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Thirulogachandar V, Govind G, Hensel G, Kale SM, Kuhlmann M, Eschen-Lippold L, Rutten T, Koppolu R, Rajaraman J, Palakolanu SR, Seiler C, Sakuma S, Jayakodi M, Lee J, Kumlehn J, Komatsuda T, Schnurbusch T, Sreenivasulu N. HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development. J Exp Bot 2024; 75:2900-2916. [PMID: 38366171 DOI: 10.1093/jxb/erae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | | | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sudhakar Reddy Palakolanu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Christiane Seiler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Shun Sakuma
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
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Yuan J, Hu J, Liu W, Chen S, Zhang F, Wang S, Zhang Z, Wang L, Xiao B, Li F, Hofreiter M, Lai X, Westbury MV, Sheng G. Camelus knoblochi genome reveals the complex evolutionary history of Old World camels. Curr Biol 2024:S0960-9822(24)00524-4. [PMID: 38754423 DOI: 10.1016/j.cub.2024.04.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/22/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.1,2 Although many remains have been unearthed,3,4,5 we know neither whether the prevalent hybridization observed between extant Camelus species2,6,7 also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C. knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C. knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.
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Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China.
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Wenhui Liu
- Institute of Environmental Archaeology, National Museum of China, East Chang'an Street 16, Beijing 100006, People's Republic of China
| | - Shungang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China
| | - Fengli Zhang
- Daqing Museum, Wenyuan Street 2, Daqing, Heilongjiang 163711, People's Republic of China
| | - Siren Wang
- Daqing Museum, Wenyuan Street 2, Daqing, Heilongjiang 163711, People's Republic of China
| | - Zhen Zhang
- Zhaoyuan Museum, Zhongyang Street 192, Daqing, Heilongjiang 166599, People's Republic of China
| | - Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Fuqiang Li
- Yifu Museum, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Michael V Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1353 Copenhagen, Denmark.
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Environmental Studies, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China.
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Chen S, Safiul Azam FM, Akter ML, Ao L, Zou Y, Qian Y. The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification. Front Plant Sci 2024; 15:1356912. [PMID: 38745930 PMCID: PMC11092384 DOI: 10.3389/fpls.2024.1356912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024]
Abstract
Introduction Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety. Methods The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum. Results and discussion The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium. Conclusion Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.
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Affiliation(s)
- Shixi Chen
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Fardous Mohammad Safiul Azam
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Mst. Lovely Akter
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Li Ao
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Yuanchao Zou
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Ye Qian
- Branch of The First Affiliated Hospital of Xinjiang Medical University, Changji, Xinjiang, China
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Maleka MF, Spies JJ. Polymorphisms in two key anthocyanic genes of clivia (Clivia miniata L.) reveal evidence of selection and possible association with flower pigmentation. J Evol Biol 2024; 37:429-441. [PMID: 38452247 DOI: 10.1093/jeb/voae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/26/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
Members of the genus Clivia show considerable variation in flower pigmentation and morphology. Such variation is affected by mutations that emerge in candidate flower development genes over time. Besides population history, mutations can further illuminate the effects of demographic events in populations in addition to population genetic parameters including selection, recombination, and linkage disequilibrium (LD). The current study aimed to find sequence variants in 2 anthocyanin biosynthetic genes (DFR and bHLH) of Clivia miniata and use the data to assess population genetic factors from a random collection of orange/red- and yellow-flowered specimens. Overall, average nucleotide diversity in the 2 anthocyanin genes was moderate (π = 0.00646), whereas haplotypes differed significantly (Hd ≥ 0.9). Gene evolution was seemingly driven by mutations (CmiDFR) or recombinations (CmibHLH001). LD decayed swiftly within the analyzed gene regions and supported the feasibility of assessing trait-variant associations via the association/linkage mapping approach. In the end, most associations were found to be spurious, but 1 haplotype in CmibHLH001 showed a promising correlation to the orange/red flower phenotype in Clivia specimens. In all, the present study is the first to measure gene-level diversity in C. miniata-data that had never been reported so far. Furthermore, the study also identified allelic and haplotypic variants that may be beneficial in future association genetic studies of Clivia. Such studies, however, consider large diverse populations to control for statistical bias intrinsic to the analysis of small datasets.
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Affiliation(s)
- Mathabatha F Maleka
- Department of Genetics, University of the Free State, Bloemfontein, Republic of South Africa
| | - Johan J Spies
- Department of Genetics, University of the Free State, Bloemfontein, Republic of South Africa
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Zhou Y, Li N, Zhou H, Zhou R, Cui S, Zheng G. Mitogenomics reveals extremely low genetic diversity in the endangered Jilin clawed salamander: Implications for its conservation. Ecol Evol 2024; 14:e11132. [PMID: 38505182 PMCID: PMC10948371 DOI: 10.1002/ece3.11132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/17/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
The Jilin clawed salamander (Onychodactylus zhangyapingi) is an endemic, endangered, and level-two protected amphibian species of China. In the context of serious threats to amphibians worldwide, conservation studies of this endangered species are urgently needed. In this study, mitogenomic conservation genetics and species distribution modeling analyses were performed for O. zhangyapingi. Sixty-three samples were collected from nine different locations, and the complete mitochondrial genome was sequenced. Population genetic analyses revealed that O. zhangyapingi exhibits only one genetic structure with extremely low nucleotide diversity. Late Pleistocene climate cooling may have led to a reduction in effective population size and extremely low mitogenomic nucleotide diversity in this salamander, and the subsequent temperature increase (~20 kya to present) provided the opportunity for rapid population growth. The continuous highly suitable region for O. zhangyapingi is only approximately 3000 km2 on the southeastern boundary of Jilin Province, China. Fortunately, there are three large forested national nature reserves within the distribution of O. zhangyapingi that can effectively protect endangered species. Our findings suggest that O. zhangyapingi is a vulnerable species with a narrow distribution and extremely low genetic diversity, and we should pay more attention to the conservation management of this species.
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Affiliation(s)
- Yu Zhou
- College of Life SciencesShenyang Normal UniversityShenyangChina
| | - Ningkun Li
- College of Life SciencesShenyang Normal UniversityShenyangChina
| | - Hongjun Zhou
- College of Life SciencesShenyang Normal UniversityShenyangChina
| | - Ruoyan Zhou
- College of Life ScienceNorthwest A&F UniversityYanglingShaanxiChina
| | - Shuyan Cui
- College of Life SciencesShenyang Normal UniversityShenyangChina
| | - Guo Zheng
- College of Life SciencesShenyang Normal UniversityShenyangChina
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Alfaro-Fernández A, Taengua R, Font-San-Ambrosio I, Sanahuja-Edo E, Peiró R, Galipienso L, Rubio L. Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain. Plants (Basel) 2024; 13:250. [PMID: 38256804 PMCID: PMC10818716 DOI: 10.3390/plants13020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
The genetic variation and population structure of gene N (nucleocapsid) and part of gene L (replicase) from 13 eggplant mottle dwarf virus (EMDV) isolates from Spain were evaluated and compared with sequences of EMDV isolates from other countries retrieved from GenBank. Phylogenetic inference of part of gene L showed three main clades, one containing an EMDV isolate from Australia and the other two containing isolates from Iran and Europe, as well as four subclades. EMDV isolates from Spain were genetically very similar and grouped in a subclade together with one isolate from Germany and one from the UK. No new recombination events were detected in addition to one recombination previously reported, suggesting that recombination is rare for EMDV. The comparison of synonymous and non-synonymous rates showed that negative selection played an important role, and only two codons were under positive selection. Genetic differentiation (Fst test), phylogenetic and nucleotide diversity analyses suggest a unique introduction of EMDV to Spain and low gene flow with other countries. In contrast, Greece and Italy showed diverse populations with high gene flow between both.
