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Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera) BMC Genet. (IF 2.9) Pub Date : 2024-03-15 Darun Naim, Asif Ahsan, Ahmed Imtiaj, Nurul Haque Mollah
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Transcriptome analysis reveals regulatory mechanisms of different drought-tolerant Gleditsia sinensis seedlings under drought stress BMC Genet. (IF 2.9) Pub Date : 2024-03-13 Fuhua Liu, Yang Zhao, Xiurong Wang, Biao Wang, Feng Xiao, Kequan He
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ONT read assembly of the black rhino genome BMC Genet. (IF 2.9) Pub Date : 2024-03-05 Ken Kraaijeveld, Koen Bossers, Nikola Petrusevski, Stef Pieterman, Linda G.R. Bruins-van Sonsbeek, Floyd Wittink
The black rhinoceros (Diceros bicornis) is an endangered mammal for which a captive breeding program is part of the conservation effort. Black rhinos in zoo’s often suffer from chronic infections and heamochromatosis. Furthermore, breeding is hampered by low male fertility. To aid a research project studying these topics, we sequenced and assembled the genome of a captive male black rhino using ONT
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De novo genome assembly of a high-protein soybean variety HJ117 BMC Genet. (IF 2.9) Pub Date : 2024-03-04 Zhi Liu, Qing Yang, Bingqiang Liu, Chenhui Li, Xiaolei Shi, Yu Wei, Yuefeng Guan, Chunyan Yang, Mengchen Zhang, Long Yan
Soybean is an important feed and oil crop in the world due to its high protein and oil content. China has a collection of more than 43,000 soybean germplasm resources, which provides a rich genetic diversity for soybean breeding. However, the rich genetic diversity poses great challenges to the genetic improvement of soybean. This study reports on the de novo genome assembly of HJ117, a soybean variety
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Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant BMC Genet. (IF 2.9) Pub Date : 2024-03-04 Lin-Fang Wu, Wei-Guang Zhu, En-Ping Yu, Hong-Lin Cao, Zheng-Feng Wang
Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant,
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Genome-wide identification and characterization of flowering genes in Citrus sinensis (L.) Osbeck: a comparison among C. Medica L., C. Reticulata Blanco, C. Grandis (L.) Osbeck and C. Clementina BMC Genet. (IF 2.9) Pub Date : 2024-02-20 Harleen Kaur, Pooja Manchanda, Gurupkar S. Sidhu, Parveen Chhuneja
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Differential lung gene expression changes in C57BL/6 and DBA/2 mice carrying an identical functional Mx1 gene reveals crucial differences in the host response BMC Genet. (IF 2.9) Pub Date : 2024-02-15 Silke Bergmann, Linda Brunotte, Klaus Schughart
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Whole genome sequence of Vibrio cholerae NB-183 isolated from freshwater in Ontario, Canada harbors a unique gene repertoire BMC Genet. (IF 2.9) Pub Date : 2024-02-15 Opeyemi U. Lawal, Noah Bryan, Mitra Soni, Yanhong Chen, Melinda Precious, Valeria R. Parreira, Lawrence Goodridge
Vibrio cholerae is an enteric pathogen that poses a significant threat to global health. It causes severe dehydrating diarrheal disease cholera in humans. V. cholerae could be acquired either from consuming contaminated seafood or direct contact with polluted waters. As part of a larger program that assesses the microbial community profile in aquatic systems, V. cholerae strain NB-183 was isolated
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Comparative analysis and characterization of the chloroplast genome of Krascheninnikovia ceratoides (Amarathaceae): a xerophytic semi-shrub exhibiting drought resistance and high-quality traits BMC Genet. (IF 2.9) Pub Date : 2024-01-29 Yuping Liu, Changyuan Zheng, Xu Su, Jinyuan Chen, Xiaoli Li, Chenglin Sun, Mir Muhammad Nizamani
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An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform BMC Genet. (IF 2.9) Pub Date : 2024-01-22 A.K. Larin, K.M. Klimina, V.A. Veselovsky, E.I. Olekhnovich, M.D. Morozov, D.I. Boldyreva, R.A. Yunes, A.I. Manolov, D.E. Fedorov, A.V. Pavlenko, Y.S. Galeeva, E.V. Starikova, E.N. Ilina
