Case-control approach to identify Plasmodium falciparum polymorphisms associated with severe malaria. by Watcharee Chokejindachai, David J Conway

“…<h4>Methodology/principal findings</h4>Assessment of LD was first made with 11 microsatellite loci widely dispersed in the parasite genome, and 16 microsatellite loci covering a approximately 140 kb region of chromosome 2 (an arbitrarily representative non-telomeric part of the genome), in a sample of 100 P. falciparum isolates. …”
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Small deletion variants have stable breakpoints commonly associated with alu elements. by Adam J de Smith, Robin G Walters, Lachlan J M Coin, Israel Steinfeld, Zohar Yakhini, Rob Sladek, Philippe Froguel, Alexandra I F Blakemore

“…We investigated the breakpoints of 20 small, common deletions, representing a subset of those originally identified by array CGH, using Agilent microarrays, in 50 healthy French Caucasian subjects. By sequencing PCR products amplified using primers designed to span the deleted regions, we determined the exact size and genomic position of the deletions in all affected samples. …”
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Morphological and molecular characterization of Halamphora vantushpaensis (Bacillariophyceae, Amphipleuraceae), a new diatom species widely dispersed on the shores of the soda Lake... by Elif Yılmaz, Romain Gastineau, Cüneyt Nadir Solak, Ewa Górecka, Rosa Trobajo, Monique Turmel, Claude Lemieux, Christian Otis, Andrzej Witkowski, David G. Mann

“…This new species is characterized morphologically by light and scanning electron microscopy, performed on both wild and cultivated samples. Two monoclonal cultures were submitted to a genome-skimming approach, giving access to the complete sequence of their nuclear rRNA cluster of genes, mitochondrial and plastid genomes. …”
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The complete plastome of a newly described species, Iris cangshanensis by Jinfeng Liu, Xianfeng Jiang

“…The chloroplast genome is 154,008 base pairs (bp) in size with 37.32% overall GC content, consisting of an 83,559 bp (35.35%) large single-copy region (LSC), a 17,937 bp (30.56%) small single-copy region (SSC), and a pair of 26,256 bp (42.78%) inverted repeat (IR) sequences. …”
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Insights to genetic characterization tools for epidemiological tracking of Francisella tularensis in Sweden. by Tara Wahab, Dawn N Birdsell, Marika Hjertqvist, Cedar L Mitchell, David M Wagner, Paul S Keim, Ingela Hedenström, Sven Löfdahl

“…This result suggests that SNP markers, highly specific to a particular reference genome, may be found most frequently among samples recovered from the same location where the reference genome originated. …”
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RAD-Seq-derived SSR markers: a new paradigm for genetic analysis and construction of genetically improved production populations in Pinus koraiensis by Pingyu Yan, Wanying Zhang, Junfei Hao, Xiaotian Miao, Jun Wu, Zixiong Xie, Zhixin Li, Lei Zhang, Hanguo Zhang

“…The objective of this initiative is to facilitate the efficient management of genetic resources within Pinus koraiensis, enable precise pedigree identification and establish a foundational framework for subsequent whole-genome sequencing and assembly strategies. To achieve this objective, a simplified genome sequencing approach was employed, utiliZing RAD-Seq technology on a sample of 100 clones of Pinus koraiensis sourced from 6 seed orchards. …”
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GRK5 intronic (CA)n polymorphisms associated with type 2 diabetes in Chinese Hainan Island. by Zhenfang Xia, Tubao Yang, Zhuansuo Wang, Jianping Dong, Chunyan Liang

“…A genome-wide association study had showed G-protein-coupled receptor kinase 5 (GRK5) rs10886471 was related to the risk of type 2 diabetes mellitus (T2DM) through upregulated GRK5 mRNA expression. …”
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Zinc Finger Domain of the PRDM9 Gene on Chromosome 1 Exhibits High Diversity in Ruminants but Its Paralog PRDM7 Contains Multiple Disruptive Mutations. by Sonika Ahlawat, Priyanka Sharma, Rekha Sharma, Reena Arora, Sachinandan De

“…PRDM9 gene encodes a protein with an immensely variable zinc-finger (ZF) domain that determines the site of meiotic recombination hotspots genome-wide. In this study, the terminal ZF domain of PRDM9 on bovine chromosome 1 and its paralog on chromosome 22 were characterized in 225 samples from five ruminant species (cattle, yak, mithun, sheep and goat). …”
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Genetic diversity and antimicrobial resistance of clinical Klebsiella pneumoniae isolates: An ISSR-PCR analysis by Poonamrani Mishra, Debasish Sahoo, Mahesh Chandra Sahu

“…The study aimed to investigate the genetic diversity of K. pneumoniae clinical isolates using Inter Simple Sequence Repeat (ISSR) primers to assess strain differentiation and evolutionary relationships. …”
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Systematic analysis of transcription start sites in avian development. by Marina Lizio, Ruslan Deviatiiarov, Hiroki Nagai, Laura Galan, Erik Arner, Masayoshi Itoh, Timo Lassmann, Takeya Kasukawa, Akira Hasegawa, Marian A Ros, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Hideya Kawaji, Oleg Gusev, Guojun Sheng

