Transcriptomics and virus-induced gene silencing identify defence-related genes during Ralstonia solanacearum infection in resistant and susceptible tobacco
In this study, transcriptome sequencing were subjected to roots after infection with the R. solanacearum in the resistant and susceptible tobacco variety. DEGs that responded to R. solanacearum infection in both resistant and susceptible tobacco contributed to pectinase and peroxidase development and were enriched in plant hormone signal transduction, signal transduction and MAPK signalling pathway KEGG terms. Core DEGs in the resistant tobacco response to R. solanacearum infection were enriched in cell wall, membrane, abscisic acid and ethylene terms. qRT-PCR indicated that Nitab4.5_0004899g0110, Nitab4.5_0004234g0080 and...
Source: Genomics - January 10, 2024 Category: Genetics & Stem Cells Authors: Zhiliang Xiao Zhengwen Liu Huifen Zhang Aiguo Yang Lirui Cheng Dan Liu Caihong Jiang Shizhou Yu Zhixiao Yang Min Ren Ruimei Geng Source Type: research
Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
Genomics. 2024 Jan;116(1):110781. doi: 10.1016/j.ygeno.2024.110781. Epub 2024 Jan 3.ABSTRACTNile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in Africa, y...
Source: Genomics - January 5, 2024 Category: Genetics & Stem Cells Authors: Diego Robledo Joel Ogwang Ezra Byakora Jennifer Nascimento Schulze Katali Kirungi Benda Clemence Fraslin Sarah Salisbury Moses Solimo Johnson Francis Mayega Beine Peter Charles Masembe Ross Houston Robert Mukiibi Source Type: research
Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
Genomics. 2024 Jan 3;116(1):110781. doi: 10.1016/j.ygeno.2024.110781. Online ahead of print.ABSTRACTNile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in A...
Source: Genomics - January 5, 2024 Category: Genetics & Stem Cells Authors: Diego Robledo Joel Ogwang Ezra Byakora Jennifer Nascimento Schulze Katali Kirungi Benda Clemence Fraslin Sarah Salisbury Moses Solimo Johnson Francis Mayega Beine Peter Charles Masembe Ross Houston Robert Mukiibi Source Type: research
Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
Genomics. 2024 Jan 3;116(1):110781. doi: 10.1016/j.ygeno.2024.110781. Online ahead of print.ABSTRACTNile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in A...
Source: Genomics - January 5, 2024 Category: Genetics & Stem Cells Authors: Diego Robledo Joel Ogwang Ezra Byakora Jennifer Nascimento Schulze Katali Kirungi Benda Clemence Fraslin Sarah Salisbury Moses Solimo Johnson Francis Mayega Beine Peter Charles Masembe Ross Houston Robert Mukiibi Source Type: research
Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
Genomics. 2024 Jan 3:110781. doi: 10.1016/j.ygeno.2024.110781. Online ahead of print.ABSTRACTNile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in Africa, ...
Source: Genomics - January 5, 2024 Category: Genetics & Stem Cells Authors: Diego Robledo Joel Ogwang Ezra Byakora Jennifer Nascimento Schulze Katali Kirungi Benda Clemence Fraslin Sarah Salisbury Moses Solimo Johnson Mayega Beine Peter Charles Masembe Ross Houston Robert Mukiibi Source Type: research
Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity
Genomics. 2024 Jan 2:110782. doi: 10.1016/j.ygeno.2024.110782. Online ahead of print.ABSTRACTThere is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the breeds spread in Chinese high-altitude regions perform significantly different frequencies of new sequences in promoters than other b...
Source: Genomics - January 4, 2024 Category: Genetics & Stem Cells Authors: Heng Du Chenguang Diao Yue Zhuo Xianrui Zheng Zhengzheng Hu Shiyu Lu Wenjiao Jin Lei Zhou Jian-Feng Liu Source Type: research
Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity
Genomics. 2024 Jan 2:110782. doi: 10.1016/j.ygeno.2024.110782. Online ahead of print.ABSTRACTThere is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the breeds spread in Chinese high-altitude regions perform significantly different frequencies of new sequences in promoters than other b...
Source: Genomics - January 4, 2024 Category: Genetics & Stem Cells Authors: Heng Du Chenguang Diao Yue Zhuo Xianrui Zheng Zhengzheng Hu Shiyu Lu Wenjiao Jin Lei Zhou Jian-Feng Liu Source Type: research
Transcriptomic analysis of the longissimus thoracis muscle in pigs has identified molecular regulatory patterns associated with meat quality
In this study, three pig breeds, Shengxianhua, Jiaxing, and Qinglian Black (SXH, JXB and QLB), were used as experimental animals. Transcriptional analysis was performed on the longissimus thoracis (LT) muscle to investigate variations in intramuscular fat (IMF), inosine monophosphate (IMP), amino acids, and muscle fiber morphology across different breeds. Ingenuity canonical pathway analysis (IPA) identified biological processes and key driver genes related to metabolism and muscle development. Additionally, weighted gene co-expression network analysis (WGCNA) revealed gene modules associated with IMP. KEGG and GO analyses...
Source: Genomics - January 3, 2024 Category: Genetics & Stem Cells Authors: Qiangqiang Chen Zhirong Chen Qian Sun Wei Zhang Fen Wu Guoliang Liu Tenghao Wang Zhen Wang Qishan Wang Jinzhi Zhang Source Type: research
Transcriptomic analysis of the longissimus thoracis muscle in pigs has identified molecular regulatory patterns associated with meat quality
In this study, three pig breeds, Shengxianhua, Jiaxing, and Qinglian Black (SXH, JXB and QLB), were used as experimental animals. Transcriptional analysis was performed on the longissimus thoracis (LT) muscle to investigate variations in intramuscular fat (IMF), inosine monophosphate (IMP), amino acids, and muscle fiber morphology across different breeds. Ingenuity canonical pathway analysis (IPA) identified biological processes and key driver genes related to metabolism and muscle development. Additionally, weighted gene co-expression network analysis (WGCNA) revealed gene modules associated with IMP. KEGG and GO analyses...
