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Attili L, Garofalo L, Puddu G, Tirone G, Pizzarelli A, Barbara N, Haring E, Lorenzini R. Genetic distinctiveness of an endangered falcon: Implications for conservation in Europe. PLoS One 2023; 18:e0295424. [PMID: 38117737 PMCID: PMC10732417 DOI: 10.1371/journal.pone.0295424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/20/2023] [Indexed: 12/22/2023] Open
Abstract
In the Falconidae, the genus Falco comprises species of large birds of prey with wide distribution worldwide. However, the European lanner falcon Falco biarmicus feldeggii is rapidly heading for global extinction following a dramatic decline caused by anthropogenic interference. Conservation projects are currently underway with the main purpose of increasing its population size in the Mediterranean basin through captive breeding and release of birds into the wild. To support the projects, and strengthen the legitimacy of conservation efforts consistently with the Evolutionary Significant Unit concept, we explored the possibility of characterising the gene pool of the European lanner and reliably distinguishing it from other falcon taxa inhabiting the Mediterranean area, which show morphological and genetic similarities. To address the issue, we examined genetic variability at the nuclear level through the analysis of 12 neutral Short Tandem Repeat loci, and, for the first time in these taxa, two single-copy functional genes, coding for the brain-derived neurotrophic factor precursor and the oocyte maturation factor, respectively. The second exon of the major histocompatibility complex class II B gene was also investigated. Additionally, to frame our data with previously published data, we assess variation at the mitochondrial level by sequencing portions of the cytochrome b, 12S rRNA gene, and the control region. Our results showed that the European lanner is highly distinct from other falcon taxa, as revealed by nuclear, but not by mitochondrial DNA. We discuss our findings focusing on their implications for the preservation of this highly endangered European bird, and highlighted the critical role of genetic information in planning and monitoring concrete interventions.
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Affiliation(s)
- Lorenzo Attili
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Grosseto, Italy
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, Rome, Italy
| | - Luisa Garofalo
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, Rome, Italy
| | - Giuseppe Puddu
- Regione Lazio, Riserva Naturale Lago di Vico, Caprarola, Viterbo, Italy
| | - Giampiero Tirone
- Regione Lazio, Riserva Naturale Lago di Vico, Caprarola, Viterbo, Italy
| | - Antonella Pizzarelli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Grosseto, Italy
| | | | | | - Rita Lorenzini
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Grosseto, Italy
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Zinevich L, Prommer M, Laczkó L, Rozhkova D, Sorokin A, Karyakin I, Bagyura J, Cserkész T, Sramkó G. Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus). Sci Rep 2023; 13:17800. [PMID: 37853004 PMCID: PMC10584951 DOI: 10.1038/s41598-023-44534-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.
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Affiliation(s)
- Liudmila Zinevich
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - Levente Laczkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Daria Rozhkova
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | - Alexander Sorokin
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - János Bagyura
- MME - BirdLife Hungary, Költő utca 21, Budapest, 1121, Hungary
| | - Tamás Cserkész
- Hungarian Natural History Museum, Baross utca 13, Budapest, 1088, Hungary
| | - Gábor Sramkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary.
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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3
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Konopiński MK, Fijarczyk AM, Biedrzycka A. Complex patterns shape immune genes diversity during invasion of common raccoon in Europe - Selection in action despite genetic drift. Evol Appl 2022; 16:134-151. [PMID: 36699132 PMCID: PMC9850017 DOI: 10.1111/eva.13517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon Procyon lotor invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific single-nucleotide polymorphism markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, that is - less genetically diverse invasive population from the Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.
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Affiliation(s)
| | - Anna M. Fijarczyk
- Laval University Département de BiologieUniversité LavalQuébecQuébecCanada
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Hu L, Long J, Lin Y, Gu Z, Su H, Dong X, Lin Z, Xiao Q, Batbayar N, Bold B, Deutschová L, Ganusevich S, Sokolov V, Sokolov A, Patel HR, Waters PD, Graves JAM, Dixon A, Pan S, Zhan X. Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator. Nat Commun 2022; 13:6413. [PMID: 36302769 PMCID: PMC9613686 DOI: 10.1038/s41467-022-34138-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.
