scholarly journals Genetic diversity analysis of Dermacentor nuttalli within Inner Mongolia, China

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Zheng Gui ◽  
Lin Wu ◽  
Hao Cai ◽  
Lan Mu ◽  
Jing-Feng Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Genetic Differentiation ◽  
Inner Mongolia ◽  
Haplotype Diversity ◽  
Fixation Index ◽  
Rrna Gene ◽  
Human Beings ◽  
Autonomous Region ◽  
Inner Mongolia Autonomous Region

Abstract Background Ticks (Arthropoda, Ixodida), after mosquitoes, are the second most prevalent vector of infectious diseases. They are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. However, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous Region of China, surprisingly, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied. Methods We characterized the haplotype distribution of Dermacentor nuttalli in four main pastoral areas of the Inner Mongolia Autonomous Region, by sampling 109 individuals (recovered from sheep) in April–August 2019. The 16S rRNA gene, cytochrome c oxidase subunit I (COI), and the internal transcribed spacer 2 region (ITS2) were amplified and sequenced from extracted DNA. Results Twenty-six haplotypes were identified using 16S rRNA sequences, 57 haplotypes were identified with COI sequences, and 75 haplotypes were identified with ITS2 sequences. Among the three genes, total haplotype diversity was greater than 0.7, while total nucleotide diversity was greater than 0.06. Neutrality tests revealed a significantly negative Tajima’s D result, while Fu's Fs was not significantly positive. Fixation index values (FST) indicated that the degree of genetic differentiation among some sampled populations was small, while for others it was moderate. Analysis of molecular variance (AMOVA) revealed that the variation within populations was greater than that among populations. The mismatch analysis of D. nuttalli exhibited double peaks. Conclusion The genetic diversity of D. nuttalli populations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation among different populations. However, genetic differentiation is cryptic and does not form a pedigree geographical structure.

scholarly journals Genetic Diversity Analysis of Dermacentor Nuttalli within Inner Mongolia, China

2020 ◽  
Author(s):  
Zheng Gui ◽  
Lin Wu ◽  
Hao Cai ◽  
Fu-Shaoyin ◽  
Jing Feng Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Inner Mongolia ◽  
Haplotype Diversity ◽  
Fixation Index ◽  
Rrna Gene ◽  
Human Beings ◽  
Autonomous Region ◽  
Negative Results ◽  
Inner Mongolia Autonomous Region

Abstract BackgroundTicks (Arthropoda, Ixodida), after mosquitoes, are the next most prevalent vector of infectious diseases; and are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. Yet, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous region of China, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied. MethodsWe characterized the haplotype distribution of Dermacentor nuttalli in four main pastoral areas of the Inner Mongolia Autonomous region, by sampling 109 individuals (recovered from sheep) in April-August 2019. The 16S rRNA gene, Cytochrome c Oxidase Subunit Ⅰ, and the Internal Transcribed Spacer 2 region were amplified and sequenced from extracted DNA.Results 82 haplotypes were identified, the most prevalent of which was H32. 12 sequences (11 of all sequences) represented the most abundant haplotypes, with a highly scattered distribution. Total haplotype diversity was 0.98318, while total nucleotide diversity was 0.11369. Neutrality tests revealed negative results in the four locations analyzed, which is indicative of an excess of recently derived haplotypes. Fixation index values (FST) indicate that the degree of genetic differentiation amongst some sampled populations were small, while others were moderate. Conclusion The genetic diversity of D.nuttalli populations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation amongst different populations. However, genetic differentiation is cryptic and does not form the pedigree geographical structure.

scholarly journals Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China

2020 ◽  
Author(s):  
Qiong Xue ◽  
Zhenqiang Zuo ◽  
Heng Zhou ◽  
Jian Zhou ◽  
Shengjie Zhang ◽  
...  
Keyword(s):  
Inner Mongolia ◽  
Type Strain ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Autonomous Region ◽  
Salt Pond ◽  
A Genome ◽  
The Family ◽  
Inner Mongolia Autonomous Region

