Strongly preserved modules between cancer tissue and cell line contribute to drug resistance analysis across multiple cancer types
Genomics. 2021 Feb 26:S0888-7543(21)00075-6. doi: 10.1016/j.ygeno.2021.02.015. Online ahead of print.ABSTRACTThe existence and emergence of drug resistance in tumor cells is the main burden of cancer treatment. Most cancer drug resistance analyses are based entirely on cell line data and ignore the discordance between human tumors and cell lines, leading to biased preclinical model transformation. Based on cancer tissue data in TCGA and cancer cell line data in CCLE, this study identified and excluded non-preserved module (NP module) between cancer tissue and cell lines. We used strongly preserved module (SP module) for cl...
Source: Genomics - March 1, 2021 Category: Genetics & Stem Cells Authors: Siyao Dong Chengyan Song Baocui Qi Xiaochen Jiang Lu Liu Yan Xu Source Type: research

Transcriptome profiling towards understanding of the morphogenesis in the scale development of blunt snout bream (Megalobrama amblycephala)
This study provides a strong reference for further exploration of the function of genes related to the molecular regulation mechanism of scale development in M. amblycephala, as well as in other fishes.PMID:33640463 | DOI:10.1016/j.ygeno.2020.12.043 (Source: Genomics)
Source: Genomics - February 28, 2021 Category: Genetics & Stem Cells Authors: Zhiqiang Wang Yongyi Jia Xin Huang Dongmei Zhu Han Liu Weimin Wang Source Type: research

Transcriptome profiling towards understanding of the morphogenesis in the scale development of blunt snout bream (Megalobrama amblycephala)
This study provides a strong reference for further exploration of the function of genes related to the molecular regulation mechanism of scale development in M. amblycephala, as well as in other fishes.PMID:33640463 | DOI:10.1016/j.ygeno.2020.12.043 (Source: Genomics)
Source: Genomics - February 28, 2021 Category: Genetics & Stem Cells Authors: Zhiqiang Wang Yongyi Jia Xin Huang Dongmei Zhu Han Liu Weimin Wang Source Type: research

Genome-wide investigation and expression analysis of MACPF gene family reveals its immune role in response to bacterial challenge of Manila clam
In this study, 18 MACPF genes (RpMACPF) were identified and classed into three types (Macrophage-expressed gene 1, Apextrin, and MACPF domain contain protein) based on gene structure and phylogenetic relationship in R. philippinarum. The length of RpMACPF proteins varied from 287 to 785 amino acids. The molecular weights and Theoretical PI values ranged from 3.2 kDa to 8.7 kDa and 4.7 to 8.6, respectively. RNA-seq data analysis revealed that 14 of 18 RpMACPF genes were highly expressed at the pediveliger larvae stage indicate RpMACPF might contribute to the early development and metamorphosis processes of the R. philippina...
Source: Genomics - February 27, 2021 Category: Genetics & Stem Cells Authors: Kunyin Jiang Zhihui Yin Yanming Zhang Qiaoyue Xu Rongchao Yu Wanlin Cong Xiwu Yan Hongtao Nie Source Type: research

Genome-wide investigation and expression analysis of MACPF gene family reveals its immune role in response to bacterial challenge of Manila clam
In this study, 18 MACPF genes (RpMACPF) were identified and classed into three types (Macrophage-expressed gene 1, Apextrin, and MACPF domain contain protein) based on gene structure and phylogenetic relationship in R. philippinarum. The length of RpMACPF proteins varied from 287 to 785 amino acids. The molecular weights and Theoretical PI values ranged from 3.2 kDa to 8.7 kDa and 4.7 to 8.6, respectively. RNA-seq data analysis revealed that 14 of 18 RpMACPF genes were highly expressed at the pediveliger larvae stage indicate RpMACPF might contribute to the early development and metamorphosis processes of the R. philippina...
Source: Genomics - February 27, 2021 Category: Genetics & Stem Cells Authors: Kunyin Jiang Zhihui Yin Yanming Zhang Qiaoyue Xu Rongchao Yu Wanlin Cong Xiwu Yan Hongtao Nie Source Type: research

hsa-miR-196a-5p overexpression is associated with MIR196A2 methylation and affects the malignant biological behavior of glioma
Genomics. 2021 Feb 23:S0888-7543(21)00072-0. doi: 10.1016/j.ygeno.2021.02.012. Online ahead of print.ABSTRACThsa-miR-196a-5p is involved in tumorigenesis and progression; however, the driving factors for hsa-miR-196a-5p overexpression and its correlation with the clinicopathological features and prognosis of patients remain unclear in glioma. Thus, this study aimed to investigate the prognostic value of hsa-miR-196a-5p and its correlation with MIR196A2 methylation in glioma. We observed that hsa-miR-196a-5p expression was upregulated in glioma. Next, 112 patients were divided into high (n = 56) and low (n = 56) hsa-miR-196...
Source: Genomics - February 26, 2021 Category: Genetics & Stem Cells Authors: Shanqiang Qu Ouwen Qiu Jing Huang Jin Liu Huafu Wang Source Type: research