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Affiliation(s)
- Ana Alfaro-Fernández
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Rafael Taengua
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
| | - Isabel Font-San-Ambrosio
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Esmeralda Sanahuja-Edo
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Rosa Peiró
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain;
| | - Luis Galipienso
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
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Fonseca EM, Pelletier TA, Decker SK, Parsons DJ, Carstens BC. Pleistocene glaciations caused the latitudinal gradient of within-species genetic diversity. Evol Lett 2023; 7:331-338. [PMID: 37829497 PMCID: PMC10565891 DOI: 10.1093/evlett/qrad030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/26/2023] [Accepted: 07/10/2023] [Indexed: 10/14/2023] Open
Abstract
Intraspecific genetic diversity is a key aspect of biodiversity. Quaternary climatic change and glaciation influenced intraspecific genetic diversity by promoting range shifts and population size change. However, the extent to which glaciation affected genetic diversity on a global scale is not well established. Here we quantify nucleotide diversity, a common metric of intraspecific genetic diversity, in more than 38,000 plant and animal species using georeferenced DNA sequences from millions of samples. Results demonstrate that tropical species contain significantly more intraspecific genetic diversity than nontropical species. To explore potential evolutionary processes that may have contributed to this pattern, we calculated summary statistics that measure population demographic change and detected significant correlations between these statistics and latitude. We find that nontropical species are more likely to deviate from neutral expectations, indicating that they have historically experienced dramatic fluctuations in population size likely associated with Pleistocene glacial cycles. By analyzing the most comprehensive data set to date, our results imply that Quaternary climate perturbations may be more important as a process driving the latitudinal gradient in species richness than previously appreciated.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Tara A Pelletier
- Department of Biology, Radford University, Radford, VA, United States
| | - Sydney K Decker
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Danielle J Parsons
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
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Mulugeta B, Ortiz R, Geleta M, Hailesilassie T, Hammenhag C, Hailu F, Tesfaye K. Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool. Front Plant Sci 2023; 14:1192356. [PMID: 37546270 PMCID: PMC10400094 DOI: 10.3389/fpls.2023.1192356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023]
Abstract
Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r2 > 0.20, P < 0.01), with an average r2 of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the Fst outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.
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Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
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Díaz-Ferguson E, Chial M, Gonzalez M, Muñoz E, Chen O, Durán O, Vega AJ, Delgado CR. Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets. Animals (Basel) 2023; 13:2272. [PMID: 37508050 PMCID: PMC10376180 DOI: 10.3390/ani13142272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima's D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas.
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Affiliation(s)
- Edgardo Díaz-Ferguson
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
| | - Magaly Chial
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Maribel Gonzalez
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Edgardo Muñoz
- Center of Marine Science and Limnology, Department of Marine Biology, University of Panama, Panama City 0824-01853, Panama
| | - Olga Chen
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Ovidio Durán
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Angel Javier Vega
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
- School of Biology, Regional Center, University of Panama, Santiago de Veraguas 0923-00125, Panama
| | - Carlos Ramos Delgado
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
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10
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Ord J, Gossmann TI, Adrian-Kalchhauser I. High nucleotide diversity accompanies differential DNA methylation in naturally diverging populations. Mol Biol Evol 2023; 40:7083720. [PMID: 36947101 PMCID: PMC10139703 DOI: 10.1093/molbev/msad068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/14/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, the link between genetic diversity and DNAme has been scarcely examined in natural populations, despite its potential to shed light on the evolutionary forces acting on methylation state. Here, we analysed reduced-representation bisulfite sequencing and whole genome pool-seq data from marine and freshwater stickleback populations to examine the relationship between DNAme variation (between- and within-population), and nucleotide diversity in the context of freshwater adaptation. We find that sites that are differentially methylated between populations have higher underlying standing genetic variation, with diversity higher among sites that gained methylation in freshwater than those that lost it. Strikingly, while nucleotide diversity is generally lower in the freshwater population as expected from a population bottleneck, this is not the case for sites which lost methylation which instead have elevated nucleotide diversity in freshwater compared to marine. Subsequently, we show that nucleotide diversity is higher among sites with ancestrally variable methylation and also positively correlates with the sensitivity to environmentally induced methylation change. The results suggest that as selection on the control of methylation state becomes relaxed, so too does selection against mutations at the sites themselves. Increased epigenetic variance in a population is therefore likely to precede genetic diversification.
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Affiliation(s)
- James Ord
- Institute for Fish and Wildlife Health, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1, 00790 Helsinki, Finland
| | - Toni I Gossmann
- Computational Systems Biology, Faculty of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Irene Adrian-Kalchhauser
- Institute for Fish and Wildlife Health, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
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11
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Cheng L, Li M, Wang Y, Han Q, Hao Y, Qiao Z, Zhang W, Qiu L, Gong A, Zhang Z, Li T, Luo S, Tang L, Liu D, Yin H, Lu S, Balbuena TS, Zhao Y. Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population. Front Plant Sci 2023; 14:1114284. [PMID: 36890899 PMCID: PMC9986275 DOI: 10.3389/fpls.2023.1114284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yachao Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Lin Qiu
- Institute of Forestry Science, Xinyang Forestry Bureau, Xinyang, Henan, China
| | - Andong Gong
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhihan Zhang
- College of Engineering and Technology, Northeast Forestry University, Harbin, China
| | - Tao Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Shanshan Luo
- College of Agriculture, Guizhou University, Guiyang, China
| | - Linshuang Tang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Daliang Liu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Hao Yin
- College of Agriculture, Guizhou University, Guiyang, China
| | - Song Lu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal, Brazil
| | - Yiyong Zhao
- College of Agriculture, Guizhou University, Guiyang, China
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12
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Konopiński MK. Average weighted nucleotide diversity is more precise than pixy in estimating the true value of π from sequence sets containing missing data. Mol Ecol Resour 2023; 23:348-354. [PMID: 36031871 DOI: 10.1111/1755-0998.13707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/03/2022] [Accepted: 07/27/2022] [Indexed: 01/04/2023]
Abstract
Nucleotide diversity remains an important statistic in population genetic/genomic studies. Although recent advances in massive sequencing make generating sequence data sets cheaper and faster, currently used technologies often introduce substantial amounts of missing nucleotides in their output. A novel method of estimating π from data sets containing missing data - pixy - has also recently been proposed. In this study, the pixy estimator, πpixy , was compared to average weighted nucleotide diversity, πW . The estimators were tested both on sequences simulated in fastsimcoal and real sequence sets. Both sets were modified by random insertion of missing nucleotides. Weighted nucleotide diversity performed better in all pairwise comparisons. It was characterized by a smaller error and a narrower distribution of the results. πpixy tends to overestimate the nucleotide diversity when both the proportion of missing data and the level of variation is low. Of the two estimators, only πW estimated the true nucleotide diversity in a part of the simulations. A simple formula for estimating πW allows for easy integration of the estimator in packages such as pixy, which would allow obtaining more precise estimates of nucleotide diversity either in a sliding window or for discrete genomic regions.
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13
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Larkin IE, Myers EA, Carstens BC, Barrow LN. Predictors of genomic diversity within North American squamates. J Hered 2023; 114:131-142. [PMID: 36638275 PMCID: PMC10078173 DOI: 10.1093/jhered/esad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023] Open
Abstract
Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for two mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; four individuals and 6,820-44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (Phylogenetically Independent Contrasts: R 2 = 0.31, p = 0.007) and GBS diversity (R 2 = 0.21; p = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species' ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.
