Seasonal monitoring of Cryptosporidium species and their genetic diversity in neonatal calves on two large‐scale farms in Xinjiang, China

Abstract Background: Neonatal dairy calves infected with Cryptosporidium can possess a significant source of zoonotic infections and disease. To assess seasonal variations in the prevalence and genetic diversity of Cryptosporidium in neonatal dairy calves, 380 fecal samples from neonatal dairy calves on two large-scale farms in Xinjiang (Alaer and Wensu) were screened for the Cryptosporidium small subunit (SSU) rRNA gene. Results: The overall prevalence of Cryptosporidium was 48.7% (185/380): 48.6% (108/222) in Alaer and 48.7% (77/158) in Wensu. Cryptosporidium was most frequent in summer (56.8%, 54/95), followed by spring (50.0%, 44/88), winter (46.8%, 44/94), and autumn (41.7%, 43/103) (P > 0.05). Cryptosporidium was significantly more prevalent in calves with diarrhea (72.4%, 113/156) than in those without (32.1%, 72/224) (P < 0.01). Based on a restriction fragment length polymorphism (RFLP) analysis, C. parvum (n = 173), C. bovis (n = 7), C. ryanae (n = 3), and co-infections of the three species (n = 2) were identified. Most (172/175) C. parvum samples were successfully sequenced at the 60-kDa glycoprotein gene (gp60), revealing two zoonotic subtypes: IIdA14G1 (n = 94) and IIdA15G1 (n = 7) in Alaer and IIdA15G1 (n = 71) in Wensu.Conclusions: These results showed that neonatal dairy calves were commonly infected with Cryptosporidium throughout the year, and there was a significant association between the occurrence of diarrhea and Cryptosporidium infection. Presence of IIdA14G1 and IIdA15G1 indicated neonatal dairy calves may be a source of zoonotic C. parvum subtypes.

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Faculty Opinions recommendation of Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.738510762.793578253 ◽

2020 ◽

Author(s):

Kang Le

Keyword(s):

Genetic Diversity ◽

Large Scale ◽

Comparative Analyses

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Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

BMC Plant Biology ◽

10.1186/s12870-021-03037-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ming Sun ◽

Zhixiao Dong ◽

Jian Yang ◽

Wendan Wu ◽

Chenglin Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Large Scale ◽

Genetic Research ◽

High Yield ◽

Yield Strain ◽

Tissue Samples ◽

Prairie Grass ◽

The Future ◽

Genomic Resource

Abstract Background Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus. Results Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding. Conclusion A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.

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Genetic Diversity and Evolution of the Biological Features of the Pandemic SARS-CoV-2

Acta Naturae ◽

10.32607/actanaturae.11337 ◽

2021 ◽

Vol 13 (3) ◽

pp. 77-89

Author(s):

Aleksandra A. Nikonova ◽

Eugene B. Faizuloev ◽

Anastasia V. Gracheva ◽

Igor Yu. Isakov ◽

Vitaly V. Zverev

Keyword(s):

Genetic Diversity ◽

Genetic Variants ◽

Large Scale ◽

Biological Properties ◽

Viral Genomes ◽

Biological Features ◽

Health Measures ◽

Common Genetic Variants ◽

Coronavirus Infection ◽

The Relationship

The new coronavirus infection (COVID-19) represents a challenge for global health. Since the outbreak began, the number of confirmed cases has exceeded 117 million, with more than 2.6 million deaths worldwide. With public health measures aimed at containing the spread of the disease, several countries have faced a crisis in the availability of intensive care units. Currently, a large-scale effort is underway to identify the nucleotide sequences of the SARS-CoV-2 coronavirus that is an etiological agent of COVID-19. Global sequencing of thousands of viral genomes has revealed many common genetic variants, which enables the monitoring of the evolution of SARS-CoV-2 and the tracking of its spread over time. Understanding the current evolution of SARS-CoV-2 is necessary not only for a retrospective analysis of the new coronavirus infection spread, but also for the development of approaches to the therapy and prophylaxis of COVID-19. In this review, we have focused on the general characteristics of SARS-CoV-2 and COVID-19. Also, we have analyzed available publications on the genetic diversity of the virus and the relationship between the diversity and the biological properties of SARS-CoV-2, such as virulence and contagiousness.

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Genetic Diversity of Cryptosporidium in Bactrian Camels (Camelus bactrianus) in Xinjiang, Northwestern China

Pathogens ◽

10.3390/pathogens9110946 ◽

2020 ◽

Vol 9 (11) ◽

pp. 946

Author(s):