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Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina BMC Genet. (IF 2.9) Pub Date : 2024-01-13 Kun Zhang, Yiheng Wang, Yue Zhang, Xiaofei Shan
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Association between human blood metabolome and the risk of hypertension BMC Genet. (IF 2.9) Pub Date : 2023-12-15 Nannan Dai, Yujuan Deng, Baishi Wang
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Draft genome of Castanopsis chinensis, a dominant species safeguarding biodiversity in subtropical broadleaved evergreen forests BMC Genet. (IF 2.9) Pub Date : 2023-12-14 Pan Chen, Ju-Yu Lian, Bin Wu, Hong-Lin Cao, Zhi-Hong Li, Zheng-Feng Wang
Castanopsis is the third largest genus in the Fagaceae family and is essentially tropical or subtropical in origin. The species in this genus are mainly canopy-dominant trees, and the key components of evergreen broadleaved forests play a crucial role in the maintenance of local biodiversity. Castanopsis chinensis, distributed from South China to Vietnam, is a representative species. It currently suffers
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Diverse WGBS profiles of longissimus dorsi muscle in Hainan black goats and hybrid goats BMC Genet. (IF 2.9) Pub Date : 2023-12-14 Yuwei Ren, Xing Chen, Xinli Zheng, Feng Wang, Ruiping Sun, Limin Wei, Yan Zhang, Hailong Liu, Yanning Lin, Lingling Hong, Xiaoxian Huang, Zhe Chao
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Association between MC1R gene and coat color segregation in Shanxia long black pig and Lulai black pig BMC Genet. (IF 2.9) Pub Date : 2023-11-30 Hao Zheng, San-ya Xiong, Shi-jun Xiao, Ze-kai Zhang, Jin-min Tu, Deng-shuai Cui, Nai-biao Yu, Zhi-yong Huang, Long-yun Li, Yuan-mei Guo
Coat color, as a distinct phenotypic characteristic of pigs, is often subject to preference and selection, such as in the breeding process of new breed. Shanxia long black pig was derived from an intercross between Berkshire boars and Licha black pig sows, and it was bred as a paternal strain with high-quality meat and black coat color. Although the coat color was black in the F1 generation of the
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Genome assembly of Erythrophleum Fordii, a special “ironwood” tree in China BMC Genet. (IF 2.9) Pub Date : 2023-11-28 Chang-Yu Wen, Ju-Yu Lian, Wei-Xiong Peng, Zheng-Feng Wang, Zhi-Gang Yang, Hong-Lin Cao
Erythrophleum is a genus in the Fabaceae family. The genus contains only about 10 species, and it is best known for its hardwood and medical properties worldwide. Erythrophleum fordii Oliv. is the only species of this genus distributed in China. It has superior wood and can be used in folk medicine, which leads to its overexploitation in the wild. For its effective conservation and elucidation of the
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Identification of genetic associations and functional SNPs of bovine KLF6 gene on milk production traits in Chinese holstein BMC Genet. (IF 2.9) Pub Date : 2023-11-28 Yanan Liu, Bo Han, Weijie Zheng, Peng Peng, Chendong Yang, Guie Jiang, Yabin Ma, Jianming Li, Junqing Ni, Dongxiao Sun
Our previous research identified the Kruppel like factor 6 (KLF6) gene as a prospective candidate for milk production traits in dairy cattle. The expression of KLF6 in the livers of Holstein cows during the peak of lactation was significantly higher than that during the dry and early lactation periods. Notably, it plays an essential role in activating peroxisome proliferator-activated receptor α (PPARα)
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Probable human origin of the SARS-CoV-2 polybasic furin cleavage motif BMC Genet. (IF 2.9) Pub Date : 2023-11-21 Antonio R. Romeu
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Can polygenic risk scores help explain disease prevalence differences around the world? A worldwide investigation BMC Genet. (IF 2.9) Pub Date : 2023-11-20 Pritesh R. Jain, Myson Burch, Melanie Martinez, Pablo Mir, Jakub P. Fichna, Cezary Zekanowski, Renata Rizzo, Zeynep Tümer, Csaba Barta, Evangelia Yannaki, John Stamatoyannopoulos, Petros Drineas, Peristera Paschou
