scholarly journals Genetic Diversity and Population Structure of Acanthochiton rubrolineatus (Polyplacophora) Based on Mitochondrial and Nuclear Gene Markers

Diversity ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 159
Author(s):  
Haowen Xu ◽  
Zhailin Chu ◽  
Jing Zhang ◽  
Meidong Jing ◽  
Ling Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
16S Rrna ◽  
Nuclear Gene ◽  
Population Expansion ◽  
Ice Age ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Markers ◽  
Southern Group

Acanthochiton rubrolineatus (Cryptoplacidae, Neoloricata, Polyplacophora) has a narrow distribution range along the seacoasts of China, the Korean Peninsula and Japan. We collected 238 samples from eight localities along the Chinese coast, and analyzed the genetic diversity and population structure with COI, 16S-rRNA and 28S-rRNA gene sequences. All analyses based on combined sequences of COI and 16S-rRNA suggested that there was evident genetic differentiation between the northern populations (YT, WH, DL, QD, LYG) and southern populations (ZS, YH, XM) of A. rubrolineatus. The haplotype distribution pattern and genetic diversity based on 28S-rRNA sequences also supported the genetic divergence between the two groups. Both groups had experienced population expansion after the ice age of Pleistocene, and an additional population bottleneck had happened in the southern group in recent history, which led to low genetic diversity of mitochondrial DNA and abnormally high diversity of nuclear DNA in this group. Our results suggested that the protection on A. rubrolineatus is necessary, and the northern and southern group should be protected separately.

Genetic diversity and population structure of penis fish (Urechis unicinctus) based on mitochondrial and nuclear gene markers

2018 ◽  
Vol 29 (8) ◽  
pp. 1261-1268 ◽  
Author(s):  
Jie Gong ◽  
Ruoping Zhao ◽  
Jiaheng Deng ◽  
Yancui Zhao ◽  
Jincheng Zuo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Nuclear Gene ◽  
Urechis Unicinctus ◽  
Gene Markers

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.

scholarly journals Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei Wang ◽  
Chunyan Ma ◽  
Longling Ouyang ◽  
Wei Chen ◽  
Ming Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Genetic Constitution ◽  
Southern Group ◽  
Population Structure Analysis ◽  
Lateolabrax Maculatus ◽  
Geographic Populations ◽  
Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

Genetic diversity of vaginal lactobacilli from women in different countries based on 16S rRNA gene sequences

2002 ◽  
Vol 92 (3) ◽  
pp. 451-459 ◽  
Author(s):  
S.I. Pavlova ◽  
A.O. Kilic ◽  
S.S. Kilic ◽  
J.-S. So ◽  
M.E. Nader-Macias ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Vaginal Lactobacilli

DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities

1992 ◽  
Vol 100 (1-3) ◽  
pp. 59-65 ◽  
Author(s):  
Paul A. Rochelle ◽  
John C. Fry ◽  
R. John Parkes ◽  
Andrew J. Weightman
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Deep Sediment

Redescription of Cerebratulus marginatus auct. (Nemertea: Pilidiophora) from Hokkaido, Japan, as a new species

Zootaxa ◽  
2020 ◽  
Vol 4819 (2) ◽  
pp. 295-315
Author(s):  
HIROSHI KAJIHARA
Keyword(s):  
16S Rrna ◽  
Vascular System ◽  
Phylogenetic Analyses ◽  
Far East ◽  
Muscle Layer ◽  
The Body ◽  
Rrna Gene ◽  
28S Rrna ◽  
Anterior Portion ◽  
Longitudinal Muscle Layer