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Affiliation(s)
- Ivy E Larkin
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH
| | - Lisa N Barrow
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH.,Current Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque NM
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14
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Ravi V, Swaminathan A, Yadav S, Arya H, Pandey R. SARS-CoV-2 Variants of Concern and Variations within Their Genome Architecture: Does Nucleotide Distribution and Mutation Rate Alter the Functionality and Evolution of the Virus? Viruses 2022; 14:v14112499. [PMID: 36423107 PMCID: PMC9694950 DOI: 10.3390/v14112499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 virus pathogenicity and transmissibility are correlated with the mutations acquired over time, giving rise to variants of concern (VOCs). Mutations can significantly influence the genetic make-up of the virus. Herein, we analyzed the SARS-CoV-2 genomes and sub-genomic nucleotide composition in relation to the mutation rate. Nucleotide percentage distributions of 1397 in-house-sequenced SARS-CoV-2 genomes were enumerated, and comparative analyses (i) within the VOCs and of (ii) recovered and mortality patients were performed. Fisher's test was carried out to highlight the significant mutations, followed by RNA secondary structure prediction and protein modeling for their functional impacts. Subsequently, a uniform dinucleotide composition of AT and GC was found across study cohorts. Notably, the N gene was observed to have a high GC percentage coupled with a relatively higher mutation rate. Functional analysis demonstrated the N gene mutations, C29144T and G29332T, to induce structural changes at the RNA level. Protein secondary structure prediction with N gene missense mutations revealed a differential composition of alpha helices, beta sheets, and coils, whereas the tertiary structure displayed no significant changes. Additionally, the N gene CTD region displayed no mutations. The analysis highlighted the importance of N protein in viral evolution with CTD as a possible target for antiviral drugs.
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Affiliation(s)
- Varsha Ravi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Aparna Swaminathan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Sunita Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Hemant Arya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence: or ; Tel.: +91-9811029551
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15
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Wang Y, Yu J, Chen YK, Wang ZC. Complete Chloroplast Genome Sequence of the Endemic and Endangered Plant Dendropanax oligodontus: Genome Structure, Comparative and Phylogenetic Analysis. Genes (Basel) 2022; 13:2028. [PMID: 36360265 PMCID: PMC9690231 DOI: 10.3390/genes13112028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2023] Open
Abstract
Dendropanax oligodontus, which belongs to the family Araliaceae, is an endemic and endangered species of Hainan Island, China. It has potential economic and medicinal value owing to the presence of phenylpropanoids, flavonoids, triterpenoids, etc. The analysis of the structure and characteristics of the D. oligodontus chloroplast genome (cpDNA) is crucial for understanding the genetic and phylogenetic evolution of this species. In this study, the cpDNA of D. oligodontus was sequenced for the first time using next-generation sequencing methods, assembled, and annotated. We observed a circular quadripartite structure comprising a large single-copy region (86,440 bp), a small single-copy region (18,075 bp), and a pair of inverted repeat regions (25,944 bp). The total length of the cpDNA was 156,403 bp, and the GC% was 37.99%. We found that the D. oligodontus chloroplast genome comprised 131 genes, with 86 protein-coding genes, 8 rRNA genes, and 37 tRNAs. Furthermore, we identified 26,514 codons, 13 repetitive sequences, and 43 simple sequence repeat sites in the D. oligodontus cpDNA. The most common amino acid encoded was leucine, with a strong A/T preference at the third position of the codon. The prediction of RNA editing sites in the protein-coding genes indicated that RNA editing was observed in 19 genes with a total of 54 editing sites, all of which involved C-to-T transitions. Finally, the cpDNA of 11 species of the family Araliaceae were selected for comparative analysis. The sequences of the untranslated regions and coding regions among 11 species were highly conserved, and minor differences were observed in the length of the inverted repeat regions; therefore, the cpDNAs were relatively stable and consistent among these 11 species. The variable hotspots in the genome included clpP, ycf1, rnK-rps16, rps16-trnQ, atpH-atpI, trnE-trnT, psbM-trnD, ycf3-trnS, and rpl32-trnL, providing valuable molecular markers for species authentication and regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. Evolutionary selection pressure analysis indicated that the atpF gene was strongly subjected to positive environmental selection. Phylogenetic analysis indicated that D. oligodontus and Dendropanax dentiger were the most closely related species within the genus, and D. oligodontus was closely related to the genera Kalopanax and Metapanax in the Araliaceae family. Overall, the cp genomes reported in this study will provide resources for studying the genetic diversity and conservation of the endangered plant D. oligodontus, as well as resolving phylogenetic relationships within the family.
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Affiliation(s)
- Yong Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jing Yu
- Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University, Haikou 570228, China
| | - Yu-Kai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Zhu-Cheng Wang
- College of Life Sciences, Cangzhou Normal University, Cangzhou 061001, China
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16
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Jiang H, Guo D, Liu Y, Zhu L, Xie F, Xie L. RNA-Seq combined with population-level analysis reveals important candidate genes related to seed size in flax ( Linum usitatissimum L.). Front Plant Sci 2022; 13:1015399. [PMID: 36388602 PMCID: PMC9641021 DOI: 10.3389/fpls.2022.1015399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Seed size is a key determinant of crop yields. Understanding the regulatory mechanisms of seed size is beneficial for improving flax seed yield. In this study, the development of large flax seeds lagged behind that of small seeds, and 1,751 protein-coding genes were differentially expressed in early seeds, torpedo-stage embryos, and endosperms of CIli2719 and Z11637 using RNA sequencing. Homologous alignment revealed that 129 differentially expressed genes (DEGs) in flax were homologous with 71 known seed size-related genes in Arabidopsis thaliana and rice (Oryza sativa L.). These DEGs controlled seed size through multiple processes and factors, among which phytohormone pathways and transcription factors were the most important. Moreover, 54 DEGs were found to be associated with seed size and weight in a DEG-based association study. Nucleotide diversity (π) analysis of seed size-related candidate DEGs by homologous alignment and association analysis showed that the π values decreased significantly during flax acclimation from oil to fiber flax, suggesting that some seed size-related candidate genes were selected in this acclimation process. These results provide important resources and genetic foundation for further research on seed size regulation and seed improvement in flax.
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17
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Catalan A, Höhna S, Lower SE, Duchen P. Inferring the demographic history of the North American firefly Photinus pyralis. J Evol Biol 2022; 35:1488-1499. [PMID: 36168726 DOI: 10.1111/jeb.14094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/13/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022]
Abstract
The firefly Photinus pyralis inhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Despite its broad distribution, its demographic history is unknown. In this study, we modelled and inferred different demographic scenarios for North American populations of P. pyralis, which were collected from Texas to New Jersey. We used a combination of ABC techniques (for multi-population/colonization analyses) and likelihood inference (dadi, StairwayPlot2, PoMo) for single-population demographic inference, which proved useful with our RAD data. We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. To estimate the age of divergence between of P. pyralis, which provides deeper insights into the history of the entire species, we assembled a multi-locus phylogenetic data covering the genus Photinus. We uncovered that the phylogenetic node leading to P. pyralis lies at the end of the Miocene. Importantly, modelling the demographic history of North American P. pyralis serves as a null model of nucleotide diversity patterns in a widespread native insect species, which will serve in future studies for the detection of adaptation events in this firefly species, as well as a comparison for future studies of other North American insect taxa.
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Affiliation(s)
- Ana Catalan
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Sebastian Höhna
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sarah E Lower
- Department of Biology, Bucknell University, Lewisburg, PA, USA
| | - Pablo Duchen
- Institute for Organismal and Molecular Evolutionary Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
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18
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Luna N, Muñoz M, Ramírez AL, Patiño LH, Castañeda SA, Ballesteros N, Ramírez JD. Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries. Viruses 2022; 14:v14061234. [PMID: 35746705 PMCID: PMC9230695 DOI: 10.3390/v14061234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/21/2023] Open
Abstract
Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage's genomic and epidemiological characteristics. However, in South America, this variant's arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health.