Complex disorders are caused by a combination of genetic, environmental and lifestyle factors, and their prevalence can vary greatly across different populations. The extent to which genetic risk, as identified by Genome Wide Association Study (GWAS), correlates to disease prevalence in different populations has not been investigated systematically. Here, we studied 14 different complex disorders and
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Transcriptomic monitoring of Douglas-fir heartwood formation BMC Genet. (IF 2.9) Pub Date : 2023-11-20 Didier Delourme, Laure Brémaud, Idelette Plazanet, Patrick Pélissier, Philippe Label, Nathalie Boizot, Christian Breton, Stéphanie Durand, Guy Costa
Molecular cues linked to heartwood formation open new (complementary) perspectives to genetic breeding programs of Douglas-fir, a tree species largely cultivated in Europe for the natural durability and civil engineering properties of its wood. RNAs from a single genotype of Douglas-fir, extracted from three distinct wood zones (outer sapwood, inner sapwood and transition zone) at four vegetative seasons
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SARS-CoV-2 helicase might interfere with cellular nonsense-mediated RNA decay: insights from a bioinformatics study BMC Genet. (IF 2.9) Pub Date : 2023-11-18 Behnia Akbari, Ehsan Ahmadi, Mohammad Reza Zabihi, Mina Roshan Zamir, Mina Sadeghi Shaker, Farshid Noorbakhsh
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Exploring the key genomic variation in monkeypox virus during the 2022 outbreak BMC Genet. (IF 2.9) Pub Date : 2023-11-16 Jie Zhu, Jian Yu, Hao Qin, Xinlei Chen, Chuanchang Wu, Xiaodan Hong, Yafei Zhang, Zhenhua Zhang
In 2022, a global outbreak of monkeypox occurred with a significant shift in its epidemiological characteristics. The monkeypox virus (MPXV) belongs to the B.1 lineage, and its genomic variations that were linked to the outbreak were investigated in this study. Previous studies have suggested that viral genomic variation plays a crucial role in the pathogenicity and transmissibility of viruses. Therefore
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Genome wide identification, structural characterization and phylogenetic analysis of High-Affinity potassium (HAK) ion transporters in common bean (Phaseolus vulgaris L.) BMC Genet. (IF 2.9) Pub Date : 2023-11-14 Afrasyab Khan, Zamarud Shah, Sajid Ali, Nisar Ahmad, Maaz Iqbal, Arif Ullah, Firdous Ayub
High-Affinity Potassium ions represent one of the most important and large group of potassium transporters. Although HAK genes have been studied in a variety of plant species, yet, remain unexplored in common bean. In the current study, 20 HAK genes were identified in common bean genome. Super-family “K_trans” domain was found in all PvHAK genes. Signals for localization of PvHAK proteins were detected
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Molecular characterization and phylogenetic analysis of the first Corynebacterium rouxii strains isolated in Brazil: a recent member of Corynebacterium diphtheriae complex BMC Genet. (IF 2.9) Pub Date : 2023-11-08 Juliana Nunes Ramos, Max Roberto Batista Araújo, Paulo Victor Pereira Baio, Lincoln Oliveira Sant’Anna, João Flávio Carneiro Veras, Érica Miranda Damásio Vieira, Mireille Ângela Bernardes Sousa, Carlos Henrique Camargo, Cláudio Tavares Sacchi, Karoline Rodrigues Campos, Marlon Benedito Nascimento Santos, Sérgio Bokermann, Luige Biciati Alvim, Louisy Sanches dos Santos, Ana Luiza de Mattos-Guaraldi
Corynebacterium diphtheriae complex was formed by the species C. diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis in the recent past. In addition to C. diphtheriae, C. ulcerans and C. pseudotuberculosis species can carry the tox gene, which encodes diphtheria toxin. Currently, three new species have been included in the complex: Corynebacterium rouxii, Corynebacterium silvaticum
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Identification of transcriptionally active transposons in Barley BMC Genet. (IF 2.9) Pub Date : 2023-11-04 Dongying Gao, Emma Fox-Fogle
