scholarly journals Genomic Characterization of Diverse Bat Coronavirus HKU10 in Hipposideros Bats

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1962
Author(s):  
Ning Wang ◽  
Chu-Ming Luo ◽  
Xing-Lou Yang ◽  
Hai-Zhou Liu ◽  
Li-Biao Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Yunnan Province ◽  
Selective Pressure ◽  
Cell Tropism ◽  
Sampling Locations ◽  
Archived Samples ◽  
Genomic Characterization ◽  
Bat Coronavirus ◽  
New Habitats

Bats have been identified as natural reservoirs of a variety of coronaviruses. They harbor at least 19 of the 33 defined species of alpha- and betacoronaviruses. Previously, the bat coronavirus HKU10 was found in two bat species of different suborders, Rousettus leschenaultia and Hipposideros pomona, in south China. However, its geographic distribution and evolution history are not fully investigated. Here, we screened this viral species by a nested reverse transcriptase PCR in our archived samples collected over 10 years from 25 provinces of China and one province of Laos. From 8004 bat fecal samples, 26 were found to be positive for bat coronavirus HKU10 (BtCoV HKU10). New habitats of BtCoV HKU10 were found in the Yunnan, Guangxi, and Hainan Provinces of China, and Louang Namtha Province in Laos. In addition to H. pomona, BtCoV HKU10 variants were found circulating in Aselliscus stoliczkanus and Hipposideros larvatus. We sequenced full-length genomes of 17 newly discovered BtCoV HKU10 strains and compared them with previously published sequences. Our results revealed a much higher genetic diversity of BtCoV HKU10, particularly in spike genes and accessory genes. Besides the two previously reported lineages, we found six novel lineages in their new habitats, three of which were located in Yunnan province. The genotypes of these viruses are closely related to sampling locations based on polyproteins, and correlated to bat species based on spike genes. Combining phylogenetic analysis, selective pressure, and molecular-clock calculation, we demonstrated that Yunnan bats harbor a gene pool of BtCoV HKU10, with H. pomona as a natural reservoir. The cell tropism test using spike-pseudotyped lentivirus system showed that BtCoV HKU10 could enter cells from human and bat, suggesting a potential interspecies spillover. Continuous studies on these bat coronaviruses will expand our understanding of the evolution and genetic diversity of coronaviruses, and provide a prewarning of potential zoonotic diseases from bats.

scholarly journals Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

2021 ◽  
Vol 9 (8) ◽  
pp. 1612
Author(s):  
Werner Ruppitsch ◽  
Andjela Nisic ◽  
Patrick Hyden ◽  
Adriana Cabal ◽  
Jasmin Sucher ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Safety Evaluation ◽  
Gene Clusters ◽  
Northern Region ◽  
Genomic Diversity ◽  
High Genetic Diversity ◽  
Pathogenic Factors ◽  
Flavor Development ◽  
Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

Genomic characterization of three Vietnamese indigenous chicken varieties using mitochondrial D-loop sequences

2019 ◽  
Vol 99 (4) ◽  
pp. 833-839
Author(s):  
Son Quang Do ◽  
Lan Thi Phuong Nguyen ◽  
Thinh Hoang Nguyen ◽  
Trung Quoc Nguyen
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Diversity Indices ◽  
Fixation Index ◽  
Indigenous Chicken ◽  
Loop Region ◽  
Red Junglefowl ◽  
D Loop ◽  
Genomic Characterization

In this study, partial mitochondrial DNA (mtDNA) D-loop sequences of three Vietnamese indigenous chicken varieties, including Mong Tien Phong, To, and Sau Ngon, were analyzed to access genetic diversity and the maternal lineages of origin. A 525 bp fragment of the mtDNA D-loop region was sequenced from a total of 61 chickens of the three varieties. A neighbor-joining phylogenetic tree was assembled from the haplotypes obtained and reference sequences of mtDNA D-loop sequences of Red Junglefowl and domestic chickens from National Center for Biotechnology Information database. Genetic diversity indices and analysis of molecular variance were performed. Evaluation of genetic relationships between the three varieties was carried out with pairwise fixation index (FST). In total, 16 haplotypes were identified in the chickens studied. These haplotypes were classified in three haplogroups (A, B, and E) with the majority grouped in haplogroup B and haplogroup E. All three chicken varieties studied were distributed into 2–3 haplogroups and all three haplogroups found in this study are also represented by Red Junglefowl. In conclusion, all three Vietnamese indigenous chicken varieties have likely originated from multiple maternal lineages and potentially descended from the Red Junglefowl.