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Affiliation(s)
- Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Angie L. Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Luz H. Patiño
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Sergio Andres Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: or
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19
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Shafat Z, Ahmed A, Parvez MK, Parveen S. Sequence to structure analysis of the ORF4 protein from Hepatitis E virus. Bioinformation 2022; 17:818-828. [PMID: 35539889 PMCID: PMC9049080 DOI: 10.6026/97320630017818] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis E virus (HEV) is the main cause of acute hepatitis worldwide. HEV accounts for up to 30% mortality rate in pregnant women, with highest incidences reported for genotype 1 (G1) HEV. The contributing factors in adverse cases during pregnancy
in women due to HEV infection is still debated. The mechanism underlying the pathogenesis of viral infection is attributed to different genomic component of HEV, i.e., open reading frames (ORFs): ORF1, ORF2, ORF3 and ORF4. Recently, ORF4 has been discovered
in enhancing the replication of GI isolates of HEV through regulation of an IRES-like RNA element. However, its characterization through computational methodologies remains unexplored. In this novel study, we provide comprehensive overview of ORF4 protein's
genetic and molecular characteristics through analyzing its sequence and different structural levels. A total of three different datasets (Human, Rat and Ferret) of ORF4 genomes were built and comparatively analyzed. Several non-synonymous mutations in
conjunction with higher entropy values were observed in rat and ferret datasets, however, limited variation was observed in human ORF4 genomes. Higher transition to tranversion ratio was observed in the ORF4 genomes. Studies have reported the association of
intrinsic disordered proteins (IDP) with drug discovery due to its role in several signaling and regulatory processes through protein-protein interactions (PPIs). As PPIs are potent drug target sources, thus the ORF4 protein was explored by analyzing its
polypeptide structure in order to shed light on its intrinsic disorder. Pressures that lead towards preponderance of disordered-promoting amino acid residues shaped the evolution of ORF4. The intrinsic disorder propensity analysis revealed ORF4 protein
(Human) as a highly disordered protein (IDP). Predominance of coils and lack of secondary structure further substantiated our findings suggesting its involvement in binding to ligand molecules. Thus, ORF4 contributes to cellular signaling processes through
protein-protein interactions, as IDPs are targets for regulation to accelerate the process of drug designing strategies against HEV infections.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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20
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Ye Z, Zhao C, Raborn RT, Lin M, Wei W, Hao Y, Lynch M. Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Mol Biol Evol 2022; 39:6553573. [PMID: 35325186 PMCID: PMC9004417 DOI: 10.1093/molbev/msac059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Chaoxian Zhao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - R Taylor Raborn
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Man Lin
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Wen Wei
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Yue Hao
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
| | - Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, 85287
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21
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Pavesi A, Romerio F. Extending the Coding Potential of Viral Genomes with Overlapping Antisense ORFs: A Case for the De Novo Creation of the Gene Encoding the Antisense Protein ASP of HIV-1. Viruses 2022; 14:v14010146. [PMID: 35062351 PMCID: PMC8781085 DOI: 10.3390/v14010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Gene overprinting occurs when point mutations within a genomic region with an existing coding sequence create a new one in another reading frame. This process is quite frequent in viral genomes either to maximize the amount of information that they encode or in response to strong selective pressure. The most frequent scenario involves two different reading frames in the same DNA strand (sense overlap). Much less frequent are cases of overlapping genes that are encoded on opposite DNA strands (antisense overlap). One such example is the antisense ORF, asp in the minus strand of the HIV-1 genome overlapping the env gene. The asp gene is highly conserved in pandemic HIV-1 strains of group M, and it is absent in non-pandemic HIV-1 groups, HIV-2, and lentiviruses infecting non-human primates, suggesting that the ~190-amino acid protein that is expressed from this gene (ASP) may play a role in virus spread. While the function of ASP in the virus life cycle remains to be elucidated, mounting evidence from several research groups indicates that ASP is expressed in vivo. There are two alternative hypotheses that could be envisioned to explain the origin of the asp ORF. On one hand, asp may have originally been present in the ancestor of contemporary lentiviruses, and subsequently lost in all descendants except for most HIV-1 strains of group M due to selective advantage. Alternatively, the asp ORF may have originated very recently with the emergence of group M HIV-1 strains from SIVcpz. Here, we used a combination of computational and statistical approaches to study the genomic region of env in primate lentiviruses to shed light on the origin, structure, and sequence evolution of the asp ORF. The results emerging from our studies support the hypothesis of a recent de novo addition of the antisense ORF to the HIV-1 genome through a process that entailed progressive removal of existing internal stop codons from SIV strains to HIV-1 strains of group M, and fine tuning of the codon sequence in env that reduced the chances of new stop codons occurring in asp. Altogether, the study supports the notion that the HIV-1 asp gene encodes an accessory protein, providing a selective advantage to the virus.
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Affiliation(s)
- Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
- Correspondence:
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22
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Galipienso L, Elvira-González L, Velasco L, Herrera-Vásquez JÁ, Rubio L. Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies. Plants (Basel) 2021; 10:plants10112295. [PMID: 34834658 PMCID: PMC8620285 DOI: 10.3390/plants10112295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
High-throughput sequencing from symptomatic tomato and pepper plants collected in Panama rendered the complete genome of the southern tomato virus (isolate STV_Panama) and bell pepper endornavirus (isolate BPEV_Panama), and almost-complete genomes of three other BPEV isolates. Tomato chlorosis virus, tomato mosaic virus, and impatiens necrotic spot virus were also detected. Analysis of the complete genome of STV and BPEV worldwide isolates revealed nucleotide diversities of 0.004246 and 0.070523, respectively. Bayesian phylogenetic analysis showed two main groups for each virus (I and II), and several subgroups for BPEV (IA, IB, IC, IIA and IIB). Isolate STV_Panama clustered with NC_12-03-08 from USA and Tom3-T from France (99.97% nucleotide identity) in Group I and BPEV_Panama was close to the Canadian isolate BPEV_Ontario (99.66% nucleotide identity) in Subgroup IB. No correlation was observed between geographic and genetic distances for both viruses. Panamanian BPEV isolates were divergent, belonging to Groups I and II (nucleotide identities > 87.33%). Evolutionary analysis showed purifying selection in all encoding regions of both viruses, being stronger in the overlapping region of both STV genes. Finally, recombination was detected in BPEV but not in STV. This is the first report of STV and BPEV in Panama.
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Affiliation(s)
- Luis Galipienso
- Plant Protection and Biotechnology Center of the Valencian Institute of Agricultural Research, 46113 Moncada, Valencia, Spain;
| | - Laura Elvira-González
- Subtropical and Mediterranean Horticulture Institute (LaMayora), 29010 Algarrobo-Costa, Málaga, Spain;
| | - Leonardo Velasco
- Churriana Center of Andalusian Institute of Agricultural Research, 29140 Churriana, Málaga, Spain;
| | | | - Luis Rubio
- Plant Protection and Biotechnology Center of the Valencian Institute of Agricultural Research, 46113 Moncada, Valencia, Spain;
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23
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Shirasawa K, Kosugi S, Sasaki K, Ghelfi A, Okazaki K, Toyoda A, Hirakawa H, Isobe S. Genome features of common vetch ( Vicia sativa) in natural habitats. Plant Direct 2021; 5:e352. [PMID: 34646975 PMCID: PMC8496506 DOI: 10.1002/pld3.352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 05/30/2023]
Abstract
Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement.
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Affiliation(s)
| | - Shunichi Kosugi
- Kazusa DNA Research InstituteKisarazuJapan
- RIKENYokohamaJapan
| | - Kazuhiro Sasaki
- Institute for Sustainable Agro‐ecosystem Services, Graduate School of Agricultural and Life SciencesThe University of TokyoNishitokyoJapan
- Japan International Research Center for Agricultural SciencesTsukubaJapan
| | - Andrea Ghelfi
- Kazusa DNA Research InstituteKisarazuJapan
- National Institute of GeneticsMishimaJapan
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24
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Hardigan MA, Lorant A, Pincot DDA, Feldmann MJ, Famula RA, Acharya CB, Lee S, Verma S, Whitaker VM, Bassil N, Zurn J, Cole GS, Bird K, Edger PP, Knapp SJ. Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry. Mol Biol Evol 2021; 38:2285-2305. [PMID: 33507311 PMCID: PMC8136507 DOI: 10.1093/molbev/msab024] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.