The genomes of many major crops including barley (Hordeum vulgare) consist of numerous transposons. Despite their important roles in crop genome evolution and morphological variations, most of these elements are silent or truncated and unable to be mobile in host genomes. Thus far, only a very limited number of active transposons were identified in plants. We analyzed the barley full-length cDNA (FLcDNA)
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Genome sequence resource for “Candidatus Liberibacter asiaticus” strain GDCZ from a historical HLB endemic region in China BMC Genet. (IF 2.9) Pub Date : 2023-11-04 Yongqin Zheng, Yun Li, Pengbin Xu, Chaoji Liu, Jianchi Chen, Xiaoling Deng, Zheng Zheng
“Candidatus Liberibacter asiaticus” (CLas) is an un-culturable α-proteobacterium that caused citrus Huanglongbing (HLB), a destructive disease threatening citrus production worldwide. In China, the presence of HLB was first reported in Chaoshan region of Guangdong province, China around a century ago. Thus, whole genome information of CLas strains from Chaoshan area become the most important resource
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Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding BMC Genet. (IF 2.9) Pub Date : 2023-11-03 Yanlin An, Xiaobo Xia, Huayan Zheng, Shirui Yu, Tingting Jing, Feng Zhang
As an important food and cash crop, identification of DNA molecular markers is of great significance for molecular marker-assisted breeding of Sorghum (Sorghum bicolor (L.) moench). Although some sorghum-related mutation databases have been published, the special SSR and SV databases still need to be constructed and updated. In this study, the quality of 18 different sorghum genomes was evaluated,
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3-D chromatin conformation, accessibility, and gene expression profiling of triple-negative breast cancer BMC Genet. (IF 2.9) Pub Date : 2023-11-02 Pere Llinàs-Arias, Miquel Ensenyat-Méndez, Javier I. J. Orozco, Sandra Íñiguez-Muñoz, Betsy Valdez, Chuan Wang, Anja Mezger, Eunkyoung Choi, Yan Zhou Tran, Liqun Yao, Franziska Bonath, Remi-André Olsen, Mattias Ormestad, Manel Esteller, Mathieu Lupien, Diego M. Marzese
Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype with limited treatment options. Unlike other breast cancer subtypes, the scarcity of specific therapies and greater frequencies of distant metastases contribute to its aggressiveness. We aimed to find epigenetic changes that aid in the understanding of the dissemination process of these cancers. Using CRISPR/Cas9, our
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Identification of genetic variants associated with anterior cruciate ligament rupture and AKC standard coat color in the Labrador Retriever BMC Genet. (IF 2.9) Pub Date : 2023-10-26 BT Lee, LA Baker, M Momen, H Terhaar, EE Binversie, SJ Sample, Peter Muir
Canine anterior cruciate ligament (ACL) rupture is a common complex disease. Prevalence of ACL rupture is breed dependent. In an epidemiological study, yellow coat color was associated with increased risk of ACL rupture in the Labrador Retriever. ACL rupture risk variants may be linked to coat color through genetic selection or through linkage with coat color genes. To investigate these associations
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Correlation study of malignant lymphoma and breast Cancer in different gender European populations: mendelian randomization analysis BMC Genet. (IF 2.9) Pub Date : 2023-10-09 Xiong Chen, GuoHuang Hu
Previous research has already indicated an elevated risk of breast cancer (BC) among survivors of malignant lymphoma, but the underlying reasons remain unknown. Our objective is to elucidate the causal relationship between malignant lymphoma and BC through Mendelian randomization (MR). Genome-wide association studies (GWAS) data from 181,125 Hodgkin lymphoma (HL) patients and 181,289 non-Hodgkin lymphoma
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Genome-wide identification, comparative analysis and functional roles in flavonoid biosynthesis of cytochrome P450 superfamily in pear (Pyrus spp.) BMC Genet. (IF 2.9) Pub Date : 2023-10-03 Wei Zhang, Hongxiang Li, Qionghou Li, Zewen Wang, Weiwei Zeng, Hao Yin, Kaijie Qi, Ying Zou, Jian Hu, Baisha Huang, Peng Gu, Xin Qiao, Shaoling Zhang
