nucleotide variability
Recently Published Documents


TOTAL DOCUMENTS

95
(FIVE YEARS 28)

H-INDEX

17
(FIVE YEARS 2)

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Jiaojun Yu ◽  
Jun Fu ◽  
Yuanping Fang ◽  
Jun Xiang ◽  
Hongjin Dong

Abstract Background Rubus is the largest genus of the family Rosaceae and is valued as medicinal, edible, and ornamental plants. Here, we sequenced and assembled eight chloroplast (cp) genomes of Rubus from the Dabie Mountains in Central China. Fifty-one Rubus species were comparatively analyzed for the cp genomes including the eight newly discovered genomes and forty-three previously reported in GenBank database (NCBI). Results The eight newly obtained cp genomes had the same quadripartite structure as the other cp genomes in Rubus. The length of the eight plastomes ranged from 155,546 bp to 156,321 bp with similar GC content (37.0 to 37.3%). The results indicated 133–134 genes were annotated for the Rubus plastomes, which contained 88 or 89 protein coding genes (PCGs), 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Among them, 16 (or 18) of the genes were duplicated in the IR region. Structural comparative analysis results showed that the gene content and order were relatively preserved. Nucleotide variability analysis identified nine hotspot regions for genomic divergence and multiple simple sequences repeats (SSRs), which may be used as markers for genetic diversity and phylogenetic analysis. Phylogenetic relationships were highly supported within the family Rosaceae, as evidenced by sub-clade taxa cp genome sequences. Conclusion Thus, the whole plastome may be used as a super-marker in phylogenetic studies of this genus.


2022 ◽  
Vol 42 (1) ◽  
Author(s):  
Nathaniel Burner ◽  
Abigail McCauley ◽  
Sreepriya Pramod ◽  
Jesse Frederick ◽  
Tyler Steede ◽  
...  

2021 ◽  
Vol 2099 (1) ◽  
pp. 012037
Author(s):  
N S Kobalo ◽  
A A Kulikov ◽  
I I Titov

Abstract The pandemic of the coronavirus infection COVID-19, which began at the end of 2019 and caused by the SARS-CoV-2 virus, has led to unprecedented consequences in the world. By the end of May 2021, in the world there were 167 million infected and 3.5 million died directly from infection [1]. SARS-CoV-2 is a beta coronavirus, so it shares many conserved fragments with other known viruses of this type [2]. Since the beginning of the spread of the COVID-19, one of the important issues of research of the SARS-CoV-2 virus has been the search for its conserved RNA motifs and their functional annotation. These motifs are potential targets for the treatment and diagnosis of a disease caused by the virus. This report examines the structural RNA fragments of SARS-CoV-2, similar to the corresponding fragments in other beta coronaviruses [2]. For these RNA motifs the nucleotide variability during the spread of the virus, depending on their secondary structure, was investigated. All the motifs display the similar background variability although contain hypervariable positions.


2021 ◽  
Author(s):  
Eliška Vrbová ◽  
Angel A. Noda ◽  
Linda Grillová ◽  
Islay Rodríguez ◽  
Allyn Forsyth ◽  
...  

Bejel (endemic syphilis) is a neglected non-venereal disease caused by Treponema pallidum subsp. endemicum (TEN). Although it is mostly present in hot, dry climates, a few cases have been found outside of these areas. The aim of this work was the sequencing and analysis of TEN isolates obtained from "syphilis patients" in Cuba, which is not considered an endemic area for bejel. Genomes were obtained by pool segment genome sequencing or direct sequencing methods, and the bioinformatics analysis was performed according to an established pipeline. We obtained four genomes with 100%, 81.7%, 52.6%, and 21.1% of broad coverage, respectively. The sequenced genomes revealed a non-clonal character, with nucleotide variability ranging between 0.2–10.3 nucleotide substitutions per 100 kbp among the TEN isolates. Nucleotide changes affected 27 genes, and the analysis of the completely sequenced genome also showed a recombination event between tprC and tprI, in TP0488 as well as in the intergenic region between TP0127–TP0129. Despite limitations in the quality of samples affecting broad sequencing coverage, the determined non-clonal character of the isolates suggests a persistent infection in the Cuban population rather than a single outbreak caused by imported case.


BMC Zoology ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Fatimat Tembotova ◽  
Ekaterina Kuchinova ◽  
Albina Amshokova ◽  
Ekaretina Kononenko

Abstract Background There are two species of Mus in the Caucasus: M. musculus and M. macedonicus. M. musculus is widespread in the Caucasus, where the species is found everywhere from the Black to the Caspian Sea. M. macedonicus is ubiquitous Transcaucasia. The most north-astern border of its distribution in the Caucasus, according to the literature, is located in the Derbent region, near the border between Dagestan and Azerbaijan. Results Cytochrome b mt-DNA of genus Mus research in this study in the Eastern Caucasus. About 70% of M. musculus haplotypes from the lowlands of Dagestan were recorded for the first time. One of these haplotypes accounts for approximately 25% of the total species diversity of haplotypes. M. macedonicus was found in only one locality, the Sarykum barchans, where this species prevails in number and accounts for 70% of the total number mice of the genus Mus. The species is characterized by low values of genetic diversity and nucleotide variability, which may indicate that the population originated from a small number of founders and may explain its relative isolation from the main range. The dating of the appearance of the ancestors of M. musculus in the east of the Russian Caucasus corresponds to 99-66 thousand years ago (at a mutation rate of 3-10% per million years). Conclusion The results obtained suggest that the history of the appearance of M. musculus in the Eastern Caucasus is more ancient and is not associated with human agricultural activities. We believe that possibly the ancestral range of M. musculus covered the eastern and western coasts of the Caspian Sea in the territory of southern Dagestan, Azerbaijan, and Iran. In this paper M. macedonicus, a Balkan-Asia Minor species, was registered for the first time in the North Caucasus. This species was registered in the center of Dagestan, where it inhabits sympatrically (on the territory) and syntopically (on the same biotope) with M. musculus. The low values of genetic diversity of M. macedonicus in the North Caucasus suggest that the population originated from a small group of founders.


