Camelid Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 24033

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Brooks Equine Genetic Lab., Department of Animal Science, Genetic Institute, University of Florida, Gainesville, FL, USA
Interests: equine genetics; genetic disorders; coat color; neurological conditions
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Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458, USA
Interests: animal molecular cytogenetics; animal genomics; genomics of reproduction; disease genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Camelids represent a small group of wild and domesticated odd-toed ungulates characterized by unique evolutionary history and unusual biological features. All species are adapted to extreme environments—the Old-World camels to deserts with extreme temperature fluctuations and high dietary salt content; the New-World camelids to high altitude conditions. They have unique features for immune defense, disease resistance, insulin metabolism, and reproduction. Domestic camelids are also valued for their milk, meat, fleece, and fiber production. In the context of global warming, the remarkable physiological adaptations and other biological features of camelids present a novel opportunity for environmentally sustainable animal husbandry.

The aim of this Special Issue is to address the genetics and molecular signatures of camelid biology. The topics include but are not limited to improvement of camelid genome assemblies and functional annotation, development of genomics tools for improved genetic selection, genetics of adaptations, immunogenetics and disease resistance, genetics of phenotypes and production traits, genetics of congenital disorders and diseases, genetics of reproduction and development, genetics of behavior, population genetics, evolution, and paleogenomics.

Dr. Samantha A. Brooks
Prof. Terje Raudsepp
Guest Editors

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Keywords

  • adaptations
  • health
  • production traits
  • population
  • evolution

Published Papers (6 papers)