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Affiliation(s)
- Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Charlotte B Acharya
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Seonghee Lee
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Sujeet Verma
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Vance M Whitaker
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 92182, USA
| | - Jason Zurn
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 92182, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Kevin Bird
- Department of Horticultural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Patrick P Edger
- Department of Horticultural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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25
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Cunha DBD, Martins KCP, Júnior JNDS, Moreira ECDO, Sampaio I, Queiroz CDCS, Leite MA, Souza AAD, Santos CAD, Vallinoto M. High genetic diversity detected in the mitochondrial Control Region of the Serra Spanish Mackerel, Scomberomorus brasiliensis (Collette, Russo & Zavala, 1978) along the Brazilian coast. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:178-185. [PMID: 37706236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The Serra Spanish mackerel, Scomberomorus brasiliensis, is one of the most important fishery resources in the western tropical Atlantic, including northern and eastern Brazil. Despite its economic importance, few genetic markers have been sequenced in this species, and little is known of its population genetics. The present study evaluated the genetic variability of 110 individuals, representing three distinct Brazilian populations (Macapá, Fortaleza and Paranaguá), based on a segment of the mitochondrial Control Region. The sequences revealed high levels of genetic diversity, and suggested marked connectivity among the studied populations. A variable repeat was also found in the 3' portion of the studied Control Region fragment, which may prove useful as a marker in future genetic population studies of S. brasiliensis.
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Affiliation(s)
- Divino Bruno da Cunha
- Universidade Federal do Sul e Sudeste do Pará - UNIFESSPA, Laboratório Multiuso, Campus de São Félix do Xingu, São Félix do Xingu, Pará, Brasil
| | - Kely Cristina Piedade Martins
- Universidade Federal do Sul e Sudeste do Pará - UNIFESSPA, Laboratório Multiuso, Campus de São Félix do Xingu, São Félix do Xingu, Pará, Brasil
| | - José Nazareno do Santos Júnior
- Universidade Federal do Sul e Sudeste do Pará - UNIFESSPA, Laboratório Multiuso, Campus de São Félix do Xingu, São Félix do Xingu, Pará, Brasil
| | | | - Iracilda Sampaio
- Laboratório de Evolução, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará (UFPA), Campus de Bragança, Bragança, PA, Brasil
| | - Cleonilde da Conceição Silva Queiroz
- Laboratório de Genética e Biologia Molecular, Centro de Ciências Exatas Naturais e Tecnológicas (CCENT), Universidade Estadual da Região Tocantina do Maranhão (UEMASUL), Imperatriz, MA, Brazil
| | - Maria Adriana Leite
- Universidade Federal do Amapá - Campus Binacional do Oiapoque, Amapá, Brasil
| | | | | | - Marcelo Vallinoto
- Laboratório de Evolução, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará (UFPA), Campus de Bragança, Bragança, PA, Brasil
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26
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Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen NO. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome Biol Evol 2021; 13:evab098. [PMID: 33964136 PMCID: PMC8214408 DOI: 10.1093/gbe/evab098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.
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Affiliation(s)
- Anna Tigano
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Arne Jacobs
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Aryn P Wilder
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Conservation Genetics, San Diego Zoo Global, Escondido, California, USA
| | - Ankita Nand
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ye Zhan
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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27
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Tisthammer KH, Dong W, Joy JB, Pennings PS. Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a. Viruses 2021; 13:511. [PMID: 33808782 PMCID: PMC8003410 DOI: 10.3390/v13030511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Understanding within-host evolution is critical for predicting viral evolutionary outcomes, yet such studies are currently lacking due to difficulty involving human subjects. Hepatitis C virus (HCV) is an RNA virus with high mutation rates. Its complex evolutionary dynamics and extensive genetic diversity are demonstrated in over 67 known subtypes. In this study, we analyzed within-host mutation frequency patterns of three HCV subtypes, using a large number of samples obtained from treatment-naïve participants by next-generation sequencing. We report that overall mutation frequency patterns are similar among subtypes, yet subtype 3a consistently had lower mutation frequencies and nucleotide diversity, while subtype 1a had the highest. We found that about 50% of genomic sites are highly conserved across subtypes, which are likely under strong purifying selection. We also compared within-host and between-host selective pressures, which revealed that Hyper Variable Region 1 within hosts was under positive selection, but was under slightly negative selection between hosts, which indicates that many mutations created within hosts are removed during the transmission bottleneck. Examining the natural prevalence of known resistance-associated variants showed their consistent existence in the treatment-naïve participants. These results provide insights into the differences and similarities among HCV subtypes that may be used to develop and improve HCV therapies.
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Affiliation(s)
- Kaho H. Tisthammer
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (J.B.J.)
| | - Jeffrey B. Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (J.B.J.)
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC V5Z 3J5, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
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28
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Myers BM, Burns KJ, Clark CJ, Brelsford A. The population genetics of nonmigratory Allen's Hummingbird ( Selasphorus sasin sedentarius) following a recent mainland colonization. Ecol Evol 2021; 11:1850-1865. [PMID: 33614008 PMCID: PMC7882939 DOI: 10.1002/ece3.7174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 02/01/2023] Open
Abstract
Allen's Hummingbird comprises two subspecies, one migratory (Selasphorus sasin sasin) and one nonmigratory (S. s. sedentarius). The nonmigratory subspecies, previously endemic to the California Channel Islands, apparently colonized the California mainland on the Palos Verdes Peninsula some time before 1970 and now breeds throughout coastal southern California. We sequenced and compared populations of mainland nonmigratory Allen's Hummingbird to Channel Island populations from Santa Catalina, San Clemente, and Santa Cruz Island. We found no evidence of founder effects on the mainland population. Values of nucleotide diversity on the mainland were higher than on the Channel Islands. There were low levels of divergence between the Channel Islands and the mainland, and Santa Cruz Island was the most genetically distinct. Ecological niche models showed that rainfall and temperature variables on the Channel Islands are similar in the Los Angeles basin and predicted continued expansion of nonmigratory Allen's Hummingbird north along the coast and inland. We also reviewed previous genetic studies of vertebrate species found on the Channel Islands and mainland and showed that broad conclusions regarding island-mainland patterns remain elusive. Challenges include the idiosyncratic nature of colonization itself as well as the lack of a comprehensive approach that incorporates similar markers and sampling strategies across taxa, which, within the context of a comparative study of island-mainland relationships, may lead to inconsistent results.
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Affiliation(s)
- Brian M. Myers
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Kevin J. Burns
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Christopher J. Clark
- Department of Evolution, Ecology, and Organismal BiologySpeith HallUniversity of CaliforniaRiversideCAUSA
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal BiologySpeith HallUniversity of CaliforniaRiversideCAUSA
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Burgarella C, Berger A, Glémin S, David J, Terrier N, Deu M, Pot D. The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns. Front Plant Sci 2021; 12:666075. [PMID: 34527004 PMCID: PMC8435843 DOI: 10.3389/fpls.2021.666075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/20/2021] [Indexed: 05/17/2023]
Abstract
Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.
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Affiliation(s)
- Concetta Burgarella
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- *Correspondence: Concetta Burgarella
| | - Angélique Berger
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sylvain Glémin
- CNRS, Univ. Rennes, ECOBIO – UMR 6553, Rennes, France
- Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jacques David
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Monique Deu
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- David Pot
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30
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Florez-Rueda AM, Scharmann M, Roth M, Städler T. Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages. Front Plant Sci 2021; 12:624442. [PMID: 33815438 PMCID: PMC8018279 DOI: 10.3389/fpls.2021.624442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/24/2021] [Indexed: 05/07/2023]
Abstract
Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.
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31
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Barrow LN, Masiero da Fonseca E, Thompson CEP, Carstens BC. Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data. Mol Ecol Resour 2020; 21:2818-2831. [PMID: 33249725 DOI: 10.1111/1755-0998.13303] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/11/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
The growing availability of genetic data sets, in combination with machine learning frameworks, offers great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we analysed repurposed data using machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this data set, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contained low genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful data sets with greater utility for understanding global biodiversity.
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Affiliation(s)
- Lisa N Barrow
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | - Coleen E P Thompson
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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32
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Rafiepour M, Ebrahimie E, Vahidi MF, Salekdeh GH, Niazi A, Dadpasand M, Liang D, Si J, Ding X, Han J, Zhang Y, Qanbari S. Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies. Genome Biol Evol 2020; 13:5976760. [PMID: 33179728 DOI: 10.1093/gbe/evaa231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 01/30/2023] Open
Abstract
The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.