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Affiliation(s)
- Li Hu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Juan Long
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Yi Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhongru Gu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Han Su
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuemin Dong
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhenzhen Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Qian Xiao
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.20513.350000 0004 1789 9964Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Batbayar Bold
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Lucia Deutschová
- grid.455051.0Raptor Protection of Slovakia, Trhová 54, SK-841 01, Bratislava, Slovakia
| | - Sergey Ganusevich
- Wild Animal Rescue Centre, Krasnostudencheskiy pr., 21-45, Moscow, 125422 Russia
| | - Vasiliy Sokolov
- grid.426536.00000 0004 1760 306XInstitute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 202-8 Marta Street, Ekaterinburg, 620144 Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 21 Zelenaya Gorka, Labytnangi, Yamalo-Nenetski District 629400 Russia
| | - Hardip R. Patel
- grid.1001.00000 0001 2180 7477The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Paul D. Waters
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052 Australia
| | | | - Andrew Dixon
- Emirates Falconers’ Club, Al Mamoura Building (A), P.O. Box 47716, Muroor Road, Abu Dhabi, UAE ,grid.511767.30000 0004 5895 0922International Wildlife Consultants, P.O. Box 19, Carmarthen, SA33 5YL UK
| | - Shengkai Pan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiangjiang Zhan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.9227.e0000000119573309Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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Kawasaki E, Wenjing D, Sawada A, Nakajima M, Momose K, Yoshino T, Amano T, Endoh D, Nakajima N, Teraoka H. Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan. Animals (Basel) 2022; 12:2293. [PMID: 36078013 PMCID: PMC9455020 DOI: 10.3390/ani12172293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Red-crowned crane Grus japonensis is an endangered species in two separate populations: the mainland population in the Eurasian continent and the island population in eastern Hokkaido, Japan. We found 11 insertion/deletion (InDel) markers in the genome of the red-crowned crane and designed primer sets across these InDels that can be analyzed with conventional agarose gel electrophoresis. Sixty-six samples of whole blood and skeletal muscle obtained from red-crowned cranes, including 12 families in eastern Hokkaido from 1994 to 2021, showed different patterns in gel images of 11 InDel PCR reactions except for two pairs. The combined non-exclusion probability of the 11 markers indicates that individuals can be determined with a probability of 99.9%. In 39 non-relative chicks, the expected heterozygosity (He) was 0.316, suggesting low genetic diversity. This might not be caused by high levels of inbreeding since the average FIS was not significantly different from zero (0.095, p = 0.075). The results suggest that the 11 InDel primer sets can be used for fairly accurate individual identification as well as genetic population analyses in red-crowned cranes in the island population.
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Affiliation(s)
- Erika Kawasaki
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Dong Wenjing
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Akira Sawada
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Momoko Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | | | | | - Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
- NPO Red-Crowned Crane Conservancy, Kushiro 085-0036, Japan
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Jaiswal S, Jagannadham J, Kumari J, Iquebal MA, Gurjar AKS, Nayan V, Angadi UB, Kumar S, Kumar R, Datta TK, Rai A, Kumar D. Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo. Front Vet Sci 2021; 8:593871. [PMID: 34222390 PMCID: PMC8253262 DOI: 10.3389/fvets.2021.593871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Juli Kumari
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anoop Kishor Singh Gurjar
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Varij Nayan
- Indian Council of Agricultural Research (ICAR)-Central Institute for Research on Buffaloes, Hisar, India
| | - Ulavappa B Angadi
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunil Kumar
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rakesh Kumar
- Animal Biotechnology Centre, Indian Council of Agricultural Research (ICAR)-National Dairy research Institute, Karnal, India
| | - Tirtha Kumar Datta
- Animal Biotechnology Centre, Indian Council of Agricultural Research (ICAR)-National Dairy research Institute, Karnal, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
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Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
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Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
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Yaro M, Munyard KA, Morgan E, Allcock RJN, Stear MJ, Groth DM. Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment. BMC Genomics 2019; 20:816. [PMID: 31699027 PMCID: PMC6836352 DOI: 10.1186/s12864-019-6198-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually. RESULTS Here, we separately sequenced and then pooled according to breed the genomes from five unrelated individuals from each of the Djallonke and Sahelian sheep breeds (sourced from Ghana), at greater than 22-fold combined coverage for each breed. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian breeds respectively, were successfully mapped to the sheep reference genome Oar v3.1. We identified approximately 11.1 million and 10.9 million single nucleotide polymorphisms (SNPs) in the Djallonke and Sahelian breeds, with approximately 15 and 16% respectively of these not previously reported in sheep. Multiple regions of reduced heterozygosity were also found; 70 co-localised within genomic regions harbouring genes that mediate disease resistance, immune response and adaptation in sheep or cattle. Thirty- three of the regions of reduced heterozygosity co-localised with previously reported genes for resistance to haemonchosis and trypanosomiasis. CONCLUSIONS Our analyses suggest that these regions of reduced heterozygosity may be signatures of selection for these economically important diseases.