The cytochrome P450 (CYP) superfamily is the largest enzyme metabolism family in plants identified to date, and it is involved in many biological processes, including secondary metabolite biosynthesis, hormone metabolism and stress resistance. However, the P450 gene superfamily has not been well studied in pear (Pyrus spp.). Here, the comprehensive identification and a comparative analysis of P450
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Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids BMC Genet. (IF 2.9) Pub Date : 2023-09-27 Abdoul-Raouf Sayadi Maazou, Melaku Gedil, Victor O. Adetimirin, Nnanna Unachukwu, Wende Mengesha, Silvestro Meseka, Abebe Menkir
The establishment of heterotic groups of inbred lines is crucial for hybrid maize breeding programs. Currently, there is no information on the heterotic patterns of the Provitamin A (PVA) inbred lines developed in the maize improvement program of the International Institute of Tropical Agriculture (IITA) to form productive PVA enriched hybrids for areas affected by vitamin A deficiency. This study
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Exploring the association between COVID-19 and male genital cancer risk in European population: evidence from mendelian randomization analysis BMC Genet. (IF 2.9) Pub Date : 2023-09-26 Dejie Wang, Yingjuan Ma, Lin Yan, Wei Gan, Yugang Han, Jiang-Shan Tan, Wenhua Zhao
Recently accumulated evidence indicates a potential association between COVID-19 and elevated susceptibility to cancer, including male genital cancer. However, the causal nature of this relationship remains unclear. In this Mendelian randomization (MR) study, we investigated the potential causal relationship between COVID-19 and male genital cancer using genetic variants as instrumental variables.
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Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa) BMC Genet. (IF 2.9) Pub Date : 2023-09-21 Gaixia Yang, Shijie Wang, Lianxiang Long, Xiaoyue Yu, Hongyu Cai, Pengyun Chen, Lijiao Gu, Minsheng Yang
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A bioinformatics screen reveals hox and chromatin remodeling factors at the Drosophila histone locus BMC Genet. (IF 2.9) Pub Date : 2023-09-21 Lauren J. Hodkinson, Connor Smith, H. Skye Comstra, Bukola A. Ajani, Eric H. Albanese, Kawsar Arsalan, Alvaro Perez Daisson, Katherine B. Forrest, Elijah H. Fox, Matthew R. Guerette, Samia Khan, Madeleine P. Koenig, Shivani Lam, Ava S. Lewandowski, Lauren J. Mahoney, Nasserallah Manai, JonCarlo Miglay, Blake A. Miller, Olivia Milloway, Nhi Ngo, Vu D. Ngo, Nicole F. Oey, Tanya A. Punjani, HaoMin SiMa
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Genome sequencing-based transcriptomic analysis reveals novel genes in Peucedanum praeruptorum BMC Genet. (IF 2.9) Pub Date : 2023-09-18 Cheng Song, Yingyu Zhang, Yunpeng Zhang, Shanyong Yi, Haoyu Pan, Ranran Liao, Yuanyuan Wang, Bangxing Han
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Overestimated prediction using polygenic prediction derived from summary statistics BMC Genet. (IF 2.9) Pub Date : 2023-09-14 David Keetae Park, Mingshen Chen, Seungsoo Kim, Yoonjung Yoonie Joo, Rebekah K. Loving, Hyoung Seop Kim, Jiook Cha, Shinjae Yoo, Jong Hun Kim
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Comparative analysis of microbial community structure in different times of Panax ginseng Rhizosphere microbiome and soil properties under larch forest BMC Genet. (IF 2.9) Pub Date : 2023-09-14 Tong Aizi, Liu Lijuan, Liu Lihua, Liu Wei, Qin Jiamei
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Gene-based burden scores identify rare variant associations for 28 blood biomarkers BMC Genet. (IF 2.9) Pub Date : 2023-09-04 Rana Aldisi, Emadeldin Hassanin, Sugirthan Sivalingam, Andreas Buness, Hannah Klinkhammer, Andreas Mayr, Holger Fröhlich, Peter Krawitz, Carlo Maj
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Complete genome sequences of Providencia bacteriophages PibeRecoleta, Stilesk and PatoteraRojo BMC Genet. (IF 2.9) Pub Date : 2023-09-01 Steven Batinovic, Hiu Tat Chan, Jason Stiles, Steve Petrovski