hsa-miR-196a-5p overexpression is associated with MIR196A2 methylation and affects the malignant biological behavior of glioma
Genomics. 2021 Feb 23:S0888-7543(21)00072-0. doi: 10.1016/j.ygeno.2021.02.012. Online ahead of print.ABSTRACThsa-miR-196a-5p is involved in tumorigenesis and progression; however, the driving factors for hsa-miR-196a-5p overexpression and its correlation with the clinicopathological features and prognosis of patients remain unclear in glioma. Thus, this study aimed to investigate the prognostic value of hsa-miR-196a-5p and its correlation with MIR196A2 methylation in glioma. We observed that hsa-miR-196a-5p expression was upregulated in glioma. Next, 112 patients were divided into high (n = 56) and low (n = 56) hsa-miR-196...
Source: Genomics - February 26, 2021 Category: Genetics & Stem Cells Authors: Shanqiang Qu Ouwen Qiu Jing Huang Jin Liu Huafu Wang Source Type: research

Widespread distribution of prophages signaling the potential for adaptability and pathogenicity evolution of Ralstonia solanacearum species complex
Genomics. 2021 Feb 21:S0888-7543(21)00071-9. doi: 10.1016/j.ygeno.2021.02.011. Online ahead of print.ABSTRACTIntegrated bacteriophages (prophages) can impact host cells, affecting their lifestyle, genomic diversity, and fitness. However, many basic aspects of how these organisms affect the host cell remain poorly understood. Ralstonia solanacearum is a gram-negative plant pathogenic bacterium that encompasses a great diversity of ecotypes regarded as a species complex (R. solanacearum Species Complex - RSSC). RSSC genomes have a mosaic structure containing numerous elements, signaling the potential for its evolution throug...
Source: Genomics - February 24, 2021 Category: Genetics & Stem Cells Authors: Osiel Silva Gon çalves Fl ávia de Oliveira Souza Fernanda Prieto Bruckner Mateus Ferreira Santana Poliane Alfenas-Zerbini Source Type: research

Molecular mechanisms of wound healing and regeneration of siphon in the Manila clam Ruditapes philippinarum revealed by transcriptomic analysis
This study shed light on the process of morphological regeneration and regenerative mechanism of siphon of R. philippinarum.PMID:33626340 | DOI:10.1016/j.ygeno.2021.02.010 (Source: Genomics)
Source: Genomics - February 24, 2021 Category: Genetics & Stem Cells Authors: Zhenxing Wang Yitian Bai Hongtao Nie Qiaoyue Xu Zhihui Yin Yanming Zhang Xuwang Yin Xiwu Yan Source Type: research

Widespread distribution of prophages signaling the potential for adaptability and pathogenicity evolution of Ralstonia solanacearum species complex
Genomics. 2021 Feb 21:S0888-7543(21)00071-9. doi: 10.1016/j.ygeno.2021.02.011. Online ahead of print.ABSTRACTIntegrated bacteriophages (prophages) can impact host cells, affecting their lifestyle, genomic diversity, and fitness. However, many basic aspects of how these organisms affect the host cell remain poorly understood. Ralstonia solanacearum is a gram-negative plant pathogenic bacterium that encompasses a great diversity of ecotypes regarded as a species complex (R. solanacearum Species Complex - RSSC). RSSC genomes have a mosaic structure containing numerous elements, signaling the potential for its evolution throug...
Source: Genomics - February 24, 2021 Category: Genetics & Stem Cells Authors: Osiel Silva Gon çalves Fl ávia de Oliveira Souza Fernanda Prieto Bruckner Mateus Ferreira Santana Poliane Alfenas-Zerbini Source Type: research

Molecular mechanisms of wound healing and regeneration of siphon in the Manila clam Ruditapes philippinarum revealed by transcriptomic analysis
This study shed light on the process of morphological regeneration and regenerative mechanism of siphon of R. philippinarum.PMID:33626340 | DOI:10.1016/j.ygeno.2021.02.010 (Source: Genomics)
Source: Genomics - February 24, 2021 Category: Genetics & Stem Cells Authors: Zhenxing Wang Yitian Bai Hongtao Nie Qiaoyue Xu Zhihui Yin Yanming Zhang Xuwang Yin Xiwu Yan Source Type: research

Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds
Genomics. 2021 Feb 18:S0888-7543(21)00066-5. doi: 10.1016/j.ygeno.2021.02.009. Online ahead of print.ABSTRACTDomestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and FST, to detect selection signatures. A total of 179, 56, and 231 regions reveal...
Source: Genomics - February 21, 2021 Category: Genetics & Stem Cells Authors: K A Saravanan Manjit Panigrahi Harshit Kumar Subhashree Parida Bharat Bhushan G K Gaur Triveni Dutt B P Mishra R K Singh Source Type: research