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Affiliation(s)
- Mostafa Rafiepour
- Institute of Biotechnology, School of Agriculture, Shiraz University, Iran.,Department of System Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Esmaeil Ebrahimie
- Institute of Biotechnology, School of Agriculture, Shiraz University, Iran.,Genomics Research Platform, School of Life Sciences, Melbourne, Victoria, Australia.,School of Animal and Veterinary Sciences, The University of Adelaide, South Australia, Australia
| | - Mohammad Farhad Vahidi
- Department of Animal Biotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of System Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ali Niazi
- Institute of Biotechnology, School of Agriculture, Shiraz University, Iran
| | - Mohammad Dadpasand
- Department of Animal Science, School of Agriculture, Shiraz University, Iran
| | - Dong Liang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Jingfang Si
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,International Livestock Research Institute (ILR), Nairobi, Kenya
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, Agricultural University, Beijing, China
| | - Saber Qanbari
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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33
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Jaramillo-Correa JP, Bagnoli F, Grivet D, Fady B, Aravanopoulos FA, Vendramin GG, González-Martínez SC. Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse. Mol Ecol 2020; 29:4797-4811. [PMID: 33063352 DOI: 10.1111/mec.15684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e., evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across 177 gene-loci in a circum-Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable nuclear microsatellites (SSRs) and gene-loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1 Ma. Comparisons with the related and parapatric maritime pine (Pinus pinaster Ait.) revealed reduced rates of adaptive evolution (α and ωa ) and a significant accumulation of genetic load. It is unlikely that these are the result from differences in mutation rate or linkage disequilibrium between the two species; instead they are the presumable outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness, and integrating such effects into predictive models.
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Affiliation(s)
- Juan P Jaramillo-Correa
- Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Francesca Bagnoli
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain
| | - Bruno Fady
- INRAE, Unité de Recherche Écologie des Forêts Méditerranéennes (URFM), Avignon, France
| | - Filippos A Aravanopoulos
- Laboratory of Forest Genetics and Tree Breeding, Department of Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Giovanni G Vendramin
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
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34
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Zhang CY, Liu TJ, Mo XL, Huang HR, Yao G, Li JR, Ge XJ, Yan HF. Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae). Plants (Basel) 2020; 9:plants9111497. [PMID: 33167549 PMCID: PMC7694494 DOI: 10.3390/plants9111497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/06/2023]
Abstract
Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (dS) and nonsynonymous (dN) substitution rate values of protein-coding genes varied approximately threefold, while the dN values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future.
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Affiliation(s)
- Cai-Yun Zhang
- Guangdong Food and Drug Vocational College, Guangzhou 510520, China; (C.-Y.Z.); (X.-L.M.)
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Correspondence:
| | - Xiao-Lu Mo
- Guangdong Food and Drug Vocational College, Guangzhou 510520, China; (C.-Y.Z.); (X.-L.M.)
| | - Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Gang Yao
- South China Limestone Plants Research Centre, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China;
| | - Jian-Rong Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (H.-R.H.); (J.-R.L.); (X.-J.G.); (H.-F.Y.)
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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35
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Calla B, Demkovich M, Siegel JP, Viana JPG, Walden KKO, Robertson HM, Berenbaum MR. Selective Sweeps in a Nutshell: The Genomic Footprint of Rapid Insecticide Resistance Evolution in the Almond Agroecosystem. Genome Biol Evol 2020; 13:5955766. [PMID: 33146372 PMCID: PMC7850051 DOI: 10.1093/gbe/evaa234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2020] [Indexed: 11/14/2022] Open
Abstract
Among the most familiar forms of human-driven evolution on ecological time scales is the rapid acquisition of resistance to pesticides by insects. Since the widespread adoption of synthetic organic insecticides in the mid-twentieth century, over 500 arthropod species have evolved resistance to at least one insecticide. Efforts to determine the genetic bases of insecticide resistance have historically focused on individual loci, but the availability of genomic tools has facilitated the screening of genome-wide characteristics. We resequenced three contemporary populations of the navel orangeworm (Amyelois transitella), the principal pest of almond orchards in California, differing in bifenthrin resistance status to examine insecticide-induced changes in the population genomic landscape of this species. We detected an exceptionally large region with virtually no polymorphisms, extending to up to 1.3 Mb in the resistant population. This selective sweep includes genes associated with pyrethroid and DDT resistance, including a cytochrome P450 gene cluster and the gene encoding the voltage-gated sodium channel para. Moreover, the sequence along the sweep is nearly identical in the genome assembled from a population founded in 1966, suggesting that the foundation for insecticide resistance may date back a half-century, when California’s Central Valley experienced massive area-wide applications of DDT for pest control.
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Affiliation(s)
- Bernarda Calla
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Mark Demkovich
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Joel P Siegel
- United States Department of Agriculture, Agricultural Research Service, Commodity Protection and Quality Research, Parlier, California
| | | | - Kim K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - May R Berenbaum
- Department of Entomology, University of Illinois at Urbana-Champaign
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36
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Zhao W, Sun YQ, Pan J, Sullivan AR, Arnold ML, Mao JF, Wang XR. Effects of landscapes and range expansion on population structure and local adaptation. New Phytol 2020; 228:330-343. [PMID: 32323335 DOI: 10.1111/nph.16619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/15/2020] [Indexed: 05/25/2023]
Abstract
Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2-19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype-environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.
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Affiliation(s)
- Wei Zhao
- Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, SE-901 87, Umeå, Sweden
| | - Yan-Qiang Sun
- Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China
| | - Jin Pan
- Department of Ecology and Environmental Science, UPSC, Umeå University, SE-901 87, Umeå, Sweden
| | - Alexis R Sullivan
- Department of Ecology and Environmental Science, UPSC, Umeå University, SE-901 87, Umeå, Sweden
| | - Michael L Arnold
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Jian-Feng Mao
- Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China
| | - Xiao-Ru Wang
- Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, SE-901 87, Umeå, Sweden
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37
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Lee J, Park J, Xi H, Park J. Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae). J Insect Sci 2020; 20:10. [PMID: 32976575 PMCID: PMC7583265 DOI: 10.1093/jisesa/ieaa090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Indexed: 05/06/2023]
Abstract
Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.
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Affiliation(s)
- Jungmo Lee
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Jonghyun Park
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
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38
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Salek Ardestani S, Aminafshar M, Zandi Baghche Maryam MB, Banabazi MH, Sargolzaei M, Miar Y. Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types. Genome 2020; 63:387-396. [PMID: 32407640 DOI: 10.1139/gen-2020-0001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.
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Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Mehdi Aminafshar
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | | | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization, Karaj 3146618361, Iran
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON NIG 2W1, Canada.,Select Sires Inc., Plain City, OH 43064, USA
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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He Y, Feng L, Jiang Y, Zhang L, Yan J, Zhao G, Wang J, Chen G, Wu B, Liu D, Huang L, Fahima T. Distribution and Nucleotide Diversity of Yr15 in Wild Emmer Populations and Chinese Wheat Germplasm. Pathogens 2020; 9:E212. [PMID: 32183066 DOI: 10.3390/pathogens9030212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/27/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease of wheat. The wild emmer gene, Yr15 (Wtk1), which confers a strong broad-spectrum resistance to Pst isolates, is composed of kinase and pseudokinase domains. The analysis of 361 wild emmer accessions from a wide range of natural habitats confirms that functional Wtk1 is distributed mainly along a narrow axis from Mt. Carmel to Mt. Hermon regions, in the northern part of Israel, where environmental conditions are favorable to the onset of stripe rust. An analysis of full-length Wtk1 DNA sequences from 49 wild emmer accessions identified three haplotypes and extremely low nucleotide diversity (π = 0.00002). The sequence diversity of Wtk1 is 9.5 times lower than that of broad-spectrum partial resistance gene Yr36 (π = 0.00019), and both are in sharp contrast to the high level of nucleotide diversity previously reported for race-specific resistance genes (e.g., Lr10 and Pm3). However, the nonfunctional wtk1 sequences possess high level of nucleotide diversity (π = 0.07). These results may reflect the different resistance mechanisms and the different evolutionary processes that shaped these resistance genes. Yr15 was absent in 189 Chinese wheat landraces and was present in only 1.02% of the 583 tested modern Chinese wheat cultivars. These results corroborate our previous results showing that Yr15 was absent in 94% of a worldwide collection of 513 wheat cultivars, therefore indicating the importance of Yr15 in wheat stripe rust resistance breeding programs in China and elsewhere around the globe.