“…Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. …”
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Case Report: Genetic evolution of Burkholderia pseudomallei during treatment leading to antibiotic resistance and disease relapse. [version 2; peer review: 2 approved] by Ko Chang, Elizabeth A. Ashley, Claire Chewapreecha, Anousone Douangnouvong, Chantisa Keeratipusana, Terry John Evans, Koukeo Phommasone, Davanh Sengdatka, Elizabeth M. Batty, Vilayouth Phimolsarnnousith

“…Several subsequent B. pseudomallei isolates from the patient were resistant to multiple antibiotics, and whole genome sequencing demonstrated that this phenotype was associated with a novel 54-kb genomic deletion. …”
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A Look into the Melting Pot: The mecC-Harboring Region Is a Recombination Hot Spot in Staphylococcus stepanovicii. by Torsten Semmler, Ewan M Harrison, Antina Lübke-Becker, Rainer G Ulrich, Lothar H Wieler, Sebastian Guenther, Ivonne Stamm, Anne-Merethe Hanssen, Mark A Holmes, Szilvia Vincze, Birgit Walther

“…Whole genome sequencing (WGS) of IMT28705 together with the mecC-negative type strain CM7717 was conducted in order to comparatively investigate the genomic region downstream of attB (GenBank accession no. …”
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A simple validation and screening method for CRISPR/Cas9-mediated gene editing in mouse embryos to facilitate genetically modified mice production. by Dawid Winiarczyk, Hossein Khodadadi, Paweł Leszczyński, Hiroaki Taniguchi

“…Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) is a genome engineering method for generating site-specific editing in target genes in a variety of species. …”
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Stable Plasmodium falciparum merozoite surface protein-1 allelic diversity despite decreasing parasitaemia in children with multiple malaria infections by Reuben M. Yaa, Kelvin M. Kimenyi, Henry Antonio Palasciano, George Obiero, L. Isabella Ochola-Oyier

“…Sequenced reads were trimmed and aligned to the P. falciparum 3D7 reference genome. …”
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Phylogenetic Analysis of Chrysochamela (Fenzl) Boiss. (Brassicaceae) Taxa Growing in Turkey by Emre Sevindik, Mehmet Yavuz Paksoy, Feyzanur Topseçer, Melike Aydoğan

“…In this study, we performed a genetic diversity analysis using RAPD (Random Amplified Polymorphic DNA) and ISSR (Inter simple sequence repeat) markers for some Chrysochamela species growing in Turkey. …”
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Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium. by Mohammad Arif, Grethel Y Busot, Rachel Mann, Brendan Rodoni, Sanzhen Liu, James P Stack

“…Discriminant analyses of recently collected and archived isolates using Multi-Locus Sequence Typing (MLST) and Inter-Simple Sequence Repeats (ISSR) identified three populations of R. toxicus; RT-I and RT-II from South Australia and RT-III from Western Australia. …”
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RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics by Yi Li, Lan Jiang, Ke Wang, Hai-Jun Wu, Rui-Heng Yang, Yu-Jing Yan, Kathryn E. Bushley, David L. Hawksworth, Zujian Wu, Yi-Jian Yao

“…Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). …”
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Hepatitis B virus X protein (HBx)-mediated immune modulation and prognostic model development in hepatocellular carcinoma. by Jianhua Zhong, Yuetong Li, Yang Liu, Jie Qiao, Yiling Wu, Xinyi Kong, Miao Qi, Yiqi Lin, Yaqi Yao, Ying Jin, Changlong Bi, Aixia Zhai

“…Through transcriptome sequencing of our HBx-expressing HepG2 cells and analysis of HCC patient data from the cancer genome atlas (TCGA) and genotype-tissue expression (GTEx), we identified seven HBx-related genes, nuclear VCP-like (NVL), WD repeat domain 75 (WDR75), NOP58 nucleolar protein (NOP58), Brix domain-containing protein 1 (BRIX1), deoxynucleotidyltransferase terminal interacting protein 2 (DNTTIP2), MKI67 FHA domain interacting nucleolar phosphoprotein (NIFK), and ribosome production factor 2 (RPF2), associated with poor prognosis. …”
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Molecular Characterization of African Swine Fever Viruses from Outbreaks in Peri-Urban Kampala, Uganda by Frank Norbert Mwiine, Joseph Nkamwesiga, Christian Ndekezi, Sylvester Ochwo

“…ASF was confirmed in 10 of the 15 suspected pig samples. Phylogenetic analysis confirmed circulation of genotype IX by both full-length E183 (p54) and partial B646L (p72) gene sequencing. …”
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Genetic marker data for sweetpotato improvementDataverse by Imana L. Power, Brian E. Scheffler, Xiaofen F. Liu, Sheron A. Simpson, Linda L. Ballard, Marshall C. Lamb, Renee S. Arias

“…., consisting of 689 simple sequence repeats (SSRs) and 79 single nucleotide polymorphisms (SNPs). …”
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