Exogenous phytohormone application and transcriptome analysis of Mikania micrantha provides insights for a potential control strategy
Genomics. 2021 Feb 18:S0888-7543(21)00059-8. doi: 10.1016/j.ygeno.2021.02.008. Online ahead of print.ABSTRACTEffective and complete control of the invasive weed Mikania micrantha is required to avoid increasing damages. We exogenously applied indole 3-acetic acid (IAA), gibberellin (GA), and N-(2-Chloro-4-pyridyl)-N'-phenylurea (CPPU), and their combinations i.e. IAA + CPPU (IC), GA + CPPU (GC), and GA + IAA + CPPU (GIC), at 5, 10, 25, 50, and 75 ppm against distilled water as a control (CK), to examine their effects on the weed. The increasing concentrations of these hormones when applied alone or in combination were fata...
Source: Genomics - February 21, 2021 Category: Genetics & Stem Cells Authors: Ning Zhao Sangzi Ze Naiyong Liu Lianrong Hu Mei Ji Qiao Li Bin Yang Source Type: research

Integrated genomic selection for rapid improvement of crops
Genomics. 2021 Feb 18:S0888-7543(21)00058-6. doi: 10.1016/j.ygeno.2021.02.007. Online ahead of print.ABSTRACTAn increase in rate of crop improvement is essential for achieving sustained food production and other needs of ever increasing population. Genomic selection (GS) is a potential breeding tool that has been successfully employed in animal breeding and is being incorporated into plant breeding. GS promises accelerated breeding cycles through a rapid selection of superior genotypes. Numerous empirical and simulation studies on GS and realized impacts on improvement in the crop yields are recently being reported. For a ...
Source: Genomics - February 21, 2021 Category: Genetics & Stem Cells Authors: Gopalareddy Krishnappa Siddanna Savadi Bhudeva Singh Tyagi Sanjay Kumar Singh Mamrutha Harohalli Masthigowda Satish Kumar Chandra Nath Mishra Hanif Khan Gangadhara Krishnappa Uday Govindareddy Gyanendra Singh Gyanendra Pratap Singh Source Type: research

Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds
Genomics. 2021 Feb 18:S0888-7543(21)00066-5. doi: 10.1016/j.ygeno.2021.02.009. Online ahead of print.ABSTRACTDomestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and FST, to detect selection signatures. A total of 179, 56, and 231 regions reveal...
Source: Genomics - February 21, 2021 Category: Genetics & Stem Cells Authors: K A Saravanan Manjit Panigrahi Harshit Kumar Subhashree Parida Bharat Bhushan G K Gaur Triveni Dutt B P Mishra R K Singh Source Type: research

Exogenous phytohormone application and transcriptome analysis of Mikania micrantha provides insights for a potential control strategy
Genomics. 2021 Feb 18:S0888-7543(21)00059-8. doi: 10.1016/j.ygeno.2021.02.008. Online ahead of print.ABSTRACTEffective and complete control of the invasive weed Mikania micrantha is required to avoid increasing damages. We exogenously applied indole 3-acetic acid (IAA), gibberellin (GA), and N-(2-Chloro-4-pyridyl)-N'-phenylurea (CPPU), and their combinations i.e. IAA + CPPU (IC), GA + CPPU (GC), and GA + IAA + CPPU (GIC), at 5, 10, 25, 50, and 75 ppm against distilled water as a control (CK), to examine their effects on the weed. The increasing concentrations of these hormones when applied alone or in combination were fata...
Source: Genomics - February 21, 2021 Category: Genetics & Stem Cells Authors: Ning Zhao Sangzi Ze Naiyong Liu Lianrong Hu Mei Ji Qiao Li Bin Yang Source Type: research

Integrated genomic selection for rapid improvement of crops
Genomics. 2021 Feb 18:S0888-7543(21)00058-6. doi: 10.1016/j.ygeno.2021.02.007. Online ahead of print.ABSTRACTAn increase in rate of crop improvement is essential for achieving sustained food production and other needs of ever increasing population. Genomic selection (GS) is a potential breeding tool that has been successfully employed in animal breeding and is being incorporated into plant breeding. GS promises accelerated breeding cycles through a rapid selection of superior genotypes. Numerous empirical and simulation studies on GS and realized impacts on improvement in the crop yields are recently being reported. For a ...
Source: Genomics - February 21, 2021 Category: Genetics & Stem Cells Authors: Gopalareddy Krishnappa Siddanna Savadi Bhudeva Singh Tyagi Sanjay Kumar Singh Mamrutha Harohalli Masthigowda Satish Kumar Chandra Nath Mishra Hanif Khan Gangadhara Krishnappa Uday Govindareddy Gyanendra Singh Gyanendra Pratap Singh Source Type: research

Comparative transcriptome analyses for metribuzin tolerance provide insights into key genes and mechanisms restoring photosynthetic efficiency in bread wheat (Triticum aestivum L.)
Genomics. 2021 Feb 16;113(3):910-918. doi: 10.1016/j.ygeno.2021.02.004. Online ahead of print.ABSTRACTWeeds are the biggest threat to cropping system sustainability in wheat. Metribuzin is a versatile herbicide for broad-spectrum weed management. Understanding key genes, mechanisms and functional markers are essential to develop higher metribuzin tolerant wheats. We identified Chuan Mai 25 (tolerant) and Ritchie (susceptible) as contrasting genotypes to metribuzin stress through dose-response analyses. Transcriptome sequencing using NovaSeq 6000 RNA-Seq platform identified a total of 77,443 genes; 59,915 known genes and 17...
Source: Genomics - February 18, 2021 Category: Genetics & Stem Cells Authors: Roopali Bhoite Ping Si Kadambot H M Siddique Guijun Yan Source Type: research

Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait
Genomics. 2021 Feb 14;113(3):900-909. doi: 10.1016/j.ygeno.2021.02.006. Online ahead of print.ABSTRACTFusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 ...
Source: Genomics - February 16, 2021 Category: Genetics & Stem Cells Authors: Chunji Li Ping Cheng Li Zheng Yongjian Li Yanhong Chen Shuheng Wen Guohui Yu Source Type: research

Predicting lncRNA-miRNA interactions based on interactome network and graphlet interaction
Genomics. 2021 Feb 12;113(3):874-880. doi: 10.1016/j.ygeno.2021.02.002. Online ahead of print.ABSTRACTIn the development and treatment of many human diseases, the regulatory roles between lncRNAs and miRNAs are important, but much remains unknown about them; moreover, experimental methods for analyzing them are expensive and time-consuming. In this work, we applied a semi-supervised interactome network-based approach to explore and forecast the latent interaction between lncRNAs and miRNAs. We constructed graphs according to the similarity of each of lncRNAs and miRNAs and determined the number of graphlet interaction isom...
Source: Genomics - February 15, 2021 Category: Genetics & Stem Cells Authors: Li Zhang Ting Liu Haoyu Chen Qi Zhao Hongsheng Liu Source Type: research

XIAP, commonly targeted by tumor suppressive miR-3607-5p and miR-3607-3p, promotes proliferation and inhibits apoptosis in hepatocellular carcinoma
Genomics. 2021 Feb 12:S0888-7543(21)00054-9. doi: 10.1016/j.ygeno.2021.02.003. Online ahead of print.ABSTRACTMicroRNAs (miRNAs) are frequently aberrantly expressed in hepatocellular carcinoma (HCC) and are involved in its development. However, their role and mechanism in HCC are still not fully elucidated. Differential expression analysis and survival analysis were performed to identify potential miRNAs in HCC and miR-3607 was identified as a candidate therapeutic target and prognostic biomarker. RT-qPCR confirmed the low expression of mature miR-3607-3p and miR-3607-5p in HCC. Functional experiments suggested that both mi...
Source: Genomics - February 15, 2021 Category: Genetics & Stem Cells Authors: Weiyang Lou Jing Chen Bisha Ding Weimin Fan Source Type: research

Genetic predictors of gene expression associated with psychiatric comorbidity in patients with inflammatory bowel disease - A pilot study
CONCLUSIONS: Our TWAS analysis has identified genes and pathways with a suggestive association with IBD patients with PC. These findings can be potentially used for illustrating the mechanism of developing PC in the patients with IBD and developing diagnosis tool or drug targets for IBD patients with PC.PMID:33588072 | DOI:10.1016/j.ygeno.2021.02.001 (Source: Genomics)
Source: Genomics - February 15, 2021 Category: Genetics & Stem Cells Authors: Allan Bruinooge Qian Liu Ye Tian Wenxin Jiang Yao Li Wei Xu Charles N Bernstein Pingzhao Hu Source Type: research

ASDB: A comprehensive omics database for Anopheles sinensis
Genomics. 2021 Feb 12:S0888-7543(21)00056-2. doi: 10.1016/j.ygeno.2021.02.005. Online ahead of print.ABSTRACTAnopheles sinensis is a key disease vector for human malaria and parasitic diseases such as malayan filariasis, and it is considered to be one of the most important malaria vectors in China and Southeast Asia. As high-throughput sequencing and assembly technology are widely used in An. sinensis, a lot of omics data have been generated, and abundant genome, mRNA transcriptome, miRNA transcriptome and resequencing results have been accumulated. In addition, lots of valuable morphological images and publications have b...
Source: Genomics - February 15, 2021 Category: Genetics & Stem Cells Authors: Yu-Juan Zhang Yang Lan Bin Chen Source Type: research

Comparative transcriptome analyses for metribuzin tolerance provide insights into key genes and mechanisms restoring photosynthetic efficiency in bread wheat (Triticum aestivum L.).
Abstract Weeds are the biggest threat to cropping system sustainability in wheat. Metribuzin is a versatile herbicide for broad-spectrum weed management. Understanding key genes, mechanisms and functional markers are essential to develop higher metribuzin tolerant wheats. We identified Chuan Mai 25 (tolerant) and Ritchie (susceptible) as contrasting genotypes to metribuzin stress through dose-response analyses. Transcriptome sequencing using NovaSeq 6000 RNA-Seq platform identified a total of 77,443 genes; 59,915 known genes and 17,528 novel genes. The functional enrichment analysis at 0 h, 24 h and 60 h her...
Source: Genomics - February 15, 2021 Category: Genetics & Stem Cells Authors: Bhoite R, Si P, Siddique KHM, Yan G Tags: Genomics Source Type: research

Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait.
Abstract Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sens...
Source: Genomics - February 13, 2021 Category: Genetics & Stem Cells Authors: Li C, Cheng P, Zheng L, Li Y, Chen Y, Wen S, Yu G Tags: Genomics Source Type: research

Predicting lncRNA-miRNA interactions based on interactome network and graphlet interaction.
Abstract In the development and treatment of many human diseases, the regulatory roles between lncRNAs and miRNAs are important, but much remains unknown about them; moreover, experimental methods for analyzing them are expensive and time-consuming. In this work, we applied a semi-supervised interactome network-based approach to explore and forecast the latent interaction between lncRNAs and miRNAs. We constructed graphs according to the similarity of each of lncRNAs and miRNAs and determined the number of graphlet interaction isomers between nodes in these two graphs. According to the two graphs and the known int...
Source: Genomics - February 12, 2021 Category: Genetics & Stem Cells Authors: Zhang L, Liu T, Chen H, Zhao Q, Liu H Tags: Genomics Source Type: research

XIAP, commonly targeted by tumor suppressive miR-3607-5p and miR-3607-3p, promotes proliferation and inhibits apoptosis in hepatocellular carcinoma.
Abstract MicroRNAs (miRNAs) are frequently aberrantly expressed in hepatocellular carcinoma (HCC) and are involved in its development. However, their role and mechanism in HCC are still not fully elucidated. Differential expression analysis and survival analysis were performed to identify potential miRNAs in HCC and miR-3607 was identified as a candidate therapeutic target and prognostic biomarker. RT-qPCR confirmed the low expression of mature miR-3607-3p and miR-3607-5p in HCC. Functional experiments suggested that both miR-3607-3p and miR-3607-5p significantly inhibited HCC proliferation and induced apoptosis. ...
Source: Genomics - February 12, 2021 Category: Genetics & Stem Cells Authors: Lou W, Chen J, Ding B, Fan W Tags: Genomics Source Type: research

Genetic predictors of gene expression associated with psychiatric comorbidity in patients with inflammatory bowel disease - A pilot study.
CONCLUSIONS: Our TWAS analysis has identified genes and pathways with a suggestive association with IBD patients with PC. These findings can be potentially used for illustrating the mechanism of developing PC in the patients with IBD and developing diagnosis tool or drug targets for IBD patients with PC. PMID: 33588072 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - February 12, 2021 Category: Genetics & Stem Cells Authors: Bruinooge A, Liu Q, Tian Y, Jiang W, Li Y, Xu W, Bernstein CN, Hu P Tags: Genomics Source Type: research

ASDB: A comprehensive omics database for Anopheles sinensis.
Abstract Anopheles sinensis is a key disease vector for human malaria and parasitic diseases such as malayan filariasis, and it is considered to be one of the most important malaria vectors in China and Southeast Asia. As high-throughput sequencing and assembly technology are widely used in An. sinensis, a lot of omics data have been generated, and abundant genome, mRNA transcriptome, miRNA transcriptome and resequencing results have been accumulated. In addition, lots of valuable morphological images and publications have been produced with the in-depth studies on An. sinensis. However, the increased quantity, va...
Source: Genomics - February 12, 2021 Category: Genetics & Stem Cells Authors: Zhang YJ, Lan Y, Chen B Tags: Genomics Source Type: research

Corrigendum to 'Fragmented mitochondrial genomes evolved in opposite directions between closely related macaque louse Pedicinus obtusus and colobus louse Pedicinus badii'.
PMID: 33549956 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - February 4, 2021 Category: Genetics & Stem Cells Authors: Fu YT, Dong Y, Wang W, Nie Y, Liu GH, Shao R Tags: Genomics Source Type: research

Performance of common genetic variants in risk prediction for colorectal cancer in Chinese: A two-stage and multicenter study.
Abstract The efficacy of susceptible variants derived from genome-wide association studies (GWAs) optimizing discriminatory accuracy of colorectal cancer (CRC) in Chinese remains unclear. In the present validation study, we assessed 75 recently identified variants from GWAs. A risk predictive model combining 19 variants using the least absolute shrinkage and selection operator (LASSO) statistics offered certain clinical advantages. This model demonstrated an area under the receiver operating characteristic (AUC) of 0.61 during training analysis and yielded robust AUCs from 0.59 to 0.61 during validation analysis i...
Source: Genomics - February 2, 2021 Category: Genetics & Stem Cells Authors: He CY, Chen LZ, Wang ZX, Sun LP, Peng JJ, Wu MQ, Wang TM, Li YQ, Yang XH, Zhou DL, Ye ZL, Ma JJ, Li XZ, Zhang PF, Ju HQ, Mo HY, Zhang ZC, Zeng ZL, Shao JY, Jia WH, Cai SJ, Yuan Y, Xu RH Tags: Genomics Source Type: research

Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes.
This study is the first chromosomal level genome of a Pleuronectidae fish (V. variegatus). The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the V. variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes. PMID: 33535123 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - January 31, 2021 Category: Genetics & Stem Cells Authors: Zhao N, Guo H, Jia L, Guo B, Zheng D, Liu S, Zhang B Tags: Genomics Source Type: research

Zrg1, A cryptococcal protein associated with regulation of growth in nutrient deprivation conditions.
Abstract Cryptococcus gattii is one of the causes of cryptococcosis, a life-threatening disease generally characterized by pneumonia and/or meningitis. Zinc is an essential element for life, being required for the activity of many proteins with catalytic and structural roles. Here, we characterize ZRG1 (zinc-related gene 1), which codes a product involved in zinc metabolism. Transcriptional profiling revealed that zinc availability regulated the expression of ZRG1, and its null mutants demonstrated impaired growth in zinc- and nitrogen-limiting conditions. Moreover, zrg1 strains displayed alterations in the expres...
Source: Genomics - January 30, 2021 Category: Genetics & Stem Cells Authors: Diehl C, Garcia AWA, Kinskovski UP, Sbaraini N, de Oliveira Schneider R, Ferrareze PAG, Gerber AL, de Vasconcelos ATR, Kmetzsch L, Vainstein MH, Staats CC Tags: Genomics Source Type: research

MicroRNA expression patterns in the brown fat of hibernating 13-lined ground squirrels.
Abstract The sequence diversity of microRNAs (miRNAs) allows these potent regulators of mRNA fate to bind multiple transcripts, giving them the power to inhibit diverse cellular processes. Therefore, miRNAs may regulate metabolic rate suppression (also termed torpor), an adaptation used by capable species to reduce energy expenditure, minimize tissue damage, and prolong life. Small RNA-sequencing of brown fat from control (37 °C) and torpid (5-8 °C) ground squirrels revealed a central role for miRNAs in torpor. Unsupervised clustering analysis of all 319 conserved miRNAs showed separation of control an...
Source: Genomics - January 30, 2021 Category: Genetics & Stem Cells Authors: Logan SM, Storey KB Tags: Genomics Source Type: research

Identification of an immune-related RNA-binding protein signature to predict survival and targeted therapy responses in liver cancer.
Abstract RNA-binding proteins (RBPs) play crucial roles in multiple cancers. However, very few RBPs and their association with immune genes have been systematically studied in liver cancer (LC). We aimed to identify an immune-related RBP signature to predict the survival of LC patients. Bioinformatics methods were used to identify differentially expressed, immune-related, and prognostic RBPs and to develop an immune-related RBP signature based on data from the Cancer Genome Atlas (TCGA) cohort. We obtained eight differentially expressed, immune-related, and prognostic RBPs to construct a risk signature. The signat...
Source: Genomics - January 29, 2021 Category: Genetics & Stem Cells Authors: Yang S, Lin S, Liu K, Liu Y, Xu P, Zheng Y, Deng Y, Zhang D, Zhai Z, Li N, Ren X, Dai Z, Kang H Tags: Genomics Source Type: research

Genomic dissection of ROS detoxifying enzyme encoding genes for their role in antioxidative defense mechanism against Tomato leaf curl New Delhi virus infection in tomato.
Abstract In the present study, genes encoding for six major classes of enzymatic antioxidants, namely superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), Peroxidase (Prx) and glutathione S-transferase (GST) are identified in tomato. Their expression was studied in tomato cultivars contrastingly tolerant to ToLCNDV during virus infection and different hormone treatments. Significant upregulation of SlGR3, SlPrx25, SlPrx75, SlPrx95, SlGST44, and SlGST96 was observed in the tolerant cultivar during disease infection. Virus-induced gene silencing of SlGR3 in the tolerant cultivar conferred disease ...
Source: Genomics - January 29, 2021 Category: Genetics & Stem Cells Authors: Sharma N, Muthamilarasan M, Dulani P, Prasad M Tags: Genomics Source Type: research

A computational approach to identify CRISPR-Cas loci in the complete genomes of the lichen-associated Burkholderia sp. PAMC28687 and PAMC26561.
Abstract The genus Burkholderia and its strains PAMC28687 and PAMC26561 are lichen-associated bacteria isolated from the Antarctic region. Our study is the first to provide the genome sequence of the Burkholderia sp. PAMC26561 strain. The genus Burkholderia includes bacteria that are pathogenic to plants, animals, and humans. Computational analysis of complete genomes of strains from the uncategorized Burkholderia group was performed using the NCBI databank and PATRIC (for genome sequence information) and CRISPRCasFinder (online and offline versions) software in order to predict the CRISPR loci and Cas genes. The ...
Source: Genomics - January 29, 2021 Category: Genetics & Stem Cells Authors: Shrestha P, Han SR, Lee JH, Park H, Oh TJ Tags: Genomics Source Type: research