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Affiliation(s)
- M. Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - K. A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - E. Morgan
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - R. J. N. Allcock
- The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA Australia
- Pathwest Laboratory Medicine WA, QEII Medical Centre, Monash Avenue, Nedlands, 6009 Australia
| | - M. J. Stear
- Agribio centre for Agribioscience, La Trobe University, Melbourne, Australia
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow, Bearsden Road, Glasgow, G61 1QH UK
| | - D. M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
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Ramkumar B, Dharaskar SP, Mounika G, Paithankar K, Sreedhar AS. Mitochondrial chaperone, TRAP1 as a potential pharmacological target to combat cancer metabolism. Mitochondrion 2019; 50:42-50. [PMID: 31669620 DOI: 10.1016/j.mito.2019.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/17/2022]
Abstract
The stress response forms the most ancient defense system in living cells. Heat shock proteins (Hsps) are highly conserved across species and play major roles in mounting the stress response. The emerging information now suggests that Hsp90 family of chaperones display additional cellular roles contributing to diseases like cancer. For this reason, pharmacological targeting of Hsp90 has emerged as a novel antitumor strategy. However, its mitochondrial homologue TRAP1 has not been implicated in cancer with conclusive mechanistic insights. Since understanding the mutational spectrum of cancer cells indicates the outcome of the disease as well as treatment response, we examined mutational spectrum of TRAP1. Our in silico analyses of TRAP1 SNPs and CNVs correlated with the aggressive cancer phenotypes, and are found to be predominant over Hsp90 itself. The increased CNVs have been correlated with increased expression of TRAP1 in metastatic cancer cells, increased ATP production, and decreased oxygen consumption rate of mitochondria. Examining TRAP1 knockdown as well as over expression in metastatic cancer cells furthered our understanding that TRAP1 likely to facilitate the altered energy metabolism in the functional compromise of mitochondrial OXPHOS. Interestingly, the increased ATP levels in the TRAP1 background are found to be independent of glucose oxidation. Our results suggest TRAP1 role in triggering the alternate energy metabolism in cancer cells. Since targeting tumor metabolism is considered as an alternate strategy to combat cancer, we propose pharmacological targeting of TRAP1 to target alternate energy metabolism.
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Affiliation(s)
- Balaji Ramkumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India
| | - Shrikant P Dharaskar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India; Academy of Scientific & Innovation Research, Government of India, India
| | - Guntipally Mounika
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India
| | - Khanderao Paithankar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India
| | - Amere Subbarao Sreedhar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India.
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10
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Abstract
American chestnut (Castanea dentata Borkh.) was a dominant tree species in its native range in eastern North America until the accidentally introduced fungus Cryphonectria parasitica (Murr.) Barr, that causes chestnut blight, led to a collapse of the species. Different approaches (e.g., genetic engineering or conventional breeding) are being used to fight against chestnut blight and to reintroduce the species with resistant planting stock. Because of large climatic differences within the distribution area of American chestnut, successful reintroduction of the species requires knowledge and consideration of local adaptation to the prevailing environmental conditions. Previous studies revealed clear patterns of genetic diversity along the northeast-southwest axis of the Appalachian Mountains, but less is known about the distribution of potentially adaptive genetic variation within the distribution area of this species. In this study, we investigated neutral and potentially adaptive genetic variation in nine American chestnut populations collected from sites with different environmental conditions. In total, 272 individuals were genotyped with 24 microsatellite (i.e., simple sequence repeat (SSR)) markers (seven genomic SSRs and 17 EST-SSRs). An FST-outlier analysis revealed five outlier loci. The same loci, as well as five additional ones, were significantly associated with environmental variables of the population sites in an environmental association analysis. Four of these loci are of particular interest, since they were significant in both methods, and they were associated with environmental variation, but not with geographic variation. Hence, these loci might be involved in (temperature-related) adaptive processes in American chestnut. This work aims to help understanding the genetic basis of adaptation in C. dentata, and therefore the selection of suitable provenances for further breeding efforts.
