zwan, Henriëtte, and 21224919 - Van der Sluis, Rencia
- Subjects
0106 biological sciences ,GENES ,PROTEINS ,Tree of life ,Genomics ,Biology ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,Evolutionary genetics ,génomique ,Evolutionsbiologi ,03 medical and health sciences ,Phylogenetics ,ACCELERATED EVOLUTION ,[SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology ,REVEALS ,genomics ,Genetics ,DIVERGENCE ,Genomes ,Genetik ,Cladistic analysis ,Selection (genetic algorithm) ,TREE ,030304 developmental biology ,Comparative genomics ,0303 health sciences ,Evolutionary Biology ,Multidisciplinary ,Phylogenetic tree ,SEQUENCES ,Human evolutionary genetics ,Cladística ,Biodiversity ,DNA ,15. Life on land ,échantillonnage ,Sampling Methods ,Biodiversitat ,DUPLICATION ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,Evolutionary biology ,1181 Ecology, evolutionary biology ,PACKAGE - Abstract
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
- Published
- 2020
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.