SHCBP1 interacting with EOGT enhances O-GlcNAcylation of NOTCH1 and promotes the development of pancreatic cancer.
Abstract O-GlcNAcylation is important in the development and progression of pancreatic ductal adenocarcinoma (PDAC). The glycosyltransferase EGF domain-specific O-linked GlcNAc transferase (EOGT) acts as a key participant in glycosylating NOTCH1. High-throughput sequencing of specimens from 30 advanced PDAC patients identified SHCBP1 and EOGT as factors of poor prognosis. We hypothesized that they could mediate PDAC progression by influencing NOTCH1 O-GlcNAcylation. Thus, 186 PDAC tissue specimens were immunostained for EOGT and SHCBP1. Pancreatic cancer cell lines and nude mouse models were used for in vitro and ...
Source: Genomics - January 27, 2021 Category: Genetics & Stem Cells Authors: Yang C, Hu JF, Zhan Q, Wang ZW, Li G, Pan JJ, Huang L, Liao CY, Huang Y, Tian YF, Shen BY, Chen JZ, Wang YD, Chen S Tags: Genomics Source Type: research

Optimizing imputation of marker data from genotyping-by-sequencing (GBS) for genomic selection in non-model species: Rubber tree (Hevea brasiliensis) as a case study.
ros D Abstract Genotyping-by-sequencing (GBS) provides the marker density required for genomic predictions (GP). However, GBS gives a high proportion of missing SNP data which, for species without a chromosome-level genome assembly, must be imputed without knowing the SNP physical positions. Here, we compared GP accuracy with seven map-independent and two map-dependent imputation approaches, and when using all SNPs against the subset of genetically mapped SNPs. We used two rubber tree (Hevea brasiliensis) datasets with three traits. The results showed that the best imputation approaches were LinkImputeR, Beagle an...
Source: Genomics - January 25, 2021 Category: Genetics & Stem Cells Authors: Munyengwa N, Le Guen V, Bille HN, Souza LM, Clément-Demange A, Mournet P, Masson A, Soumahoro M, Kouassi D, Cros D Tags: Genomics Source Type: research

Gut milieu shapes the bacterial communities of invasive silver carp.
Abstract Silver carp is an invasive fish present in the Gobindsagar reservoir, India and has a profound impact on aquaculture. Understanding taxonomic diversity and functional attributes of gut microbiota will provide insights into the important role of bacteria in metabolism of silver carp that facilitated invasion of this exotic species. Microbial composition in foregut, midgut, hindgut and water samples was analysed using 16S rRNA gene amplicon sequencing. The bacterial communities of water samples were distinct from gut microbiota, and unique microbial assemblages were present in different regions of gut depic...
Source: Genomics - January 25, 2021 Category: Genetics & Stem Cells Authors: Khurana H, Sharma M, Bharti M, Singh DN, Negi RK Tags: Genomics Source Type: research

Genome-wide supermatrix analyses of maples (Acer, Sapindaceae) reveal recurring inter-continental migration, mass extinction, and rapid lineage divergence.
Abstract Acer (Sapindaceae) is an exceptional study system for understanding the evolutionary history, divergence, and assembly of broad-leaved deciduous forests at higher latitudes. Maples stand out due to their high diversity, disjunct distribution pattern across the northern continents, and rich fossil record dating back to the Paleocene. Using a genome-wide supermatrix combining plastomes and nuclear sequences (~585 kb) for 110 Acer taxa, we built a robust time-calibrated hypothesis investigating the evolution of maples, inferring ancestral ranges, reconstructing diversification rates over time, and explorin...
Source: Genomics - January 25, 2021 Category: Genetics & Stem Cells Authors: Areces-Berazain F, Hinsinger DD, Strijk JS Tags: Genomics Source Type: research

Transcriptome analysis of immune-related genes in Sesarmops sinensis hepatopancreas in reaction to peptidoglycan challenge.
In conclusion, in addition to enriching the existing transcriptome data of S. sinensis, this study also clarified the immune response of S. sinensis to PGN stimulation, which will help us to further understand the crustacean's immune system. PMID: 33503506 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - January 24, 2021 Category: Genetics & Stem Cells Authors: Li YT, Tang BP, Zhang SP, Tang YY, Wang G, Jiang SH, Ge BM, Zhang DZ, Zhou CL, Liu QN, Zhang ML Tags: Genomics Source Type: research

Comparative analyses of hypothalamus transcriptomes reveal fertility-, growth-, and immune-related genes and signal pathways in different ploidy cyprinid fish.
In this study, high-throughput sequencing was used to conduct the transcriptome analysis of the female hypothalamus of diploid RCC, diploid common carp (Cyprinus carpio L., CC) and TCC. The key functional expression genes of the hypothalamus were obtained through functional gene annotation and differential gene expression screening. A total of 71.56 G data and 47,572 genes were obtained through sequencing and genome mapping, respectively. The Fuzzy Analysis Clustering assigned the differentially expressed genes (DEGs) into eight groups, two of which, overdominance expression (6005, 12.62%) and underdominance expression (...
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: Li S, Zhou Y, Yang C, Fan S, Huang L, Zhou T, Wang Q, Zhao R, Tang C, Tao M, Liu S Tags: Genomics Source Type: research