scholarly journals Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1956
Author(s):  
María Asunción García-Atance ◽  
Carlos Carleos ◽  
Susana Dunner ◽  
Paulina G. Eusebi ◽  
Castor José Rivero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
Inbreeding Coefficients ◽  
Genomic Tools ◽  
Conservation Plan ◽  
Genomic Characterization ◽  
Conservation Plans ◽  
Genetic Signatures

A set of five local bovine breeds in danger of extinction named Cachena, Caldelá, Limiá, Frieiresa, and Vianesa and included in the group of Morenas Gallegas are located in the Autonomous Community of Galicia at the Northwest of Spain. Local authorities launched a conservation plan at the end of the 21th century in order to preserve this important genetic reservoir. However, Morenas Gallegas bovine breeds never have been analyzed with genomic tools and this information may be crucial to develop conservation plans. The aim of the study was to analyze their genetic diversity and genetic relationships with a set of local and cosmopolitan European bovine breeds using single nucleotide polymorphisms. Our results show own genetic signatures for the Morenas Gallegas breeds which form a separate cluster when compared to the Spanish breeds analyzed, with the exception of the Cachena breed. The genetic diversity levels of the Morenas Gallegas were intermediate or high, and low inbreeding coefficients can be found except for the Frieiresa breed (11%). Vianesa breed evidenced two lineages depending on the Frieiresa component influence. The Morenas Gallegas bovine breeds group represent an important Spanish bovine genetic reservoir and despite their classification within a single generic group, the five breeds show their own genetic uniqueness.

scholarly journals Genomic characterization of mithun (Bos frontalis) populations using high density SNP array

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Anupama Mukherjee ◽  
Sabyasachi Mukherjee ◽  
Imsusosang Longkumer ◽  
Moonmoon Mech ◽  
Nazrul Haque ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Principal Component ◽  
High Density ◽  
Population Substructure ◽  
Polymorphic Snps ◽  
Cross Validation Error ◽  
Baseline Information ◽  
Genomic Characterization

Mithun (Bos frontalis) is a bovine species found in the four North-Eastern Hilly States of India viz., Nagaland, Arunachal, Manipur and Mizoram. The 770k BovineHDBeadChip (Illumina, CA), which is basically a highdensity SNP array was utilized for genomic characterization of four mithun populations and to study genetic diversity present in the populations. SNP genotyping of a total 24 samples representing four mithun populations as per their geographic locations were carried out. The results indicated that the majority of polymorphic SNPs were found to be in HWE. Observed heterozygosity ranged between 0.263±0.040 (Nagaland) to 0.299±0.044 (Arunachal). Inbreeding coefficient ranged from 0.087±0.139 for Nagaland to 0.186±0.053 for Manipur mithun. The result of the Principal Component Analysis (PCA) indicated all the mithuns were distributed together in close proximity and no clear separation of the four populations was observed.The first and second principal components (PC1 and PC2) explained 9.59% and 88.0% of the total variation, respectively. The results of the STRUCTURE analysis also showed no population substructure as inferred from an increasing plot of cross validation error, similar to PCA. In our knowledge, this is the first study on genomic characterization of any Indian livestock species, through analysis of population structure and genetic diversity using high density SNP array. The baseline information generated in our study will help in developing proper strategies for implementing genomic selection and conservation of mithun.

Genomic characterization of γ-terpinene synthase from Thymus caespititius

Planta Medica ◽  
2011 ◽  
Vol 77 (12) ◽  
Author(s):  
AS Lima ◽  
B Lukas ◽  
J Novak ◽  
AC Figueiredo ◽  
LG Pedro ◽  
...  
Keyword(s):  
Genomic Characterization
Sign in / Sign up

Export Citation Format

Share Document