Yangwenna Cao ◽

Zhaohui Cui ◽

Qiang Zhou ◽

Bo Jing ◽

Chunyan Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Sequence Analysis ◽

Small Subunit ◽

Cryptosporidium Species ◽

Northwestern China ◽

Rrna Gene ◽

Cryptosporidium Spp ◽

Gene Sequence Analysis ◽

Bactrian Camels ◽

Ssu Rrna Gene Sequence

Cryptosporidium species are ubiquitous enteric protozoan pathogens of vertebrates distributed worldwide. The purpose of this study was to gain insight into the zoonotic potential and genetic diversity of Cryptosporidium spp. in Bactrian camels in Xinjiang, northwestern China. A total of 476 fecal samples were collected from 16 collection sites in Xinjiang and screened for Cryptosporidium by PCR. The prevalence of Cryptosporidium was 7.6% (36/476). Six Cryptosporidium species, C. andersoni (n = 24), C. parvum (n = 6), C. occultus (n = 2), C. ubiquitum (n = 2), C. hominis (n = 1), and C. bovis (n = 1), were identified based on sequence analysis of the small subunit (SSU) rRNA gene. Sequence analysis of the gp60 gene identified six C. parvum isolates as subtypes, such as If-like-A15G2 (n = 5) and IIdA15G1 (n = 1), two C. ubiquitum isolates, such as subtype XIIa (n = 2), and one C. hominis isolate, such as Ixias IkA19G1 (n = 1). This is the first report of C. parvum, C. hominis, C. ubiquitum, and C. occultus in Bactrian camels in China. These results indicated that the Bactrian camel may be an important reservoir for zoonotic Cryptosporidium spp. and these infections may be a public health threat in this region.

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A clue to invasion success: genetic diversity quickly rebounds after introduction bottlenecks

Biological Invasions ◽

10.1007/s10530-020-02426-y ◽

2020 ◽

Author(s):

Peter Kaňuch ◽

Åsa Berggren ◽

Anna Cassel-Lundhagen

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Large Scale ◽

Invasion Biology ◽

Invasion Success ◽

Founder Population ◽

Establishment Success ◽

Propagule Size ◽

Introduced Populations ◽

Species Invasiveness

AbstractOne of the fundamental questions in invasion biology is to understand the genetic mechanisms behind success or failure during the establishment of a species. However, major limitations to understanding are usually a lack of spatiotemporal population data and information on the populations’ colonisation history. In a large-scale, detailed study on the bush-cricket Metrioptera roeselii 70 groups of founders were introduced in areas outside the species’ distribution range. We examined how (1) the number of founders (2–32 individuals), (2) the time since establishment (7 or 15 years after introduction) and (3) possible gene flow affected establishment success and temporal genetic changes of the introduced populations. We found higher establishment success in introductions with larger propagule sizes but genetic diversity indices were only partly correlated to propagule size. As expected, introduced populations were more similar to their founder population the larger the propagule size was. However, even if apparent at first, most of the differentiation in the small propagule introductions disappeared over time. Surprisingly, genetic variability was regained to a level comparable to the large and outbreeding founder population only 15 generations after severe demographic bottlenecks. We suggest that the establishment of these populations could be a result of several mechanisms acting in synergy. Here, rapid increase in genetic diversity of few introductions could potentially be attributed to limited gene flow from adjacent populations, behavioural adaptations and/or even increased mutation rate. We present unique insights into genetic processes that point towards traits that are important for understanding species’ invasiveness.

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First Report on the Prevalence and Subtype Distribution of Blastocystis sp. in Edible Marine Fish and Marine Mammals: A Large Scale-Study Conducted in Atlantic Northeast and on the Coasts of Northern France

Microorganisms ◽

10.3390/microorganisms8030460 ◽

2020 ◽

Vol 8 (3) ◽

pp. 460 ◽

Cited By ~ 3

Author(s):

Nausicaa Gantois ◽

Angélique Lamot ◽

Yuwalee Seesao ◽

Colette Creusy ◽

Luen-Luen Li ◽

...

Keyword(s):

Genetic Diversity ◽

Marine Fish ◽

Marine Mammals ◽

Large Scale ◽

Zoonotic Transmission ◽

Northern France ◽

Natural Hosts ◽

Blastocystis Sp ◽

Large Scale Survey ◽

Polymerase Chain

Blastocystis is frequently identified in humans and animal hosts and exhibits a large genetic diversity with the identification of 17 subtypes (STs). Despite its zoonotic potential, its prevalence and ST distribution in edible marine fish and marine mammals remain unknown. A large-scale survey was thus conducted by screening 345 fish caught in Atlantic Northeast and 29 marine mammals stranded on the coasts of northern France for the presence of the parasite using real-time Polymerase Chain Reaction PCR. The prevalence of the parasite was about 3.5% in marine fish. These animals were mostly colonized by poikilotherm-derived isolates not identified in humans and corresponding to potential new STs, indicating that fish are natural hosts of Blastocystis. Marine fishes are also carriers of human STs and represent a likely limited source of zoonotic transmission. 13.8% of the marine mammals tested were colonized and 6 different STs were identified including 3 potential new STs. The risk of zoonotic transmission through marine mammals is insignificant due to the lack of repeated contact with humans. The present survey represents the first data regarding the prevalence and ST distribution of Blastocystis in marine fish and marine mammals and provides new insights into its genetic diversity, host range and transmission.

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Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽

10.3390/f11111185 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1185

Author(s):

Helena Eklöf ◽

Carolina Bernhardsson ◽

Pär K. Ingvarsson

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Picea Abies ◽

Norway Spruce ◽

Large Scale ◽

Genotyping By Sequencing ◽

Complexity Reduction ◽

Exome Capture ◽

Genome Wide ◽

Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

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Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

Scientific Reports ◽

10.1038/s41598-020-75553-0 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Manosh Kumar Biswas ◽

Mita Bagchi ◽

Ujjal Kumar Nath ◽

Dhiman Biswas ◽

Sathishkumar Natarajan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Large Scale ◽

Polymorphic Information Content ◽

Pcr Amplification ◽

Efficient Manner ◽

Lilium Species ◽

Population Structure Analysis ◽

Wide Range ◽

Functional Molecular Markers

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

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