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11
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Liu Y, Liu S, Yeh CF, Zhang N, Chen G, Que P, Dong L, Li SH. The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies. Sci Rep 2018; 8:15723. [PMID: 30356056 PMCID: PMC6200822 DOI: 10.1038/s41598-018-33646-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/21/2018] [Indexed: 11/24/2022] Open
Abstract
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chia-Fen Yeh
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Guoling Chen
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China.
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12
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Hou X, Xu P, Lin Z, D'Urban-Jackson J, Dixon A, Bold B, Xu J, Zhan X. Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population. Integr Zool 2018; 13:553-568. [PMID: 29316314 DOI: 10.1111/1749-4877.12305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.
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Affiliation(s)
- Xian Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,School of Nature Conservation, Beijing Forestry University, Beijing, China
| | | | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Andrew Dixon
- Emirates Falconers' Club, Abu Dhabi, United Arab Emirates.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China
| | - Batbayar Bold
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Wildlife Science and Conservation Center, Ulaanbaatar, Mongolia
| | - Jiliang Xu
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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13
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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14
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Förster DW, Bull JK, Lenz D, Autenrieth M, Paijmans JLA, Kraus RHS, Nowak C, Bayerl H, Kuehn R, Saveljev AP, Sindičić M, Hofreiter M, Schmidt K, Fickel J. Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species. Mol Ecol Resour 2018; 18:1356-1373. [PMID: 29978939 DOI: 10.1111/1755-0998.12924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 11/29/2022]
Abstract
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.
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Affiliation(s)
- Daniel W Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - James K Bull
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marijke Autenrieth
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Helmut Bayerl
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany
| | - Ralph Kuehn
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany.,Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, New Mexico
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Magda Sindičić
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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15
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Pan S, Zhang T, Rong Z, Hu L, Gu Z, Wu Q, Dong S, Liu Q, Lin Z, Deutschova L, Li X, Dixon A, Bruford MW, Zhan X. Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai-Tibetan Plateau in a predatory bird. Mol Ecol 2017; 26:2993-3010. [PMID: 28277617 DOI: 10.1111/mec.14090] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/10/2017] [Accepted: 02/28/2017] [Indexed: 01/04/2023]
Abstract
Low oxygen and temperature pose key physiological challenges for endotherms living on the Qinghai-Tibetan Plateau (QTP). Molecular adaptations to high-altitude living have been detected in the genomes of Tibetans, their domesticated animals and a few wild species, but the contribution of transcriptional variation to altitudinal adaptation remains to be determined. Here we studied a top QTP predator, the saker falcon, and analysed how the transcriptome has become modified to cope with the stresses of hypoxia and hypothermia. Using a hierarchical design to study saker populations inhabiting grassland, steppe/desert and highland across Eurasia, we found that the QTP population is already distinct despite having colonized the Plateau <2000 years ago. Selection signals are limited at the cDNA level, but of only seventeen genes identified, three function in hypoxia and four in immune response. Our results show a significant role for RNA transcription: 50% of upregulated transcription factors were related to hypoxia responses, differentiated modules were significantly enriched for oxygen transport, and importantly, divergent EPAS1 functional variants with a refined co-expression network were identified. Conservative gene expression and relaxed immune gene variation may further reflect adaptation to hypothermia. Our results exemplify synergistic responses between DNA polymorphism and RNA expression diversity in coping with common stresses, underpinning the successful rapid colonization of a top predator onto the QTP. Importantly, molecular mechanisms underpinning highland adaptation involve relatively few genes, but are nonetheless more complex than previously thought and involve fine-tuned transcriptional responses and genomic adaptation.