2021 ◽  
Vol 12 ◽  
Author(s):  
Concetta Burgarella ◽  
Angélique Berger ◽  
Sylvain Glémin ◽  
Jacques David ◽  
Nancy Terrier ◽  
...  

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.


2021 ◽  
Vol 12 ◽  
Author(s):  
Chunyu Tian ◽  
Xiansong Li ◽  
Zinian Wu ◽  
Zhiyong Li ◽  
Xiangyang Hou ◽  
...  

Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.


2021 ◽  
Author(s):  
Leabaneng Tawe ◽  
Wonderful T. Choga ◽  
Giacomo M. Paganotti ◽  
Ontlametse T. Bareng ◽  
Tlhalefo D. Ntereke ◽  
...  

Abstract Background The variation of human papillomavirus (HPV) genotypes shapes the risks of cervical cancer and these variations are not well defined in Africa. Nucleotide changes within the L1 gene, nucleotide variability, and phylogeny were explored in relation to HIV in samples from Botswana and Kenya. Methods A total of 98 HPV-positive cervical samples were sequenced to identify different HPV variants. Phylogenetic inferences were used to determine HPV genotypes and investigate the clustering of sequences between women living with HIV (WLWHIV) and -women not living with HIV (WNLWHIV). Results Out of 98 generated sequences, 83.7% (82/98) participants had high-risk(HR) HPV genotypes while 16.3% (16/98) had low-risk (LR) HPV genotypes. Among participants with HR-HPV genotypes, 47.6% (39/82) were coinfected with HIV. The prevalence of HR-HPV genotypes was statistically higher in the Botswana population compared to Kenya (p-value < 0.001). Multiple amino acid mutations were identified in both countries. Genetic diversity differed considerably among WLWHIV and WNLWHIV. The mean pairwise distances between HPV-16 between HIV and HIV/HPV as well as for HPV-18 were statistically significant. Six (6) new deleterious mutations were identified in the HPV genotypes based on the sequencing of the L1 region, HPV-16 (L441P, S343P), HPV-18 (S424P), HPV-45 (Q366H, Y365F), and HPV-84 (F458L). The majority of the patients with these mutations were co-infected with HIV. Conclusions Genomic diversity and different genomic variants of HPV sequences were demonstrated. Candidate novel mutations within the L1 gene were identified in both countries which can be further investigated using functional assays.


2021 ◽  
Vol 11 (1) ◽  
pp. 42-51
Author(s):  
Kamrul Ahmed Khan ◽  
Md. Alimul Islam ◽  
Abdullah Al Momen Sabuj ◽  
Md. Abul Bashar ◽  
Md. Saiful Islam ◽  
...  

Background: Duck viral enteritis, commonly known as duck plague (DP), is an acute and contagious fatal disease in ducks, geese, and swans caused by the DP virus (DPV). It poses a serious threat to the growth of duck farming in the Haor (wetland) areas of Bangladesh. Aim: This study aimed to detect the circulating DPV by molecular characterization, followed by phylogenetic analysis, targeting the UL30 gene in infected ducks from five Haor districts in Bangladesh and to observe the variation in the genome sequence between the field virus and vaccine strain of DPV. Methods: A total of 150 samples (liver, 50; intestine, 50; and oropharyngeal tissue, 50) were collected from DP-suspected sick/dead ducks from 50 affected farms in Kishoreganj, Netrokona, B. Baria, Habiganj, and Sunamganj districts in Bangladesh. For the identification of DPV in collected samples, polymerase chain reaction (PCR) was utilized. Nucleotide sequences of the amplified UL30 gene were compared with those of other DPV strains available in GenBank. Results: Of the 150 samples, 90 (60%) were found to be positive for DPV, as confirmed by PCR. Organ-wise prevalence was higher in the liver (72%), followed by the intestine (64%) and oropharyngeal tissue (44%). Regarding areas, the highest and lowest prevalence in the liver and intestine was observed in Habiganj and B. Baria, respectively, whereas the highest and lowest prevalence in the oropharyngeal tissue was observed in B. Baria and Habiganj, respectively. Two isolates, BAU/KA/DPV(B1)/2014 from Kishoreganj and BAU/KA/DPV(B4)/2014 from Sunamganj were sequenced, and phylogenetic analysis revealed that these isolates are evolutionarily closely related to Chinese isolates of DPV. Additionally, the isolates of DPV BAU/KA/DPV(B1)/2014 and BAU/KA/DPV(B4)/2014 showed the highest (98%) similarity to each other. The nucleotide sequence of the isolate BAU/KA/DPV(B1)/2014 exhibited higher nucleotide variability (246 nucleotides) than that of the vaccine strain (accession no. EU082088), which may affect protein function and additional drug sensitivity. Conclusion: Based on the findings of the molecular study, it can be assumed that the Bangladeshi isolates and all Chinese isolates of DPV may have a common ancestry.


Sign in / Sign up

Export Citation Format

Share Document