The heteronemertean Cerebratulus orochi sp. nov. is described based on material collected intertidally at a muddy beach in Akkeshi, northern Japan. For the last 80 years, the species has been confused with Cerebratulus marginatus Renier, 1804; the latter was originally described from the Adriatic and once believed to occur in many places in the northern hemisphere including Japan. Cerebratulus orochi sp. nov. is morphologically different from all the congeners including C. marginatus by the following combination of characters: several layers of diagonal-muscle meshwork coated with connective tissue, proximo-distally distributed in cross section from the distal portion of the body-wall outer longitudinal muscle layer to the cutis-gland zone throughout the anterior portion of the body from the precerebral to the foregut regions; the cephalic vascular system consisting of lateral and mid-dorsal vessels; and the sub-rhynchocoelic vessel possessing a pair of antero-lateral diverticula before the former forks posteriorly into a pair of lower lateral vessels in the post-cerebral, pre-oral region. Previous records of C. marginatus from Japanese waters are no longer considered to be substantiated. Multi-locus phylogenetic analyses based on the mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI), as well as the nuclear 18S rRNA, 28S rRNA, and histone H3 genes among heteronemerteans comprising the “Cerebratulus clade” indicated that C. orochi sp. nov. was closely related to C. cf. marginatus from the US Pacific coast. A MegaBLAST search at the NCBI website with the 16S rRNA gene sequence from C. orochi sp. nov. followed by a couple of species delimitation analyses suggests that larvae of the species are also distributed in Vostok Bay, Far East Russia.

scholarly journals Highly Specific Sewage-DerivedBacteroidesQuantitative PCR Assays Target Sewage-Polluted Waters

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Shuchen Feng ◽  
Sandra L. McLellan
Keyword(s):  
Population Structure ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Samples ◽  
Rrna Gene ◽  
Content Type ◽  
Hypervariable Regions ◽  
Animal Hosts ◽  
Pcr Assays ◽  
The 16S Rrna Gene

ABSTRACTThe identification of sewage contamination in water has primarily relied on the detection of human-associatedBacteroidesusing markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e.,Bacteroides dorei) and otherBacteroidesorganisms (e.g.,Bacteroides thetaiotaomicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined theBacteroidespopulation structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundantBacteroidesin untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts (n = 76) and uncontaminated water samples (n = 30) demonstrated the high specificity of the assays for sewage. FreshwaterBacteroideswere also identified in uncontaminated water samples, demonstrating that measures of totalBacteroidesdo not reflect fecal pollution. A comparison of two previously described humanBacteroidesassays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derivedBacteroidesprovided an independent measure of sewage-impacted waters.IMPORTANCEBacteroidesare major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure ofBacteroideswithin sewage to contextualize the well-studied HF183 marker for a human-associatedBacteroides. The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundantBacteroidesin sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.

scholarly journals Combined Ribotyping and Random Multiprimer DNA Analysis To Probe the Population Structure of Listeria monocytogenes

2002 ◽  
Vol 68 (6) ◽  
pp. 2849-2857 ◽  
Author(s):  
L. Mereghetti ◽  
P. Lanotte ◽  
V. Savoye-Marczuk ◽  
N. Marquet-Van Der Mee ◽  
A. Audurier ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Listeria Monocytogenes ◽  
Genetic Structure ◽  
Dna Analysis ◽  
Division I ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Clustering Methods ◽  
Division Ii

ABSTRACT To improve our understanding of the genetic links between strains originating from food and strains responsible for human diseases, we studied the genetic diversity and population structure of 130 epidemiologically unrelated Listeria monocytogenes strains. Strains were isolated from different sources and ecosystems in which the bacterium is commonly found. We used rRNA gene restriction fragment length polymorphism analysis with two endonucleases and random multiprimer DNA analysis with seven oligonucleotide primers to study multiple genetic features of each strain. We used three clustering methods to identify genetic links between individual strains and to determine the precise genetic structure of the population. The combined results confirmed that L. monocytogenes strains can be divided into two major phylogenetic divisions. The method used allowed us to demonstrate that the genetic structure and diversity of the two phylogenetic divisions differ. Division I is the most homogeneous and can easily be divided into subgroups with dissimilarity distances of less than 0.30. Each of these subgroups mainly, or exclusively, contains a single serotype (1/2b, 4b, 3b, or 4a). The serotype 4a lineage appears to form a branch that is highly divergent from the phylogenetic group containing serotypes 1/2b, 4b, and 3b. Division II contains strains of serotypes 1/2a, 1/2c, and 3a. It exhibits more genetic diversity with no peculiar clustering. The fact that division II is more heterogeneous than division I suggests that division II evolved from a common ancestor earlier than division I. A significant association was found between division I and human strains, suggesting that strains from division I are better adapted to human hosts.

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