Source: Genomics - January 3, 2024 Category: Genetics & Stem Cells Authors: Qiangqiang Chen Zhirong Chen Qian Sun Wei Zhang Fen Wu Guoliang Liu Tenghao Wang Zhen Wang Qishan Wang Jinzhi Zhang Source Type: research
Identification of circular RNA-Dcaf6 as a therapeutic target for optic nerve crush-induced RGC degeneration
Genomics. 2023 Dec 30:110776. doi: 10.1016/j.ygeno.2023.110776. Online ahead of print.ABSTRACTThe death of retinal ganglion cells (RGCs) can cause irreversible injury in visual function. Clarifying the mechanism of RGC degeneration is critical for the development of therapeutic strategies. Circular RNAs (circRNAs) are important regulators in many biological and pathological processes. Herein, we performed circRNA microarrays to identify dysregulated circRNAs following optic nerve crush (ONC). The results showed that 221 circRNAs were differentially expressed between ONC retinas and normal retinas. Notably, the levels of ci...
Source: Genomics - January 1, 2024 Category: Genetics & Stem Cells Authors: Yuke Ji Jing Li Sha Liu Junya Zhu Jin Yao Ke-Ran Li Biao Yan Source Type: research
Expression of accessory genes in Salmonella requires the presence of the Gre factors
Genomics. 2023 Dec 30:110777. doi: 10.1016/j.ygeno.2023.110777. Online ahead of print.ABSTRACTGenomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are func...
Source: Genomics - January 1, 2024 Category: Genetics & Stem Cells Authors: Tania Gaviria-Cantin Lloren ç Fernández-Coll Andr és Felipe Vargas Carlos Jonay Jim énez Cristina Madrid Carlos Balsalobre Source Type: research
Transcriptional and functional analysis of plasma exosomal microRNAs in acute viral myocarditis
CONCLUSIONS: Hsa-miR-548a-3p and hsa-miR-500b-5p could serve as a promising biomarker of AVMC. Exosomal miRNAs may have substantial roles in the mechanisms of AVMC.PMID:38163573 | DOI:10.1016/j.ygeno.2023.110775 (Source: Genomics)
Source: Genomics - January 1, 2024 Category: Genetics & Stem Cells Authors: Qinchao Wu Chao Huang Ruolan Chen Daisong Li Guoliang Zhang Haichu Yu Yonghong Li Bingxue Song Ning Zhang Bing Li Xianming Chu Source Type: research
Identification of rat Vstm1 with conservative anti-inflammatory effect between rat and human homologs
Genomics. 2023 Dec 30:110774. doi: 10.1016/j.ygeno.2023.110774. Online ahead of print.ABSTRACTHuman VSTM1 (also known as SIRL1) is an inhibitory immune checkpoint receptor involved in leukocyte activation. Identification of the homologous genes in other species, such as mice and rats, will undoubtedly contribute to functional studies and clinical applications. Here, we successfully cloned the Vstm1 gene in rats, as supported by high-throughput sequencing data. However, Vstm1 is degenerated to a pseudogene in the mouse genome. Rat Vstm1 mRNA contains a complete open reading frame (ORF) of 630 nucleotides encoding 209 amino ...
Source: Genomics - January 1, 2024 Category: Genetics & Stem Cells Authors: Yuzhe Hu Yingzhe Sun Ting Li Wenling Han Pingzhang Wang Source Type: research
Necroptosis-related genes allow novel insights into predicting graft loss and diagnosing delayed graft function in renal transplantation
Genomics. 2023 Dec 30:110778. doi: 10.1016/j.ygeno.2023.110778. Online ahead of print.ABSTRACTIschemia-reperfusion injury (IRI) is an inevitable pathophysiological phenomenon in kidney transplantation. Necroptosis is an undoubtedly important contributing mechanism in renal IRI. We first screened differentially expressed necroptosis-related genes (DENRGs) from public databases. Eight DENRGs were validated by independent datasets and verified by qRT-PCR in a rat IRI model. We used univariate and multivariate Cox regression analyses to establish a prognostic signature, and graft survival analysis was performed. Immune infiltr...
Source: Genomics - January 1, 2024 Category: Genetics & Stem Cells Authors: Jiale Wang Cuinan Lu Jingwen Wang Ying Wang Huanjing Bi Jin Zheng Xiaoming Ding Source Type: research
Identification of circular RNA-Dcaf6 as a therapeutic target for optic nerve crush-induced RGC degeneration
Genomics. 2023 Dec 30:110776. doi: 10.1016/j.ygeno.2023.110776. Online ahead of print.ABSTRACTThe death of retinal ganglion cells (RGCs) can cause irreversible injury in visual function. Clarifying the mechanism of RGC degeneration is critical for the development of therapeutic strategies. Circular RNAs (circRNAs) are important regulators in many biological and pathological processes. Herein, we performed circRNA microarrays to identify dysregulated circRNAs following optic nerve crush (ONC). The results showed that 221 circRNAs were differentially expressed between ONC retinas and normal retinas. Notably, the levels of ci...
Source: Genomics - January 1, 2024 Category: Genetics & Stem Cells Authors: Yuke Ji Jing Li Sha Liu Junya Zhu Jin Yao Ke-Ran Li Biao Yan Source Type: research