Providencia is a genus of gram-negative bacteria within the order Enterobacterales, closely related to Proteus and Morganella. While ubiquitous in the environment, some species of Providencia, such as P. rettgeri and P. stuartii, are considered emerging nosocomial pathogens and have been implicated in urinary tract infection, gastrointestinal illness, and travelers’ diarrhea. Given their intrinsic
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Relationship between DNA methylation changes and skeletal muscle mass BMC Genet. (IF 2.9) Pub Date : 2023-08-31 Jeong-An Gim, Sang-Yeob Lee, Seung Chan Kim, Kyung-Wan Baek, Sung Hyo Seo, Jun-Il Yoo
Sarcopenia is a disease diagnosed in the elderly. In patients with sarcopenia, the muscle mass decreases every year. The occurrence of sarcopenia is greatly affected by extrinsic factors such as eating habits, exercise, and lifestyle. The present study aimed to determine the relationship between muscle mass traits and genes affected by epigenetic factors with three different adjustment methods using
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Genetic screening in a Brazilian cohort with inborn errors of immunity BMC Genet. (IF 2.9) Pub Date : 2023-08-17 Cristina Santos Ferreira, Ronaldo da Silva Francisco Junior, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimarães, Flavia Amendola Anisio de Carvalho, Bárbara Carvalho Santos dos Reis, Fernanda Pinto-Mariz, Monica Soares de Souza, Zilton Farias Meira de Vasconcelos, Ekaterini Simões Goudouris, Ana Tereza Ribeiro Vasconcelos
Inherited genetic defects in immune system-related genes can result in Inborn Errors of Immunity (IEI), also known as Primary Immunodeficiencies (PID). Diagnosis of IEI disorders is challenging due to overlapping clinical manifestations. Accurate identification of disease-causing germline variants is crucial for appropriate treatment, prognosis, and genetic counseling. However, genetic sequencing is
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Extant thrips diverged in the early tertiary period BMC Genet. (IF 2.9) Pub Date : 2023-08-16 Chunying Wu, Hongrui Zhang
Thysanoptera, commonly known as thrips, are diverse tiny insects whose earliest fossil record dates back to the Triassic period. Since there are few studies on the divergence time of taxa under Thysanoptera, this study used 13 mitochondrial coding protein genes to reconstruct the phylogenetic tree with divergence time of 26 species of this order and show a reliable phylogenetic relationship of thrips
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Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus BMC Genet. (IF 2.9) Pub Date : 2023-08-12 Xue Ding, Yifei Zhang, Die Li, Jia Xu, Chang Wu, Xiaojuan Cui, Yuandong Sun
Distant hybridization is an important breeding technique for creating new strains with superior traits by integrating two different genomes. Successful hybridization of Megalobrama amblycephala (Blunt snout bream, BSB, 2n = 48) and Culter alburnus (Topmouth culter, TC, 2n = 48) was achieved to establish hybrid lineages (BT and TB), which provide valuable materials for exploring the mechanisms of distant
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Comprehensive analysis of m6A regulators and relationship with tumor microenvironment, immunotherapy strategies in colorectal adenocarcinoma BMC Genet. (IF 2.9) Pub Date : 2023-08-11 Jian Ji, Shichao Liu, Yongyuan Liang, Guixi Zheng
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Transcriptome analysis during vernalization in wheat (Triticum aestivum L.) BMC Genet. (IF 2.9) Pub Date : 2023-08-10 Jiao Wang, Lei Sun, Hongwei Zhang, Bo Jiao, Haibo Wang, Shuo Zhou
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An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea BMC Genet. (IF 2.9) Pub Date : 2023-08-09 Yaqi Li, Xiang Hu, Mingkun Xiao, Jiaxiong Huang, Yuqiang Lou, Faguang Hu, Xingfei Fu, Yanan Li, Hongyan He, Jinhuan Cheng
The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural
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A novel SNP in NKX1-2 gene is associated with carcass traits in Dezhou donkey BMC Genet. (IF 2.9) Pub Date : 2023-08-07 Xinrui Wang, Tianqi Wang, Huili Liang, Liyuan Wang, Faheem Akhtar, Xiaoyuan Shi, Wei Ren, Bingjian Huang, Xiyan Kou, Yinghui Chen, Yandong Zhan, Changfa Wang
At present, donkey meat in the market shows an imbalance between supply and demand, and there is an urgent need to cultivate a meat-type Dezhou donkey breed. On the one hand, it can improve the imbalance in the market, and on the other hand, it can promote the rapid development of the donkey industry. This study aimed to reveal significant genetic variation in the NK1 homeobox 2 gene (NKX1-2) of Dezhou
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Transcriptomic comparison of bone marrow CD34 + cells and peripheral blood neutrophils from ET patients with JAK2 or CALR mutations BMC Genet. (IF 2.9) Pub Date : 2023-08-07 Ana Guijarro-Hernández, José Luis Vizmanos
Essential thrombocythemia (ET) is one of the most common types of Ph-negative myeloproliferative neoplasms, an infrequent group of blood cancers that arise from a CD34 + hematopoietic stem cell (HSC) in the bone marrow (BM) primarily due to driver mutations in JAK2, CALR or MPL. These aberrations result in an overproduction of mature myeloid cells in peripheral blood (PB). To date, no targeted therapies
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The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese holstein cattle BMC Genet. (IF 2.9) Pub Date : 2023-08-07 Xiao Wang, Yahui Gao, Cong-jun Li, Lingzhao Fang, George E. Liu, Xiuxin Zhao, Yuanpei Zhang, Gaozhan Cai, Guanghui Xue, Yan Liu, Lingling Wang, Fan Zhang, Kun Wang, Miao Zhang, Rongling Li, Yundong Gao, Jianbin Li
This study was performed in the frame of a more extensive study dedicated to the integrated analysis of the single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells (PBMCs) with a large-scale GWAS of 45 complex traits in Chinese Holstein cattle. Lipopolysaccharide (LPS) is a crucial mediator of chronic inflammation to modulate immune responses. PBMCs include
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Genetic dissection of root architectural plasticity and identification of candidate loci in response to drought stress in bread wheat BMC Genet. (IF 2.9) Pub Date : 2023-07-26 Nurealam Siddiqui, Melesech T. Gabi, Mohammad Kamruzzaman, Abebaw M. Ambaw, Tesfaye J. Teferi, Said Dadshani, Jens Léon, Agim Ballvora
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The G2-Like gene family in Populus trichocarpa: identification, evolution and expression profiles BMC Genet. (IF 2.9) Pub Date : 2023-07-05 Ruihua Wu, Lin Guo, Yueyang Guo, Lehang Ma, Kehang Xu, Boyu Zhang, Liang Du
The Golden2-like (GLK) transcription factors are plant-specific transcription factors (TFs) that perform extensive and significant roles in regulating chloroplast development. Here, genome-wide identification, classification, conserved motifs, cis-elements, chromosomal locations, evolution and expression patterns of the PtGLK genes in the woody model plant Populus trichocarpa were analyzed in detail
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Assessing whole-exome sequencing data from undiagnosed Brazilian patients to improve the diagnostic yield of inborn errors of immunity BMC Genet. (IF 2.9) Pub Date : 2023-06-30 Cristina Santos Ferreira, Ronaldo da Silva Francisco Junior, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimarães, Flávia Anisio Amendola, Fernanda Pinto-Mariz, Monica Soares de Souza, Patrícia Carvalho Batista Miranda, Zilton Farias Meira de Vasconcelos, Ekaterini Simões Goudouris, Ana Tereza Ribeiro Vasconcelos
Inborn error of immunity (IEI) comprises a broad group of inherited immunological disorders that usually display an overlap in many clinical manifestations challenging their diagnosis. The identification of disease-causing variants from whole-exome sequencing (WES) data comprises the gold-standard approach to ascertain IEI diagnosis. The efforts to increase the availability of clinically relevant genomic
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Pairwise comparative analysis of six haplotype assembly methods based on users’ experience BMC Genet. (IF 2.9) Pub Date : 2023-06-29 Shuying Sun, Flora Cheng, Daphne Han, Sarah Wei, Alice Zhong, Sherwin Massoudian, Alison B. Johnson
