Article
Genetics & Heredity
Chi Zhang, Kun Zhang, Ying Peng, Jianshe Zhou, Yifan Liu, Bingjian Liu
Summary: The complete mitochondrial genomes of three Garra species were studied, along with the mechanisms of rearrangements that occur in their genomes. It was found that these species had rearranged mitochondrial genomes compared to other fish, possibly through a process of replication and loss. These findings provide a foundation for future phylogenetic studies.
FRONTIERS IN GENETICS
(2022)
Article
Veterinary Sciences
Osman Furkan Urhan, Ufuk Erol, Kursat Altay
Summary: This study aimed to assess the prevalence, distribution, and phylogeny of T.vitulorum in water buffaloes in Sivas, Turkey. The results showed a high infection rate of T.vitulorum, especially in calves aged 0-6 months. Molecular analysis also revealed a high similarity between the DNA sequences of T.vitulorum isolates from this study and those in GenBank. These findings provide important insights into the life cycle and epidemiology of the parasite.
RESEARCH IN VETERINARY SCIENCE
(2023)
Article
Genetics & Heredity
Olga Koshkina, Tatiana Deniskova, Arsen Dotsev, Elisabeth Kunz, Marina Selionova, Ivica Medugorac, Natalia Zinovieva
Summary: Russia has a rich variety of local sheep breeds, but their genetic diversity and maternal origin have not been thoroughly investigated. This study analyzes the mitochondrial genomes of Russian sheep breeds from different regions, revealing their diversity and phylogeny.
Article
Agriculture, Dairy & Animal Science
Sihua Jin, Jingjing Xia, Fumin Jia, Lijun Jiang, Xin Wang, Xuling Liu, Xing Liu, Zhaoyu Geng
Summary: Characterization of the complete mitochondrial genome of Pingpu Yellow chicken revealed high genetic diversity and potentially three maternal lineages, indicating the breed's close relation to Luhua and Nandan chickens.
Article
Agriculture, Dairy & Animal Science
Hang Wang, Qian Wen, Tongfei Wang, Fanrong Ran, Meng Wang, Xulei Fan, Shujun Wei, Zhonghu Li, Jiangli Tan
Summary: This study describes the mtgenomes of four wasps and provides new evidence for the two-origin hypothesis of eusociality in the Vespidae. The results contribute to the understanding of species evolution and phylogeny in the family Vespidae.
Article
Biochemistry & Molecular Biology
Alexandros Heraclides, Eva Fernandez-Dominguez
Summary: This study evaluates the use of two tools (ANGSD and schmutzi) for reconstructing high-quality ancient mitogenomes from ancient human genomic data. The results show that filtering improves mtDNA consensus calling and haplogroup prediction accuracy. The study also finds a strong correlation between the number of sequence reads and bases and overall sample quality.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Ebubekir Dirican, Seyda Tuba Savrun, Ismail Erkan Aydin, Gonca Gulbay, Ulku Karaman
Summary: This study investigates mutations in the CYB and ATPase-6 genes of mtDNA in COVID-19 patients and explores the association between these mutations and clinical outcomes.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Virology
Reimar Johne, Simon H. Tausch, Rainer G. Ulrich, Katja Schilling-Loeffler
Summary: Rotaviruses are responsible for diarrhea in humans and animals. A new strain, RVK, was identified in common shrews in Germany and was found to be a separate species with low sequence identity to other rotavirus reference strains. Phylogenetic analysis showed that RVK and RVC formed a common branch within the RVA-like phylogenetic clade. Comparison of nucleotide sequences of other RVK strains from common shrews in Germany indicated high sequence variability within the putative species. RVK represents a novel rotavirus species closely related to RVC.
Article
Genetics & Heredity
Xu Wang, Hao Zhang, Ian Kitching, Zhen-Bang Xu, Yi-Xin Huang
Summary: This study analyzed the mitochondrial genomes of Sphingidae to investigate the phylogenetic relationships and genomic differences among different subfamilies within this moth family. The results supported the monophyly of all four recognized subfamilies and suggested a revised placement of Langiinae within the family.
Article
Biochemical Research Methods
Lang Zhou, Tingze Feng, Shuangbin Xu, Fangluan Gao, Tommy T. Lam, Qianwen Wang, Tianzhi Wu, Huina Huang, Li Zhan, Lin Li, Yi Guan, Zehan Dai, Guangchuang Yu
Summary: The identification of conserved and variable regions in multiple sequence alignment is crucial for accelerating gene function understanding. ggmsa, an R package, provides various display methods to mine comprehensive sequence features, supports correlation analysis, and offers a new visualization method for genome alignment, aiding researchers in discovering MSA patterns and making decisions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Yang Young Lu, Jiaxing Bai, Yiwen Wang, Ying Wang, Fengzhu Sun
Summary: CRAFT is a search engine for genomic and metagenomic data that allows for fast comparison of DNA sequences in massive sequence repositories while mapping the data into a smaller embedding space to save storage space. By compressing the data, CRAFT is able to perform queries in seconds or minutes, achieving comparable performance to six state-of-the-art alignment-free measures.
Article
Biology
Nicola Zadra, Annapaola Rizzoli, Omar Rota-Stabelli
Summary: The study reveals a strong incongruence between nuclear and mitochondrial markers in the phylogeny of Aedini mosquitoes, suggesting potential evolutionary events or hybridization history as explanations. The findings may guide future research in phylogenomic studies of Aedini mosquitoes.
Article
Biodiversity Conservation
Tulio F. Villalobos-Guerrero, Jyothi Kara, Carol Simon, Izwandy Idris
Summary: This study conducted a thorough taxonomic review of the genus Neanthes in southern Africa, revealing previous misidentifications and errors in descriptions. Further evaluation is needed to determine the taxonomic status of the Neanthes species in the region.
MARINE BIODIVERSITY
(2022)
Article
Forestry
Xue-Jiao Zhang, Kang-Jia Liu, Ya-Chao Wang, Jian He, Yuan-Mi Wu, Zhi-Xiang Zhang
Summary: High genetic diversity and low differentiation in Salix present challenges in taxonomy and systematics. The chloroplast genomes of three shrubby willows were sequenced and analyzed, revealing high similarity among them. Phylogenetic analysis placed these willows in specific clades, providing insights into the evolutionary history of Salicaceae.
Article
Forestry
Huijuan Zhou, Xiaoxiao Gao, Keith Woeste, Peng Zhao, Shuoxin Zhang
Summary: Chloroplast (cp) DNA genomes of Castanea species show similar genomic structures with differences in gene loss and pseudogenization in certain genes. These findings contribute to a better understanding of the evolutionary history and phylogenetic relationships of chestnut species.
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.