A haloalkaliphilic strain XQ-INN 246T was isolated from the sediment of a salt pond in Inner Mongolia Autonomous Region, China. Cells of the strain were rods, motile and strictly aerobic. The strain was able to grow in the presence of 2.6–5.3 M NaCl (optimum concentration is 4.4 M) at 30–50 °C (optimum temperature is 42 °C) and pH 7.0–10.0 (optimum pH is 8.0–8.5). The whole genome sequencing of strain XQ-INN 246T revealed a genome size of 4.52 Mbp and a DNA G+C content of 62.06 mol%. Phylogenetic tree based on 16S rRNA gene sequences and concatenated amino acid sequences of 122 single-copy conserved proteins revealed a robust lineage of the strain XQ-INN 246T with members of related genera of the family Natrialbaceae . The strain possessed the polar lipids of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Based on phylogenetic analysis, phenotypic characteristics, chemotaxonomic properties and genome relatedness, the isolate was proposed as the type strain of a novel species of a new genus within the family Natrialbaceae, for which the name Salinadaptatus halalkaliphilus gen. nov., sp. nov. is proposed. The type strain is XQ-INN 246T (=CGMCC 1.16692T=JCM 33751T).

scholarly journals Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

2015 ◽  
Vol 16 (3) ◽  
pp. 489 ◽  
Author(s):  
C. MAGGI ◽  
M. GONZÁLEZ-WANGÜEMERT
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Haplotype Diversity ◽  
Western Mediterranean ◽  
Mediterranean Coast ◽  
Morphological Data ◽  
Coi Gene ◽  
Fixation Index ◽  
Morphological Description ◽  
Western Mediterranean Sea

Parastichopus regalis (Cuvier, 1817) is the most expensive seafood product on the catalonian market (NE Spain), with prices around 130 €/Kg (fresh weight). Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI) and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia). We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST), AMOVA and correspondence analysis (CA) based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites) would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1) an accurate assessment of the stocks status along the Spanish coasts; 2) the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3) the founding of protected areas (i.e. not take zones) to conserve healthy populations and favour the recruitment on the nearby areas.

scholarly journals Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA

2019 ◽  
Vol 62 (1) ◽  
pp. 325-333 ◽  
Author(s):  
Linjun Yan ◽  
Yifan She ◽  
Mauricio A. Elzo ◽  
Chunlei Zhang ◽  
Xingtang Fang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Cattle Breeds ◽  
Chinese Cattle

Abstract. The objective of this research was to characterize the genetic diversity and phylogenetic diversity among 12 cattle breeds (10 Chinese breeds and two foreign taurine breeds as controls) utilizing gene mtDNA 16S rRNA. The complete sequences of the mtDNA 16S rRNA genes of the 251 animals were 1570 bp long. The mean percentages of the four nitrogen bases were 37.8 % for adenine (A), 23.7 % for thymine (T), 20.9 % for cytosine (C), and 17.6 % for guanine (G). The mtDNA 16S rRNA gene base percentages had a strong bias towards A + T. All detected nucleotide variations in gene mtDNA 16S rRNA were either transitions (62.3 %) or transversions (37.7 %); no indels (insertions and deletions) were found. A total of 40 haplotypes were constructed based on these mutations. A total of 36 haplotypes of these 40 haplotypes were present in 10 Chinese cattle breeds. The haplotype diversity of all Chinese cattle populations was 0.903±0.077, while the nucleotide diversity was 0.0071±0.0039. Kimura's two-parameter genetic distances between pairs of the studied 12 breeds ranged from 0.001 to 0.010. The phylogenetic analysis assigned the 10 Chinese breeds to two distinct lineages that likely differed in their percentage of Bos taurus and Bos indicus ancestry.

scholarly journals Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil (Lens culinaris Medik.)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 15
Author(s):  
Badreddine Sijilmassi ◽  
Abdelkarim Filali-Maltouf ◽  
Hassan Boulahyaoui ◽  
Aymane Kricha ◽  
Kenza Boubekri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rhizobium Leguminosarum ◽  
Sequence Similarity ◽  
P Value ◽  
Rrna Gene ◽  
Research Station ◽  
Symbiotic Efficiency ◽  
Rhizobium Strains

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.

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