Stage-specific transcriptomic analysis of the model cestode Hymenolepis microstoma.
Abstract Most parasitic flatworms go through different life stages with important physiological and morphological changes. In this work, we used a transcriptomic approach to analyze the main life-stages of the model tapeworm Hymenolepis microstoma (eggs, cysticercoids, and adults). Our results showed massive transcriptomic changes in this life cycle, including key gene families that contribute substantially to the expression load in each stage. In particular, different members of the cestode-specific hydrophobic ligand-binding protein (HLBP) family are among the most highly expressed genes in each life stage. We a...
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: Preza M, Calvelo J, Langleib M, Hoffmann F, Castillo E, Koziol U, Iriarte A Tags: Genomics Source Type: research

Polymorphisms of AMY1A gene and their association with growth, carcass traits and feed intake efficiency in chickens.
Abstract Investigations on the association between chicken traits and genetic variations can provide basic information to improve production performance in chickens. In our previous work, we genotyped 450 male chickens with a 600 K SNP array [1] and found that several SNPs in the genomic regions of the amylase alpha 1A (AMY1A) gene were significantly associated with feed intake efficiency and carcass traits. Given the lower accuracy of the SNP array, we performed direct sequencing with male and female chickens to further test chicken AMY1A polymorphisms and investigate their association with 17 traits in chicken...
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: Zhang Z, Zhong H, Lin S, Liang L, Ye S, Xu Z, Ji C, Zhang Z, Zhang D, Zhang X Tags: Genomics Source Type: research

Global 3'UTR shortening and down-regulation of repeated element related piRNA play crucial roles in boys with cryptorchidism.
CONCLUSION: In summary, our findings also provided the first landscape of gene regulation in cryptorchidism, especially in terms of post-transcriptional regulations. PMID: 33485952 [PubMed - as supplied by publisher] (Source: Genomics)
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: Ge W, Chen M, Tian W, Chen J, Zhao Y, Xian H, Chen J, Xu Y Tags: Genomics Source Type: research

Dissecting the molecular responses of lentil to individual and combined drought and heat stresses by comparative transcriptomic analysis.
Abstract Lentil cultivation could be challenged by combined heat and drought stress in semi-arid regions. We used RNA-seq approach to profile transcriptome changes of Lens culinaris exposed to individual and combined heat and drought stresses. It was determined that most of the differentially expressed genes observed in response to combined stress, could not be identified by analysis of transcriptome exposed to corresponding individual stresses. Interestingly, this study results revealed that the expression of ribosome generation and protein biosynthesis and starch degradation pathways related genes were uniquely ...
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: Hosseini SZ, Ismaili A, Firouzabadi FN, Fallahi H, Rezaeinejad A, Sohrabi SS Tags: Genomics Source Type: research

Analysis of organellar genomes in brown algae reveals an independent introduction of similar foreign sequences into the mitochondrial genome.
l;ckner G Abstract Kelp species (Laminariales, Phaeophyceae) are globally widespread along temperate to Polar rocky coastal lines. Here we analyse the mitochondrial and chloroplast genomes of Laminaria rodriguezii, in comparison to the organellar genomes of other kelp species. We also provide the complete mitochondrial genome sequence of another endemic kelp species from a Polar habitat, the Arctic Laminaria solidungula. We compare phylogenetic trees derived from twenty complete mitochondrial and seven complete chloroplast kelp genomes. Interestingly, we found a stretch of more than 700 bp in the mitochondrial g...
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: Rana S, Valentin K, Riehl J, Blanfuné A, Reynes L, Thibaut T, Bartsch I, Eichinger L, Glöckner G Tags: Genomics Source Type: research

A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines.
Abstract Single-cell transcriptomics (SCT) is a tour de force in the era of big omics data that has led to the accumulation of massive cellular transcription data at an astounding resolution of single cells. It provides valuable insights into cells previously unachieved by bulk cell analysis and is proving crucial in uncovering cellular heterogeneity, identifying rare cell populations, distinct cell-lineage trajectories, and mechanisms involved in complex cellular processes. SCT data is highly complex and necessitates advanced statistical and computational methods for analysis. This review provides a comprehensive...
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: Nayak R, Hasija Y Tags: Genomics Source Type: research

Common genes and pathways involved in the response to stressful stimuli by astrocytes: A meta-analysis of genome-wide expression studies.
l-Pachón A Abstract Astrocytes play pivotal roles in the brain and they become reactive under stress conditions. Here, we carried out, for the first time, an integrative meta-analysis of genome-wide expression profiling of astrocytes from human and mouse exposed to different stressful stimuli (hypoxia, infections by virus and bacteria, cytokines, ethanol, among others). We identified common differentially expressed genes and pathways in human and murine astrocytes. Our results showed that astrocytes induce expression of genes associated with stress response and immune system regulation when they are exposed...
Source: Genomics - January 21, 2021 Category: Genetics & Stem Cells Authors: González-Giraldo Y, Forero DA, Barreto GE, Aristizábal-Pachón A Tags: Genomics Source Type: research