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Affiliation(s)
- Shengkai Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China.,Institute of Zoology Joint Laboratory for Biocomplexity Research, Cardiff University, Beichen West Road, Beijing, 100101, China.,University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | | | - Li Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China.,University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhongru Gu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China.,University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China
| | - Shanshan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Qiong Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China.,State Key Laboratory of Earth Surface Processes and Resource Ecology & MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China
| | - Lucia Deutschova
- Raptor Protection of Slovakia, Kuklovská 5, SK-841 04, Bratislava 4, Slovakia
| | - Xinhai Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China
| | - Andrew Dixon
- Institute of Zoology Joint Laboratory for Biocomplexity Research, Cardiff University, Beichen West Road, Beijing, 100101, China.,International Wildlife Consultants Ltd., PO Box 19, Carmarthen, SA33 5YL, UK.,Environment Agency-Abu Dhabi, PO Box 45553, Al Mamoura Building (A), Muroor Road, Abu Dhabi, United Arab Emirates
| | - Michael W Bruford
- Institute of Zoology Joint Laboratory for Biocomplexity Research, Cardiff University, Beichen West Road, Beijing, 100101, China.,Organisms and Environment Division, Cardiff School of Bioscience, Cardiff University, Cardiff, CF10 3AX, UK
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Beijing, 100101, China.,Institute of Zoology Joint Laboratory for Biocomplexity Research, Cardiff University, Beichen West Road, Beijing, 100101, China
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16
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Ren J, Chen L, Jin X, Zhang M, You FM, Wang J, Frenkel V, Yin X, Nevo E, Sun D, Luo MC, Peng J. Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides. FRONTIERS IN PLANT SCIENCE 2017; 8:258. [PMID: 28352272 PMCID: PMC5348526 DOI: 10.3389/fpls.2017.00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 05/06/2023]
Abstract
Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ FST ≤ 0.15) or high genetic differentiation (FST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different FST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.
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Affiliation(s)
- Jing Ren
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou UniversityDezhou, China
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Xiaoli Jin
- Department of Agronomy and the Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang UniversityHangzhou, China
| | - Miaomiao Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food CanadaWinnipeg, MB, Canada
| | - Jirui Wang
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Vladimir Frenkel
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Xuegui Yin
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Dongfa Sun
- Department of Agronomy, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Junhua Peng
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
- The State Key Lab of Crop Breeding Technology Innovation and Integration, China National Seed Group Co. Ltd.Wuhan, China
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17
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Maurer A, Draba V, Pillen K. Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2507-18. [PMID: 26936829 PMCID: PMC4809299 DOI: 10.1093/jxb/erw070] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Flowering time is a key agronomic trait that plays an important role in crop yield. There is growing interest in dissecting the developmental subphases of flowering to better understand and fine-tune plant development and maximize yield. To do this, we used the wild barley nested association mapping (NAM) population HEB-25, comprising 1420 BC1S3 lines, to map quantitative trait loci (QTLs) controlling five developmental traits, plant height, and thousand grain weight. Genome-wide association studies (GWAS) enabled us to locate a total of 89 QTLs that genetically regulate the seven investigated traits. Several exotic QTL alleles proved to be highly effective and potentially useful in barley breeding. For instance, thousand grain weight was increased by 4.5 g and flowering time was reduced by 9.3 days by substituting Barke elite QTL alleles for exotic QTL alleles at the denso/sdw1 and the Ppd-H1 loci, respectively. We showed that the exotic allele at the semi-dwarf locus denso/sdw1 can be used to increase grain weight since it uncouples the negative correlation between shoot elongation and the ripening phase. Our study demonstrates that nested association mapping of HEB-25 can help unravel the genetic regulation of plant development and yield formation in barley. Moreover, since we detected numerous useful exotic QTL alleles in HEB-25, we conclude that the introgression of these wild barley alleles into the elite barley gene pool may enable developmental phases to be specifically fine-tuned in order to maximize thousand grain weight and, potentially, yield in the long term.
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Affiliation(s)
- Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Vera Draba
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany. Interdisciplinary Center for Crop Plant Research (IZN), Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany.
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