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Ogutu C, Cherono S, Ntini C, Mollah MD, Zhao L, Belal MA, Han Y. Evolutionary rate variation among genes involved in galactomannan biosynthesis in Coffea canephora. Ecol Evol 2020; 10:2559-2569. [PMID: 32185001 PMCID: PMC7069334 DOI: 10.1002/ece3.6084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/08/2019] [Accepted: 12/09/2019] [Indexed: 12/03/2022] Open
Abstract
The endosperm cell walls of mature coffee seeds accumulate large amounts of mannan storage polysaccharides, which serve as nutrient reserve for embryo and contribute to beverage quality. Our study investigated the evolutionary patterns of key galactomannan (GM) biosynthesis genes using d N/d S ratio, synteny, and phylogenetic analysis and detected heterogeneity in rate of evolution among gene copies. Selection ratio index revealed evidence of positive selection in the branch editing gene Coffea canephora alpha (α) galactosidase (Cc-alpha Gal) at Cc11_g15950 copy (ω = 1.12), whereas strong purifying selection on deleterious mutations was observed in the Coffea canephora uridine diphosphate (UDP)-glucose 4'-epimerase (Cc-UG4E) and Coffea canephora mannose-1P guanylytransferase (Cc-MGT) genes controlling the crucial nucleotide carbon sugar building blocks flux in the pathway. Relatively low sequence diversity and strong syntenic linkages were detected in all GM pathway genes except in Cc-alpha Gal, which suggests a correlation between selection pressure and nucleotide diversity or synteny analysis. In addition, phylogenetic analysis revealed independent evolution or expansion of GM pathway genes in different plant species, with no obvious inferable clustering patterns according to either gene family or congruent with evolutionary plants lineages tested due to high dynamic nature and specific biochemical cell wall modification requirements. Altogether, our study shows a significant high rate of evolutionary variation among GM pathway genes in the diploid C. canephora and demonstrates the inherent variation in evolution of gene copies and their potential role in understanding selection rates in a homogenously connected metabolic pathway.
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Affiliation(s)
- Collins Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Sino‐African Joint Research CenterChinese Academy of SciencesWuhanChina
| | - Sylvia Cherono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Charmaine Ntini
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mohammad Dulal Mollah
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mohammad A. Belal
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Sino‐African Joint Research CenterChinese Academy of SciencesWuhanChina
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Sun YQ, Zhao W, Xu CQ, Xu Y, El-Kassaby YA, De La Torre AR, Mao JF. Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis. Front Genet 2020; 10:1405. [PMID: 32117429 PMCID: PMC7027398 DOI: 10.3389/fgene.2019.01405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/23/2019] [Indexed: 12/30/2022] Open
Abstract
Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.
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Affiliation(s)
- Yan-Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Chao-Qun Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yulan Xu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Kunming, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | | | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Apuli RP, Bernhardsson C, Schiffthaler B, Robinson KM, Jansson S, Street NR, Ingvarsson PK. Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula). G3 (Bethesda) 2020; 10:299-309. [PMID: 31744900 DOI: 10.1534/g3.119.400504] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.
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Kim Y, Shin J, Cho SS, Hwang YP, Choi C. Development and Application of InDel Markers for Authentication of the Korean Herbs Zanthoxylum schinifolium and Zanthoxylum piperitum. Foods 2019; 8:E658. [PMID: 31835363 DOI: 10.3390/foods8120658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/01/2022] Open
Abstract
Zanthoxylum schinifolium and Zanthoxylum piperitum are the sources of the well-known traditional Korean herbal medicines “sancho” (prickly ash) and “chopi” (Korean pepper), respectively. Sancho and chopi are often indiscriminately mixed due to the similar appearance of the herbal materials when used as spices and herbal medicines. Moreover, commercial sancho and chopi products often contain adulterants, which is insufficient to ensure food efficacy and safety. In this study, we developed hypervariable insertion/deletion (InDel) markers to distinguish between sancho and chopi products by comparing the complete chloroplast genome sequences of four Zanthoxylum species deposited in the National Center for Biotechnology Information (NCBI) GenBank. Comparative analyses of the nucleotide diversity (Pi) of these Zanthoxylum genomes revealed four hypervariable divergent sites (trnH-psbA, psbZ-trnG, trnfM-rps14, and trnF-ndhK) with Pi > 0.025 among 520 windows. Of these four regions, including two genic and two intergenic regions, only psbZ-trnG yielded accurate PCR amplification results between commercial sancho and chopi products from the Korean herbal medicine market. We therefore selected psbZ-trnG, an InDel-variable locus with high discriminatory powers, as a candidate DNA barcode locus. This InDel marker could be used as a valuable, simple, and efficient tool for identifying these medicinal herbs, thereby increasing the safety of these spices and herbal materials in the food market.
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Carvalho SB, Torres J, Tarroso P, Velo-Antón G. Genes on the edge: A framework to detect genetic diversity imperiled by climate change. Glob Chang Biol 2019; 25:4034-4047. [PMID: 31230387 DOI: 10.1111/gcb.14740] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 05/10/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
Ongoing global warming is disrupting several ecological and evolutionary processes, spanning different levels of biological organization. Species are expected to shift their ranges as a response to climate change, with relevant implications to peripheral populations at the trailing and leading edges. Several studies have analyzed the exposure of species to climate change but few have explored exposure at the intraspecific level. We introduce a framework to forecast exposure to climate change at the intraspecific level. We build on existing methods by combining correlative species distribution models, a model of species range dynamics, and a model of phylogeographic interpolation. We demonstrate the framework by applying it to 20 Iberian amphibian and reptile species. Our aims were to: (a) identify which species and intraspecific lineages will be most exposed to future climate change; (b) test if nucleotide diversity at the edges of species ranges are significantly higher or lower than on the overall range; and (c) analyze if areas of higher species gain, loss, and turnover coincide with those predicted for lineages richness and nucleotide diversity. We found that about 80% of the studied species are predicted to contract their range. Within each species, some lineages were predicted to contract their range, while others were predicted to maintain or expand it. Therefore, estimating the impacts of climate change at the species level only can underestimate losses at the intraspecific level. Some species had significant high amount of nucleotide at the trailing or leading edge, or both, but we did not find a consistent pattern across species. Spatial patterns of species richness, gain, loss, and turnover were fairly concurrent with lineages richness and nucleotide diversity. Our results support the need for increased attention to intraspecific diversity regarding monitoring and conservation strategies under climate change.
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Affiliation(s)
- Sílvia Benoliel Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - João Torres
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - Pedro Tarroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
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Li P, Wei J, Wang H, Fang Y, Yin S, Xu Y, Liu J, Yang Z, Xu C. Natural Variation and Domestication Selection of ZmPGP1 Affects Plant Architecture and Yield-Related Traits in Maize. Genes (Basel) 2019; 10:E664. [PMID: 31480272 DOI: 10.3390/genes10090664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
ZmPGP1, involved in the polar auxin transport, has been shown to be associated with plant height, leaf angle, yield traits, and root development in maize. To explore natural variation and domestication selection of ZmPGP1, we re-sequenced the ZmPGP1 gene in 349 inbred lines, 68 landraces, and 32 teosintes. Sequence polymorphisms, nucleotide diversity, and neutral tests revealed that ZmPGP1 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 11 variants significantly associated with 4 plant architecture and 5 ear traits. SNP1473 was the most significant variant for kernel length and ear grain weight. The frequency of an increased allele T was 40.6% in teosintes, and it was enriched to 60.3% and 89.1% during maize domestication and improvement. This result revealed that ZmPGP1 may be selected in the domestication and improvement process, and significant variants could be used to develop functional markers to improve plant architecture and ear traits in maize.