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Research

14 pages, 1732 KiB  
Article
A Deadly Cargo: Gene Repertoire of Cytotoxic Effector Proteins in the Camelidae
by Ján Futas, Jan Oppelt, Pamela Anna Burger and Petr Horin
Genes 2021, 12(2), 304; https://doi.org/10.3390/genes12020304 - 21 Feb 2021
Cited by 3 | Viewed by 2314
Abstract
Cytotoxic T cells and natural killer cells can kill target cells based on their expression and release of perforin, granulysin, and granzymes. Genes encoding these molecules have been only poorly annotated in camelids. Based on bioinformatic analyses of genomic resources, sequences corresponding to [...] Read more.
Cytotoxic T cells and natural killer cells can kill target cells based on their expression and release of perforin, granulysin, and granzymes. Genes encoding these molecules have been only poorly annotated in camelids. Based on bioinformatic analyses of genomic resources, sequences corresponding to perforin, granulysin, and granzymes were identified in genomes of camelids and related ungulate species, and annotation of the corresponding genes was performed. A phylogenetic tree was constructed to study evolutionary relationships between the species analyzed. Re-sequencing of all genes in a panel of 10 dromedaries and 10 domestic Bactrian camels allowed analyzing their individual genetic polymorphisms. The data showed that all extant Old World camelids possess functional genes for two pore-forming proteins (PRF1, GNLY) and six granzymes (GZMA, GZMB, GZMH, GZMK, GZMM, and GZMO). All these genes were represented as single copies in the genome except the GZMH gene exhibiting interspecific differences in the number of loci. High protein sequence similarities with other camelid and ungulate species were observed for GZMK and GZMM. The protein variability in dromedaries and Bactrian camels was rather low, except for GNLY and chymotrypsin-like granzymes (GZMB, GZMH). Full article
(This article belongs to the Special Issue Camelid Genomics)
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18 pages, 3344 KiB  
Article
Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray
by Marcos Calderon, Manuel J. More, Gustavo A. Gutierrez and Federico Abel Ponce de León
Genes 2021, 12(2), 291; https://doi.org/10.3390/genes12020291 - 19 Feb 2021
Cited by 12 | Viewed by 4641
Abstract
Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic [...] Read more.
Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection. Full article
(This article belongs to the Special Issue Camelid Genomics)
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21 pages, 3149 KiB  
Article
An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome
by Matthew J. Jevit, Brian W. Davis, Caitlin Castaneda, Andrew Hillhouse, Rytis Juras, Vladimir A. Trifonov, Ahmed Tibary, Jorge C. Pereira, Malcolm A. Ferguson-Smith and Terje Raudsepp
Genes 2021, 12(1), 105; https://doi.org/10.3390/genes12010105 - 16 Jan 2021
Cited by 3 | Viewed by 3881
Abstract
The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for [...] Read more.
The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology. Full article
(This article belongs to the Special Issue Camelid Genomics)
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11 pages, 2956 KiB  
Article
Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran
by Morteza Bitaraf Sani, Javad Zare Harofte, Ahmad Bitaraf, Saeid Esmaeilkhanian, Mohammad Hossein Banabazi, Nader Salim, Abbas Teimoori, Ali Shafei Naderi, Mohammad Ali Faghihi, Pamela Anna Burger, Mohammad Silawi and Afsaneh Taghipour Sheshdeh
Genes 2020, 11(6), 599; https://doi.org/10.3390/genes11060599 - 29 May 2020
Cited by 6 | Viewed by 3485
Abstract
The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and [...] Read more.
The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran’s camels was estimated to be 89. Predicted Tajima’s D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran’s dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries. Full article
(This article belongs to the Special Issue Camelid Genomics)
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12 pages, 907 KiB  
Article
Genetic Diversity and Population Structure of Llamas (Lama glama) from the Camelid Germplasm Bank—Quimsachata
by Gabriela F. Paredes, Claudia E. Yalta-Macedo, Gustavo A. Gutierrez and Eudosio A. Veli-Rivera
Genes 2020, 11(5), 541; https://doi.org/10.3390/genes11050541 - 12 May 2020
Cited by 6 | Viewed by 4063
Abstract
Llamas (Lama glama) are invaluable resources of Peru. Despite their importance, their population is decreasing. The Camelid Germplasm Bank—Quimsachata was created as a guardian of this South American camelid (SAC) species and established a bank of llamas from their two types, [...] Read more.
Llamas (Lama glama) are invaluable resources of Peru. Despite their importance, their population is decreasing. The Camelid Germplasm Bank—Quimsachata was created as a guardian of this South American camelid (SAC) species and established a bank of llamas from their two types, Ch’aku and Q’ara. However, these populations need to present high genetic diversity to be considered suitable conservation stocks. Thus, in the present study, 13 microsatellites specific for the SAC were used to assess the current genetic variability and differentiation of the llama population from the Bank. The global population showed high genetic diversity with a total of 157 different alleles, with an average of 12.08 alleles per microsatellite, an expected and observed heterozygosity of 0.758 and 0.707, respectively, and an average polymorphic information content (PIC) of 0.723. Although considered as two different breeds and managed separately, the genetic differentiation between Ch’aku and Q’ara was low (FST = 0.01). Accordingly, the gene flow value was high (Nm = 30.5). Overall, our results indicate the existence of high genetic variation among individuals, and thus, this llama population could be considered a suitable genetic stock for their conservation and for sustainability programs. Additionally, the 13 microsatellites can be used to study other Peruvian llama populations and monitor the genetic variability of llamas from the Camelid Germplasm Bank—Quimsachata. Full article
(This article belongs to the Special Issue Camelid Genomics)
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12 pages, 1404 KiB  
Article
Cytogenetic Mapping of 35 New Markers in the Alpaca (Vicugna pacos)
by Mayra N. Mendoza, Terje Raudsepp, Manuel J. More, Gustavo A. Gutiérrez and F. Abel Ponce de León
Genes 2020, 11(5), 522; https://doi.org/10.3390/genes11050522 - 8 May 2020
Cited by 7 | Viewed by 4658
Abstract
Alpaca is a camelid species of broad economic, biological and biomedical interest, and an essential part of the cultural and historical heritage of Peru. Recently, efforts have been made to improve knowledge of the alpaca genome, and its genetics and cytogenetics, to develop [...] Read more.
Alpaca is a camelid species of broad economic, biological and biomedical interest, and an essential part of the cultural and historical heritage of Peru. Recently, efforts have been made to improve knowledge of the alpaca genome, and its genetics and cytogenetics, to develop molecular tools for selection and breeding. Here, we report cytogenetic mapping of 35 new markers to 19 alpaca autosomes and the X chromosome. Twenty-eight markers represent alpaca SNPs, of which 17 are located inside or near protein-coding genes, two are in ncRNA genes and nine are intergenic. The remaining seven markers correspond to candidate genes for fiber characteristics (BMP4, COL1A2, GLI1, SFRP4), coat color (TYR) and development (CHD7, PAX7). The results take the tally of cytogenetically mapped markers in alpaca to 281, covering all 36 autosomes and the sex chromosomes. The new map assignments overall agree with human–camelid conserved synteny data, except for mapping BMP4 to VPA3, suggesting a hitherto unknown homology with HSA14. The findings validate, refine and correct the current alpaca assembly VicPac3.1 by anchoring unassigned sequence scaffolds, and ordering and orienting assigned scaffolds. The study contributes to the improvement in the alpaca reference genome and advances camelid molecular cytogenetics. Full article
(This article belongs to the Special Issue Camelid Genomics)
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