Article
Microbiology
Mir Asif Iquebal, Sarika Jaiswal, Vineet Kumar Mishra, Rahul Singh Jasrotia, Ulavappa B. Angadi, Bhim Pratap Singh, Ajit Kumar Passari, Purbajyoti Deka, Ratna Prabha, Dhananjaya P. Singh, Vijai Kumar Gupta, Rukam Singh Tomar, Harinder Singh Oberoi, Anil Rai, Dinesh Kumar
Summary: Identification and diversity analysis of fungi pose great challenges, as traditional methods have limitations in differentiating between all groups and cryptic species. This study introduces a novel whole genome sequence-based microsatellite database, FungSatDB, containing >19M loci from >1900 fungal species/strains. Evaluation of genotyping efficacy through both in silico and in vitro PCR demonstrates successful differentiation of fungal species from eight countries across four continents. This database has the potential to accelerate fungal genomic research in various fields.
Article
Genetics & Heredity
Da Eun Nam, Min Ju Cha, Yae Dam Kim, Manisha Awasthi, Yuno Do, Sam-Geun Kong, Ki Wha Chung
Summary: This study aimed to determine the cultivar-specific combined genotypes (CGs) of short sequence repeats (SSRs) in C. goeringii. More than 4000 samples from 67 cultivars were collected and the genotypes of 12 SSRs were determined. The study found that approximately 30% of C. goeringii may not be genuine cultivars.
Article
Plant Sciences
Ambika Baldev Gaikwad, Ratna Kumari, Sheel Yadav, Parimalan Rangan, Dhammaprakash Pandhari Wankhede, K. V. Bhat
Summary: Small cardamom, the third most expensive spice in the world, has a high genetic potential that has not been fully utilized. In this study, the draft whole genome sequence of cardamom variety Njallani Green Gold was reported. The genome displayed a high repeat content and various gene family expansions and contractions. SSR markers were identified and used for diversity analysis, revealing a high degree of admixtures in the cardamom population. The SSR loci information has been developed into a public database for the cardamom community.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Education, Scientific Disciplines
Hai-feng Tian, Qiao-mu Hu, Zhong Li
Summary: The study characterized SSRs in the assembled genome of M. albus and developed polymorphic SSRs for future breeding programs. High genetic diversity but excess of homozygotes were found in one breeding population, providing baseline information for future breeding programs. The SSR markers will be useful for genetic mapping and diversity analysis studies in swamp eel.
Article
Agronomy
Cristina Isabel Fernandez-Otero, Ana Maria Ramos-Cabrer, Julio Enrique Lopez-Diaz, Santiago Pereira-Lorenzo
Summary: The CIAM-AGACAL research center has been conserving the phytogenetic resources of grassland species from northwest Spain, with a focus on red clover, one of the most cultivated forage legumes in the world. The study evaluated the diversity among cultivars and natural clover populations at morphological and molecular level, revealing intra-specific variability and moderate genetic differentiation among Spanish red clover cultivars. Additionally, a certain relationship between phenotypic and genotypic variation was detected.
Article
Biology
Khandakar Abu Md Mostafizar Rahman, Abdul Shukor Juraimi, Md Rezwan Molla, Muhammad Asyraf Md Hatta, Zulkefly BIN Sulaiman, Shamima Sultana, Ahmed Gaber, Benukar Biswas, Akbar Hossain
Summary: This study conducted genetic diversity analysis of sweet potato germplasms using microsatellite DNA markers. The results showed that sweet potato germplasms have a broad genetic base and demonstrated a high level of genetic relationships and polymorphism. These findings are significant for germplasm management, improvement of breeding strategies, and the development of new cultivars.
Article
Biodiversity Conservation
Jacopo Calevo, Roberta Gargiulo, Leif Bersweden, Juan Viruel, Cristina Gonzalez-Montelongo, Khellaf Rebbas, Lamia Boutabia, Michael F. Fay
Summary: Orchis patens sensu lato is a threatened species with complex population structure, exhibiting significant genetic differentiation between Italy, Algeria, and the Canary Islands, highlighting the need for immediate conservation actions to prevent further fragmentation and decline.
BIODIVERSITY AND CONSERVATION
(2021)
Article
Biology
Sonu Kumar, Ashutosh Singh, Asheesh Shanker
Summary: Microsatellites, also known as simple sequence repeats, are repetitive tracts in a DNA sequence that play key roles in species identification and phylogeny. The pSATdb database has been developed to provide comprehensive information on length variation of mitochondrial microsatellites across different genera. The identified microsatellites stored in pSATdb will be useful in various genomics studies.
LIFE SCIENCE ALLIANCE
(2022)
Article
Parasitology
Laura Soresinetti, Irene Arnoldi, Agata Negri, Giovanni Naro, Alice Michelutti, Fabrizio Montarsi, Andrea Mosca, Claudio Bandi, Paolo Gabrieli, Sara Epis
Summary: The study identified 11 polymorphic microsatellite markers in the invasive mosquito species Ae. koreicus in Italy, which could be used to investigate the genetic structure and invasion routes of this species in Europe and other non-native areas.
PARASITES & VECTORS
(2023)
Article
Forestry
Farooq Ahmad, Sanja Baric
Summary: This study identified the population structure of C. parasitica causing chestnut blight in the northern Italian region of South Tyrol using multilocus microsatellite markers, revealing high genetic diversity and regional sexual reproduction and introduction events.
Article
Biotechnology & Applied Microbiology
Rezwanuzzaman Laskar, Md Gulam Jilani, Safdar Ali
Summary: The analysis of SSRs in 98 genomes from four genera of the Polyomaviridae family revealed a high prevalence of mono-nucleotide repeats, with T and A being the most common motifs. The distribution of SSRs was mainly in the coding region, especially in the Large T Antigen gene. Viruses with humans and related species as hosts showed a distinct SSR pattern in the AT region, suggesting a predictive marker for host determination during viral evolution.
Article
Genetics & Heredity
Naveen Duhan, Simardeep Kaur, Rakesh Kaundal
Summary: ranchSATdb is a web resource that contains 15,520,263 putative SSR markers, providing a comprehensive tool for marker selection, visualization, and similarity analysis. Users can browse SSRs by various criteria, retrieve nucleotide sequences, generate custom primers, and validate them. The database also includes a SSR prediction pipeline called miSATminer and regularly adds new species.
Article
Biochemistry & Molecular Biology
Steven M. Mussmann, Alexis S. Harrison, Wade D. Wilson
Summary: A total of 21 novel microsatellite loci were identified and used to assess the population genetic parameters of the endangered Gila topminnow and prioritize conservation efforts.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Sajjad Asaf, Waqar Ahmad, Ahmed Al-Harrasi, Abdul Latif Khan
Summary: The study sequenced and analyzed the complete chloroplast genome of Ziziphus hajarensis, revealing its genetic features and providing insights into its evolution and phylogenetic position among Rhamnaceae species.
Article
Biochemistry & Molecular Biology
Luxian Liu, Shook Ling Low, Shota Sakaguchi, Yu Feng, Binjie Ge, Kamil Konowalik, Pan Li
Summary: In this study, polymorphic cpSSRs and nSSRs markers for Crossostephium chinense were developed using genome skimming sequencing. These genomic resources have the potential for population genetics and conservation studies in C. chinense and related species like Artemisia.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.