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Hwang EY, Wei H, Schroeder SG, Fickus EW, Quigley CV, Elia P, Araya S, Dong F, Costa L, Ferreira ME, Cregan PB, Song Q. Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species. G3 (Bethesda) 2019; 9:2325-36. [PMID: 31097479 DOI: 10.1534/g3.119.400220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have estimated the average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity. The other perennials, except for G. tomentella, had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except for G. cyrtoloba and G. stenophita which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Most genic sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced a very similar evolution as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.
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Nguete Nguiffo D, Mpoame M, Wondji CS. Genetic diversity and population structure of goliath frogs ( Conraua goliath) from Cameroon. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:657-663. [PMID: 31092076 DOI: 10.1080/24701394.2019.1615060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The goliath frog (Conraua goliath) is an Endangered species exclusively found in Cameroon and Equatorial Guinea. Climate change, deforestation and overhunting are principal causes driving this species to extinction. Therefore, a better understanding of the genetic diversity and population structure of this species is necessary to improve conservation efforts. Here we used two mitochondrial genes (Cytochrome Oxidase subunit 1 (COI) and 16S) extracted from 54 C. goliath individuals from six localities in Cameroon to examine their genetic diversity. The result shows a low DNA substitution between the sequences. There were four 16S and two COI haplotypes in total. Overall, genetic diversity was very low for all the genes with nucleotide diversity of 0.00106 and 0.00007 for 16S and COI respectively. The Tajima D and Fu Fs statistics were negative. The TCS haplotype network revealed a predominant and ancestral haplotype (H1) for these genes which is distributed in the 6 populations. Pairwise genetic differentiation (FST) generated between these populations using 16S revealed very high differentiation between populations from Nkam and Mungo Administrative Divisions in Cameroon. In contrast, we observed low differentiation among the geographically clustered Mungo and Nkam populations. Overall, human activities and perhaps climate change can appear to have depleted genetic diversity in the scattered populations that remain of this amphibian. To sustain the Goliath frog, we suggest to the Cameroonian government to implement more effective strategies to conserve and manage remnant populations of this iconic species through more effort against poaching which contribute to reduce the genetic diversity.
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Affiliation(s)
- Daniel Nguete Nguiffo
- a Research Unit of Biology and Applied Ecology, Department of Animal Biology, Faculty of Science , University of Dschang , Dschang , Cameroon.,b Centre for Research in Infectious Diseases (CRID) , Dschang , Cameroon
| | - Mbida Mpoame
- a Research Unit of Biology and Applied Ecology, Department of Animal Biology, Faculty of Science , University of Dschang , Dschang , Cameroon
| | - Charles S Wondji
- b Centre for Research in Infectious Diseases (CRID) , Dschang , Cameroon.,c Vector Biology Department , Liverpool School of Tropical Medicine , Liverpool , UK
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Han Z, Li W, Zhu W, Sun S, Ye K, Xie Y, Wang Z. Near-complete genome assembly and annotation of the yellow drum ( Nibea albiflora) provide insights into population and evolutionary characteristics of this species. Ecol Evol 2019; 9:568-575. [PMID: 30680137 PMCID: PMC6342179 DOI: 10.1002/ece3.4778] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 01/03/2023] Open
Abstract
Yellow drum (Nibea albiflora) is an important fish species in capture fishery and aquaculture in East Asia. We herein report the first and near-complete genome assembly of an ultra-homologous gynogenic female yellow drum using Illumina short sequencing reads. In summary, a total of 154.2 Gb of raw reads were generated via whole-genome sequencing and were assembled to 565.3 Mb genome with a contig N50 size of 50.3 kb and scaffold N50 size of 2.2 Mb (BUSCO completeness of 97.7%), accounting for 97.3%-98.6% of the estimated genome size of this fish. We further identified 22,448 genes using combined methods of ab initio prediction, RNAseq annotation, and protein homology searching, of which 21,614 (96.3%) were functionally annotated in NCBI nr, trEMBL, SwissProt, and KOG databases. We also investigated the nucleotide diversity (around 1/390) of aquacultured individuals and found the genetic diversity of the aquacultured population decreased due to inbreeding. Evolutionary analyses illustrated significantly expanded and extracted gene families, such as myosin and sodium: neurotransmitter symporter (SNF), could help explain swimming motility of yellow drum. The presented genome will be an important resource for future studies on population genetics, conservation, understanding of evolutionary history and genetic breeding of the yellow drum and other Nibea species.
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Affiliation(s)
- Zhaofang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Wen Zhu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Sha Sun
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Kun Ye
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Yangjie Xie
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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Wu F, Jiang H, Beattie GAC, Holford P, Chen J, Wallis CM, Zheng Z, Deng X, Cen Y. Population diversity of Diaphorina citri (Hemiptera: Liviidae) in China based on whole mitochondrial genome sequences. Pest Manag Sci 2018; 74:2569-2577. [PMID: 29688605 DOI: 10.1002/ps.5044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Diaphorina citri (Asian citrus psyllid; ACP) transmits 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing (HLB). ACP has been reported in 11 provinces/regions in China, yet its population diversity remains unclear. In this study, we evaluated ACP population diversity in China using representative whole mitochondrial genome (mitogenome) sequences. Additional mitogenome sequences outside China were also acquired and evaluated. RESULTS The sizes of the 27 ACP mitogenome sequences ranged from 14 986 to 15 030 bp. Along with three previously published mitogenome sequences, the 30 sequences formed three major mitochondrial groups (MGs): MG1, present in southwestern China and occurring at elevations above 1000 m; MG2, present in southeastern China and Southeast Asia (Cambodia, Indonesia, Malaysia, and Vietnam) and occurring at elevations below 180 m; and MG3, present in the USA and Pakistan. Single nucleotide polymorphisms in five genes (cox2, atp8, nad3, nad1 and rrnL) contributed mostly in the ACP diversity. Among these genes, rrnL had the most variation. CONCLUSION Mitogenome sequences analyses revealed two major phylogenetic groups of ACP present in China as well as a possible unique group present currently in Pakistan and the USA. The information could have significant implications for current ACP control and HLB management. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Fengnian Wu
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - Hongyan Jiang
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - G Andrew C Beattie
- School of Science and Health, Western Sydney University, Penrith, Australia
| | - Paul Holford
- School of Science and Health, Western Sydney University, Penrith, Australia
| | - Jianchi Chen
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Christopher M Wallis
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Zheng Zheng
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - Xiaoling Deng
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - Yijing Cen
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
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Li MR, Shi FX, Li YL, Jiang P, Jiao L, Liu B, Li LF. Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer). Genome Biol Evol 2018; 9:2159-2169. [PMID: 28922794 PMCID: PMC5737880 DOI: 10.1093/gbe/evx160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 11/15/2022] Open
Abstract
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions. In complement, the 45s rDNA, chloroplast and mitochondrial genomes were included to perform phylogenetic and population genetic analyses. The observed spatial genetic structure between northern cultivated ginseng (NCG) and southern cultivated ginseng (SCG) accessions suggested multiple independent origins of cultivated ginseng. Genome-wide scanning further demonstrated that NCG and SCG have undergone distinct selection pressures during the domestication process, with more genes identified in the NCG (97 genes) than in the SCG group (5 genes). Functional analyses revealed that these genes are involved in diverse pathways, including DNA methylation, lignin biosynthesis, and cell differentiation. These findings suggested that the SCG and NCG groups have distinct demographic histories. Candidate genes identified are useful for future molecular breeding of cultivated ginseng.
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Affiliation(s)
- Ming-Rui Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Feng-Xue Shi
- Northeast Normal University Natural History Museum, Changchun, China
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lili Jiao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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