Advances in methods of genome analyses, nucleotide analyses, and implications of variants

2022 ◽  
pp. 41-61
Author(s):  
Moyra Smith
Keyword(s):  
Genome Analyses

scholarly journals Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiawei Zhou ◽  
Shuo Zhang ◽  
Jie Wang ◽  
Hongmei Shen ◽  
Bin Ai ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Population Level ◽  
Gene Content ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Chloroplast Evolution ◽  
Chloroplast Genomes ◽  
Genome Features ◽  
Genome Annotations ◽  
Genome Analyses

AbstractThe chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.

scholarly journals Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Komal Jain ◽  
Teresa Tagliafierro ◽  
Adriana Marques ◽  
Santiago Sanchez-Vicente ◽  
Alper Gokden ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Fold Increase ◽  
The United States ◽  
Genomic Research ◽  
Babesia Microti ◽  
Hybridization Capture ◽  
Mouse Tissues ◽  
Genome Analyses ◽  
Capture Sequencing

AbstractInadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.

scholarly journals Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus

2021 ◽  
Vol 9 (3) ◽  
pp. 499
Author(s):  
Majid Rasool Kamli ◽  
Nada A. Y. Alzahrani ◽  
Nahid H. Hajrah ◽  
Jamal S. M. Sabir ◽  
Adeel Malik
Keyword(s):  
Heavy Metal ◽  
Enzyme Activities ◽  
Heavy Metal Resistance ◽  
Industrial Applications ◽  
Metal Resistance ◽  
The Family ◽  
Antiviral Activities ◽  
Genome Level ◽  
Genome Analyses ◽  
Unique Species

Bacteria belonging to the genus Aneurinibacillus within the family Paenibacillaceae are Gram-positive, endospore-forming, and rod-shaped bacteria inhabiting diverse environments. Currently, there are eight validly described species of Aneurinibacillus; however, several unclassified species have also been reported. Aneurinibacillus spp. have shown the potential for producing secondary metabolites (SMs) and demonstrated diverse types of enzyme activities. These features make them promising candidates with industrial implications. At present, genomes of 9 unique species from the genus Aneurinibacillus are available, which can be utilized to decipher invaluable information on their biosynthetic potential as well as enzyme activities. In this work, we performed the comparative genome analyses of nine Aneurinibacillus species representing the first such comprehensive study of this genus at the genome level. We focused on discovering the biosynthetic, biodegradation, and heavy metal resistance potential of this under-investigated genus. The results indicate that the genomes of Aneurinibacillus contain SM-producing regions with diverse bioactivities, including antimicrobial and antiviral activities. Several carbohydrate-active enzymes (CAZymes) and genes involved in heavy metal resistance were also identified. Additionally, a broad range of enzyme classes were also identified in the Aneurinibacillus pan-genomes, making this group of bacteria potential candidates for future investigations with industrial applications.

Genome analyses and androgen quantification for an infant with 5α-reductase type 2 deficiency

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Kazuhisa Akiba ◽  
Keiko Aso ◽  
Yukihiro Hasegawa ◽  
Maki Fukami
Keyword(s):  
Disorders Of Sex Development ◽  
Reference Value ◽  
Ambiguous Genitalia ◽  
Chinese Patients ◽  
Sex Development ◽  
Liquid Chromatography Tandem Mass ◽  
Exon 1 ◽  
Genome Analyses ◽  
Immune Assays

Abstract Objectives 5α-reductase type 2 deficiency due to biallelic SRD5A2 variants is a common form of 46,XY disorders of sex development. Case presentation A Chinese neonate presented with ambiguous genitalia. He carried a homozygous likely_pathogenic SRD5A2 variant (c.650C>A, p.A217E). His apparently nonconsanguineous parents were heterozygotes for the variant. The variant has previously been identified in two Chinese patients. Our patient carried 14.2 Mb loss-of-heterogeneity regions distributed in the genome. The SRD5A2 variant in this family was invariably coupled with two polymorphisms in exon 1 and intron 1. In the patient, blood testosterone (T)/5α-dihydrotestosterone (5αDHT) ratios were elevated before and during mini puberty, and were higher when measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS) than measured by conventional immune assays. Conclusions This study provides evidence for the founder effect of an SRD5A2 variant. Furthermore, our data indicate that there is a need to establish a new reference value for T/5αDHT ratios using LC-MS/MS.

D-galactose catabolism in archaea: operation of the DeLey–Doudoroff pathway in Haloferax volcanii

2020 ◽  
Vol 367 (1) ◽  
Author(s):  
Julia-Beate Tästensen ◽  
Ulrike Johnsen ◽  
Andreas Reinhardt ◽  
Marius Ortjohann ◽  
Peter Schönheit
Keyword(s):  
Transcriptional Regulator ◽  
High Specificity ◽  
Comprehensive Analysis ◽  
Haloferax Volcanii ◽  
Knock Out ◽  
Genes Encoding ◽  
Functional Involvement ◽  
Genome Analyses ◽  
Galactose Dehydrogenase ◽  
Substrate Binding Protein

ABSTRACT The haloarchaeon Haloferax volcanii was found to grow on D-galactose as carbon and energy source. Here we report a comprehensive analysis of D-galactose catabolism in H. volcanii. Genome analyses indicated a cluster of genes encoding putative enzymes of the DeLey–Doudoroff pathway for D-galactose degradation including galactose dehydrogenase, galactonate dehydratase, 2-keto-3-deoxygalactonate kinase and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase. The recombinant galactose dehydrogenase and galactonate dehydratase showed high specificity for D-galactose and galactonate, respectively, whereas KDPGal aldolase was promiscuous in utilizing KDPGal and also the C4 epimer 2-keto-3-deoxy-6-phosphogluconate as substrates. Growth studies with knock-out mutants indicated the functional involvement of galactose dehydrogenase, galactonate dehydratase and KDPGal aldolase in D-galactose degradation. Further, the transcriptional regulator GacR was identified, which was characterized as an activator of genes of the DeLey–Doudoroff pathway. Finally, genes were identified encoding components of an ABC transporter and a knock-out mutant of the substrate binding protein indicated the functional involvement of this transporter in D-galactose uptake. This is the first report of D-galactose degradation via the DeLey–Doudoroff pathway in the domain of archaea.

scholarly journals Adaptation, Ecology, and Evolution of the Halophilic Stromatolite ArchaeonHalococcus hamelinensisInferred through Genome Analyses

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Reema K. Gudhka ◽  
Brett A. Neilan ◽  
Brendan P. Burns
Keyword(s):  
Unknown Function ◽  
Energy Production ◽  
Extreme Environment ◽  
Evolutionary Significance ◽  
Base Pairs ◽  
Protein Coding ◽  
Inorganic Ion ◽  
Damage Repair ◽  
Genome Analyses

Halococcus hamelinensiswas the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome ofH. hamelinensisconsisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of theH. hamelinensisgenome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome ofH. hamelinensisalso revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes ofH. hamelinensisagainst various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

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