A haplotype is a set of DNA variants inherited together from one parent or chromosome. Haplotype information is useful for studying genetic variation and disease association. Haplotype assembly (HA) is a process of obtaining haplotypes using DNA sequencing data. Currently, there are many HA methods with their own strengths and weaknesses. This study focused on comparing six HA methods or algorithms:
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Association between SUMF1 polymorphisms and COVID-19 severity BMC Genet. (IF 2.9) Pub Date : 2023-06-21 Shaohui Liang, Huixia Gao, Tongxin He, Li Li, Xin Zhang, Lei Zhao, Jie Chen, Yanyan Xie, Jie Bao, Yong Gao, Erhei Dai, Yuling Wang
Evidence shows that genetic factors play important roles in the severity of coronavirus disease 2019 (COVID-19). Sulfatase modifying factor 1 (SUMF1) gene is involved in alveolar damage and systemic inflammatory response. Therefore, we speculate that it may play a key role in COVID-19. We found that rs794185 was significantly associated with COVID-19 severity in Chinese population, under the additive
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A multi-tissue gene expression dataset for hibernating brown bears BMC Genet. (IF 2.9) Pub Date : 2023-06-08 Blair W. Perry, Michael W. Saxton, Heiko T. Jansen, Corey R. Quackenbush, Brandon D. Evans Hutzenbiler, Charles T. Robbins, Joanna L. Kelley, Omar E. Cornejo
Complex physiological adaptations often involve the coordination of molecular responses across multiple tissues. Establishing transcriptomic resources for non-traditional model organisms with phenotypes of interest can provide a foundation for understanding the genomic basis of these phenotypes, and the degree to which these resemble, or contrast, those of traditional model organisms. Here, we present
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Correction: Processing genome-wide association studies within a repository of heterogeneous genomic datasets BMC Genet. (IF 2.9) Pub Date : 2023-06-05 Anna Bernasconi, Arif Canakoglu, Federico Comolli
BMC Genomic Data (2023) 24:13 https://doi.org/10.1186/s12863-023-01111-y Following publication of the original article [1], it was reported that the article entitled “Processing genome-wide association studies within a repository of heterogeneous genomic datasets” was published in the regular issue of this journal instead of in the supplement issue. The details of the supplement in which this article
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The shared genetic architecture of smoking behaviours and psychiatric disorders: evidence from a population-based longitudinal study in England BMC Genet. (IF 2.9) Pub Date : 2023-05-30 Olesya Ajnakina, Andrew Steptoe
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DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals BMC Genet. (IF 2.9) Pub Date : 2023-05-27 Karina Banasik, Peter L. Møller, Tanya R. Techlo, Peter C. Holm, G. Bragi Walters, Andrés Ingason, Anders Rosengren, Palle D. Rohde, Lisette J. A. Kogelman, David Westergaard, Troels Siggaard, Piotr J. Chmura, Mona A. Chalmer, Ólafur Þ. Magnússon, Guðmundur Á. Þórisson, Hreinn Stefánsson, Daníel F. Guðbjartsson, Kári Stefánsson, Jes Olesen, Simon Winther, Morten Bøttcher, Søren Brunak, Thomas Werge
Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8
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2018–2019 field seasons of the Maize Genomes to Fields (G2F) G x E project BMC Genet. (IF 2.9) Pub Date : 2023-05-25 Dayane Cristina Lima, Alejandro Castro Aviles, Ryan Timothy Alpers, Bridget A. McFarland, Shawn Kaeppler, David Ertl, Maria Cinta Romay, Joseph L. Gage, James Holland, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode Edwards, Sherry Flint-Garcia, Candice N. Hirsch, Elizabeth Hood, David C. Hooker, Joseph E. Knoll, Judith M. Kolkman, Sanzhen Liu, John McKay, Richard Minyo, Danilo E. Moreta, Seth
This report provides information about the public release of the 2018–2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy