Pub Date : 2024-05-01DOI: 10.1016/j.ygeno.2024.110851
Yingxiao Su , Siqi He , Qian Chen , Hechun Zhang , Chang Huang , Qian Zhao , Yabin Pu , Xiaohong He , Lin Jiang , Yuehui Ma , Qianjun Zhao
Skeletal muscle satellite cells (SMSCs) play an important role in regulating muscle growth and regeneration. Chromatin accessibility allows physical interactions that synergistically regulate gene expression through enhancers, promoters, insulators, and chromatin binding factors. However, the chromatin accessibility altas and its regulatory role in ovine myoblast differentiation is still unclear. Therefore, ATAC-seq and RNA-seq analysis were performed on ovine SMSCs at the proliferation stage (SCG) and differentiation stage (SCD). 17,460 DARs (differential accessibility regions) and 3732 DEGs (differentially expressed genes) were identified. Based on joint analysis of ATAC-seq and RNA-seq, we revealed that PI3K-Akt, TGF-β and other signaling pathways regulated SMSCs differentiation. We identified two novel candidate genes, FZD5 and MAP2K6, which may affect the proliferation and differentiation of SMSCs. Our data identify potential cis regulatory elements of ovine SMSCs. This study can provide a reference for exploring the mechanisms of the differentiation and regeneration of SMSCs in the future.
{"title":"Integrative ATAC-seq and RNA-seq analysis of myogenic differentiation of ovine skeletal muscle satellite cell","authors":"Yingxiao Su , Siqi He , Qian Chen , Hechun Zhang , Chang Huang , Qian Zhao , Yabin Pu , Xiaohong He , Lin Jiang , Yuehui Ma , Qianjun Zhao","doi":"10.1016/j.ygeno.2024.110851","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110851","url":null,"abstract":"<div><p>Skeletal muscle satellite cells (SMSCs) play an important role in regulating muscle growth and regeneration. Chromatin accessibility allows physical interactions that synergistically regulate gene expression through enhancers, promoters, insulators, and chromatin binding factors. However, the chromatin accessibility altas and its regulatory role in ovine myoblast differentiation is still unclear. Therefore, ATAC-seq and RNA-seq analysis were performed on ovine SMSCs at the proliferation stage (SCG) and differentiation stage (SCD). 17,460 DARs (differential accessibility regions) and 3732 DEGs (differentially expressed genes) were identified. Based on joint analysis of ATAC-seq and RNA-seq, we revealed that PI3K-Akt, TGF-β and other signaling pathways regulated SMSCs differentiation. We identified two novel candidate genes, <em>FZD5</em> and <em>MAP2K6</em>, which may affect the proliferation and differentiation of SMSCs. Our data identify potential cis regulatory elements of ovine SMSCs. This study can provide a reference for exploring the mechanisms of the differentiation and regeneration of SMSCs in the future.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000727/pdfft?md5=6ce4f86f98e15320a6568a3f58a7e04a&pid=1-s2.0-S0888754324000727-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140825140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-01DOI: 10.1016/j.ygeno.2024.110847
Wenxiao Chen , Jinghong Hu , Jing Chen , Yuanyuan Guo , Yongjian Hong , Houkai Xia
Background
Bufo gargarizans Cantor, a widely distributed amphibian species in Asia, produces and releases toxins through its retroauricular and granular glands. Although various tissues have been sequenced, the molecular mechanisms underlying the toxin production remain unclear. To elucidate these mechanisms, abdominal skin (non-toxic secretory glands) and retroauricular gland (toxic secreting glands) samples were collected at different time points (3, 6, 12, 24, and 36 months) for RNA sequencing (RNA-seq) and analysis.
Results
In comparison to the S group during the same period, a total of 3053, 3026, 1516, 1028, and 2061 differentially expressed genes (DEGs) were identified across five developmental stages. Gene Ontology (GO) analysis revealed that DEGs were primarily enriched in biological processes including cellular processes, single-organism processes, metabolic processes, and biological regulation. In terms of cellular components, the DEGs were predominantly localized in the cell and cell parts, whereas molecular function indicated significant enrichment in binding and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the metabolism and synthesis of various substances, such as lipid metabolism, cofactor and vitamin metabolism, tryptophan metabolism, steroid biosynthesis, and primary bile acid biosynthesis, were accompanied by the development of toads. Additionally, using trend analysis, we discovered candidate genes that were upregulated in the retroauricular glands during development, and the abundance of these genes in the abdominal skin was extremely low. Finally, we identified 26 genes that are likely to be involved in toxin production and that are likely to be involved in toxin anabolism.
Conclusion
Overall, these results provide new insights into the genes involved in toxin production in B. gargarizans, which will improve our understanding of the molecular mechanisms underlying toxigenic gene expression.
{"title":"Spatio-temporal analysis of toxigenic genes expression in the growing Bufo gargarizans based on RNA sequencing data","authors":"Wenxiao Chen , Jinghong Hu , Jing Chen , Yuanyuan Guo , Yongjian Hong , Houkai Xia","doi":"10.1016/j.ygeno.2024.110847","DOIUrl":"10.1016/j.ygeno.2024.110847","url":null,"abstract":"<div><h3>Background</h3><p><em>Bufo gargarizans</em> Cantor, a widely distributed amphibian species in Asia, produces and releases toxins through its retroauricular and granular glands. Although various tissues have been sequenced, the molecular mechanisms underlying the toxin production remain unclear. To elucidate these mechanisms, abdominal skin (non-toxic secretory glands) and retroauricular gland (toxic secreting glands) samples were collected at different time points (3, 6, 12, 24, and 36 months) for RNA sequencing (RNA-seq) and analysis.</p></div><div><h3>Results</h3><p>In comparison to the S group during the same period, a total of 3053, 3026, 1516, 1028, and 2061 differentially expressed genes (DEGs) were identified across five developmental stages. Gene Ontology (GO) analysis revealed that DEGs were primarily enriched in biological processes including cellular processes, single-organism processes, metabolic processes, and biological regulation. In terms of cellular components, the DEGs were predominantly localized in the cell and cell parts, whereas molecular function indicated significant enrichment in binding and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the metabolism and synthesis of various substances, such as lipid metabolism, cofactor and vitamin metabolism, tryptophan metabolism, steroid biosynthesis, and primary bile acid biosynthesis, were accompanied by the development of toads. Additionally, using trend analysis, we discovered candidate genes that were upregulated in the retroauricular glands during development, and the abundance of these genes in the abdominal skin was extremely low. Finally, we identified 26 genes that are likely to be involved in toxin production and that are likely to be involved in toxin anabolism.</p></div><div><h3>Conclusion</h3><p>Overall, these results provide new insights into the genes involved in toxin production in <em>B. gargarizans</em>, which will improve our understanding of the molecular mechanisms underlying toxigenic gene expression.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000685/pdfft?md5=33cfce8aa693b41dd8a3f1f51a2090f6&pid=1-s2.0-S0888754324000685-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140849830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-01DOI: 10.1016/j.ygeno.2024.110856
Bingjie Jiang , Siqi Lu , Yan Li , M.F. Badran , Yalun Dong , Pao Xu , Jun Qiang , Yifan Tao
Temperature is one of the most important non-genetic sex differentiation factors for fish. The technique of high temperature-induced sex reversal is commonly used in Nile tilapia (Oreochromis niloticus) culture, although the molecular regulatory mechanisms involved in this process remain unclear. The brain is an essential organ for the regulation of neural signals involved in germ cell differentiation and gonad development. To investigate the regulatory roles of miRNAs-mRNAs in the conversion of female to male Nile tilapia gender under high-temperature stress, we compared RNA-Seq data from brain tissues between a control group (28 °C) and a high temperature-treated group (36 °C). The result showed that a total of 123,432,984 miRNA valid reads, 288,202,524 mRNA clean reads, 1128 miRNAs, and 32,918 mRNAs were obtained. Among them, there were 222 significant differentially expressed miRNAs (DE miRNAs) and 810 differentially expressed mRNAs (DE mRNAs) between the two groups. Eight DE miRNAs and eight DE mRNAs were randomly selected, and their expression patterns were validated by qRT-PCR. The miRNA-mRNA co-expression network demonstrated that 40 DE miRNAs targeted 136 protein-coding genes. Functional enrichment analysis demonstrated that these genes were involved in several gonadal differentiation pathways, including the oocyte meiosis signaling pathway, progesterone-mediated oocyte maturation signaling pathway, cell cycle signaling pathway and GnRH signaling pathway. Then, an interaction network was constructed for 8 miRNAs (mir-137-5p, let-7d, mir-1388-5p, mir-124-4-5p, mir-1306, mir-99, mir-130b and mir-21) and 10 mRNAs (smc1al, itpr2, mapk1, ints8, cpeb1b, bub1, fbxo5, mmp14b, cdk1 and hrasb) involved in the oocyte meiosis signaling pathway. These findings provide novel information about the mechanisms underlying miRNA-mediated sex reversal in female Nile tilapia.
{"title":"Integrative analysis of miRNA-mRNA expression in the brain during high temperature-induced masculinization of female Nile tilapia (Oreochromis niloticus)","authors":"Bingjie Jiang , Siqi Lu , Yan Li , M.F. Badran , Yalun Dong , Pao Xu , Jun Qiang , Yifan Tao","doi":"10.1016/j.ygeno.2024.110856","DOIUrl":"10.1016/j.ygeno.2024.110856","url":null,"abstract":"<div><p>Temperature is one of the most important non-genetic sex differentiation factors for fish. The technique of high temperature-induced sex reversal is commonly used in Nile tilapia (<em>Oreochromis niloticus</em>) culture, although the molecular regulatory mechanisms involved in this process remain unclear. The brain is an essential organ for the regulation of neural signals involved in germ cell differentiation and gonad development. To investigate the regulatory roles of miRNAs-mRNAs in the conversion of female to male Nile tilapia gender under high-temperature stress, we compared RNA-Seq data from brain tissues between a control group (28 °C) and a high temperature-treated group (36 °C). The result showed that a total of 123,432,984 miRNA valid reads, 288,202,524 mRNA clean reads, 1128 miRNAs, and 32,918 mRNAs were obtained. Among them, there were 222 significant differentially expressed miRNAs (DE miRNAs) and 810 differentially expressed mRNAs (DE mRNAs) between the two groups. Eight DE miRNAs and eight DE mRNAs were randomly selected, and their expression patterns were validated by qRT-PCR. The miRNA-mRNA co-expression network demonstrated that 40 DE miRNAs targeted 136 protein-coding genes. Functional enrichment analysis demonstrated that these genes were involved in several gonadal differentiation pathways, including the oocyte meiosis signaling pathway, progesterone-mediated oocyte maturation signaling pathway, cell cycle signaling pathway and GnRH signaling pathway. Then, an interaction network was constructed for 8 miRNAs (mir-137-5p, let-7d, mir-1388-5p, mir-124-4-5p, mir-1306, mir-99, mir-130b and mir-21) and 10 mRNAs (<em>smc1al</em>, <em>itpr2</em>, <em>mapk1</em>, <em>ints8</em>, <em>cpeb1b</em>, <em>bub1</em>, <em>fbxo5</em>, <em>mmp14b</em>, <em>cdk1</em> and <em>hrasb</em>) involved in the oocyte meiosis signaling pathway. These findings provide novel information about the mechanisms underlying miRNA-mediated sex reversal in female Nile tilapia.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000776/pdfft?md5=850201f30352d5e79e448537eb85d3c4&pid=1-s2.0-S0888754324000776-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140908516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-01DOI: 10.1016/j.ygeno.2024.110855
Yicheng Yang , Yuan Shao , Chenchen Pei , Yangyang Liu , Min Zhang , Xi Zhu , Jinshan Li , Lifei Feng , Guanghua Li , Keke Li , Yunxiang Liang , Yingjun Li
Clostridium butyricum is a Gram-positive anaerobic bacterium known for its ability to produce butyate. In this study, we conducted whole-genome sequencing and assembly of 14C. butyricum industrial strains collected from various parts of China. We performed a pan-genome comparative analysis of the 14 assembled strains and 139 strains downloaded from NCBI. We found that the genes related to critical industrial production pathways were primarily present in the core and soft-core gene categories. The phylogenetic analysis revealed that strains from the same clade of the phylogenetic tree possessed similar antibiotic resistance and virulence factors, with most of these genes present in the shell and cloud gene categories. Finally, we predicted the genes producing bacteriocins and botulinum toxins as well as CRISPR systems responsible for host defense. In conclusion, our research provides a desirable pan-genome database for the industrial production, food application, and genetic research of C. butyricum.
{"title":"Pangenome analyses of Clostridium butyricum provide insights into its genetic characteristics and industrial application","authors":"Yicheng Yang , Yuan Shao , Chenchen Pei , Yangyang Liu , Min Zhang , Xi Zhu , Jinshan Li , Lifei Feng , Guanghua Li , Keke Li , Yunxiang Liang , Yingjun Li","doi":"10.1016/j.ygeno.2024.110855","DOIUrl":"10.1016/j.ygeno.2024.110855","url":null,"abstract":"<div><p><em>Clostridium butyricum</em> is a Gram-positive anaerobic bacterium known for its ability to produce butyate. In this study, we conducted whole-genome sequencing and assembly of 14<em>C. butyricum</em> industrial strains collected from various parts of China. We performed a pan-genome comparative analysis of the 14 assembled strains and 139 strains downloaded from NCBI. We found that the genes related to critical industrial production pathways were primarily present in the core and soft-core gene categories. The phylogenetic analysis revealed that strains from the same clade of the phylogenetic tree possessed similar antibiotic resistance and virulence factors, with most of these genes present in the shell and cloud gene categories. Finally, we predicted the genes producing bacteriocins and botulinum toxins as well as CRISPR systems responsible for host defense. In conclusion, our research provides a desirable pan-genome database for the industrial production, food application, and genetic research of <em>C. butyricum</em>.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000764/pdfft?md5=b70980c1f3e695590bb35fae06aae96e&pid=1-s2.0-S0888754324000764-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140862638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-01DOI: 10.1016/j.ygeno.2024.110859
Yihui Gong , Xuan Luo , Ting Zhang , Guihua Zhou , Jingyi Li , Bin Zhang , Peng Li , Hua Huang
Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate the functions of the mitochondrial (mt) genome of Luffa cylindrica. The mt genome of L. cylindrica contained two chromosomes with lengths of 380,879 bp and 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 pseudogene, were identified. About 90.63% of the codons ended with A or U bases, and 98.63% of monomers contained A/T, which contributed to the high A/T content (55.91%) of the complete mt genome. Six genes (ATP8, CCMFC, NAD4, RPL10, RPL5 and RPS4) showed positive selection. Phylogenetic analysis indicates that L. cylindrica is closely related to L. acutangula. The present results provide the mt genome of L. cylindrica, which may facilitate possible genetic variation, evolutionary, and molecular breeding studies of L. cylindrica.
{"title":"Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica)","authors":"Yihui Gong , Xuan Luo , Ting Zhang , Guihua Zhou , Jingyi Li , Bin Zhang , Peng Li , Hua Huang","doi":"10.1016/j.ygeno.2024.110859","DOIUrl":"10.1016/j.ygeno.2024.110859","url":null,"abstract":"<div><p>Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate the functions of the mitochondrial (mt) genome of <em>Luffa cylindrica</em>. The mt genome of <em>L. cylindrica</em> contained two chromosomes with lengths of 380,879 bp and 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 pseudogene, were identified. About 90.63% of the codons ended with A or U bases, and 98.63% of monomers contained A/T, which contributed to the high A/T content (55.91%) of the complete mt genome. Six genes (<em>ATP8, CCMFC, NAD4, RPL10, RPL5</em> and <em>RPS</em>4) showed positive selection. Phylogenetic analysis indicates that L. <em>cylindrica</em> is closely related to <em>L. acutangula</em>. The present results provide the mt genome of L. <em>cylindrica</em>, which may facilitate possible genetic variation, evolutionary, and molecular breeding studies of L. <em>cylindrica</em>.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000806/pdfft?md5=1c6eb87519146fab240119875fc8163b&pid=1-s2.0-S0888754324000806-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140944706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-01DOI: 10.1016/j.ygeno.2024.110849
Guo-Le Qin , Chuan-Ming Fu , Fan Tang , Jian Yin , De-Long Guan , Chen-Yu Shi
Paulownia fortunei is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance Paulownia germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common Paulownia. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common Paulownia, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis, and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during Paulownia breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity.
{"title":"Population genomics analysis reveals footprints of selective breeding in a rapid-growth variety of Paulownia fortunei with apical dominance","authors":"Guo-Le Qin , Chuan-Ming Fu , Fan Tang , Jian Yin , De-Long Guan , Chen-Yu Shi","doi":"10.1016/j.ygeno.2024.110849","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110849","url":null,"abstract":"<div><p><em>Paulownia fortunei</em> is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance <em>Paulownia</em> germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common <em>Paulownia</em>. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common <em>Paulownia</em>, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis, and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during <em>Paulownia</em> breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000703/pdfft?md5=177ff9f7358e8c8b41b4ae8cd4f3ff97&pid=1-s2.0-S0888754324000703-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140816008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-01DOI: 10.1016/j.ygeno.2024.110846
Xiao Yan , Kaihong Xu , Zhijuan Xu , Cong Shi , Binbin Lai , Hao Wu , Shujun Yang , Lixia Sheng , Keting Wang , Yuhan Zheng , Guifang Ouyang , Di Yang
Period circadian regulator 3 (PER3) functions as a tumor suppressor in various cancers. However, the role of PER3 in multiple myeloma (MM) has not been reported yet. Through this study, we aimed to investigate the potential role of PER3 in MM and the underlying mechanisms. RT-qPCR and western blotting were used to determine the mRNA and protein expression levels of PER3. Glyoxylate reductase 1 homolog (GLYR1) was predicted to be a transcription factor of PER3. The binding sites of GLYR1 on the promoter region of PER3 were analyzed using UCSC and confirmed using luciferase and chromatin immunoprecipitation assays. Viability, apoptosis, and metathesis were determined using CCK-8, colony formation, TUNEL, and transwell assays. We found that PER3 expression decreased in MM. Low PER3 levels may predict poor survival rates; PER3 overexpression suppresses the viability and migration of MM cells and promotes apoptosis. Moreover, GLYR1 transcriptionally activates PER3, and the knockdown of PER3 alleviates the effects of GLYR1 and induces its malignant behavior in MM cells. To conclude, GLYR1 upregulates PER3 and suppresses the aggressive behavior of MM cells, suggesting that GLYR1/PER3 signaling may be a potential therapeutic target for MM.
周期昼夜节律调节因子3(PER3)在多种癌症中发挥着肿瘤抑制因子的作用。然而,PER3在多发性骨髓瘤(MM)中的作用尚未见报道。本研究旨在探讨 PER3 在 MM 中的潜在作用及其内在机制。研究采用 RT-qPCR 和 Western 印迹法测定 PER3 的 mRNA 和蛋白表达水平。据预测,乙醛酸还原酶1同源物(GLYR1)是PER3的转录因子。使用 UCSC 分析了 GLYR1 在 PER3 启动子区域的结合位点,并使用荧光素酶和染色质免疫共沉淀试验进行了确认。使用 CCK-8、菌落形成、TUNEL 和透孔试验测定了细胞的活力、凋亡和变态反应。我们发现,PER3 在 MM 中的表达量减少。PER3水平低可能预示着存活率低;PER3过表达会抑制MM细胞的活力和迁移,并促进细胞凋亡。此外,GLYR1 可转录激活 PER3,而 PER3 的敲除可减轻 GLYR1 的影响并诱导 MM 细胞的恶性行为。总之,GLYR1能上调PER3并抑制MM细胞的侵袭行为,这表明GLYR1/PER3信号转导可能是MM的潜在治疗靶点。
{"title":"GLYR1 transcriptionally regulates PER3 expression to promote the proliferation and migration of multiple myeloma","authors":"Xiao Yan , Kaihong Xu , Zhijuan Xu , Cong Shi , Binbin Lai , Hao Wu , Shujun Yang , Lixia Sheng , Keting Wang , Yuhan Zheng , Guifang Ouyang , Di Yang","doi":"10.1016/j.ygeno.2024.110846","DOIUrl":"10.1016/j.ygeno.2024.110846","url":null,"abstract":"<div><p>Period circadian regulator 3 (PER3) functions as a tumor suppressor in various cancers. However, the role of PER3 in multiple myeloma (MM) has not been reported yet. Through this study, we aimed to investigate the potential role of PER3 in MM and the underlying mechanisms. RT-qPCR and western blotting were used to determine the mRNA and protein expression levels of PER3. Glyoxylate reductase 1 homolog (GLYR1) was predicted to be a transcription factor of PER3. The binding sites of GLYR1 on the promoter region of PER3 were analyzed using UCSC and confirmed using luciferase and chromatin immunoprecipitation assays. Viability, apoptosis, and metathesis were determined using CCK-8, colony formation, TUNEL, and transwell assays. We found that PER3 expression decreased in MM. Low PER3 levels may predict poor survival rates; PER3 overexpression suppresses the viability and migration of MM cells and promotes apoptosis. Moreover, GLYR1 transcriptionally activates PER3, and the knockdown of PER3 alleviates the effects of GLYR1 and induces its malignant behavior in MM cells. To conclude, GLYR1 upregulates PER3 and suppresses the aggressive behavior of MM cells, suggesting that GLYR1/PER3 signaling may be a potential therapeutic target for MM.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000673/pdfft?md5=1db0208b29c310e79e0ade3ca93b6973&pid=1-s2.0-S0888754324000673-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140760169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-24DOI: 10.1016/j.ygeno.2024.110848
Qishen Gu , Xing Lv , Dongmei Zhang, Yan Zhang, Xingyi Wang, Huifeng Ke, Jun Yang, Bin Chen, Liqiang Wu, Guiyin Zhang, Xingfen Wang, Zhengwen Sun, Zhiying Ma
Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090, GhM_D05G1692, GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.
{"title":"Deepening genomic sequences of 1081 Gossypium hirsutum accessions reveals novel SNPs and haplotypes relevant for practical breeding utility","authors":"Qishen Gu , Xing Lv , Dongmei Zhang, Yan Zhang, Xingyi Wang, Huifeng Ke, Jun Yang, Bin Chen, Liqiang Wu, Guiyin Zhang, Xingfen Wang, Zhengwen Sun, Zhiying Ma","doi":"10.1016/j.ygeno.2024.110848","DOIUrl":"10.1016/j.ygeno.2024.110848","url":null,"abstract":"<div><p>Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, <em>GhM_A12G0090</em>, <em>GhM_D05G1692</em>, <em>GhM_D12G3135</em> were identified and <em>GhM_D11G2208</em> function was identified in <em>Arabidopsis</em>. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000697/pdfft?md5=f76293895f88f3992a94100b07d3c7ba&pid=1-s2.0-S0888754324000697-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140788432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-11DOI: 10.1016/j.ygeno.2024.110842
Elena Espinosa , Rocio Bautista , Rafael Larrosa , Oscar Plata
The recent advent of long read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), have led to substantial improvements in accuracy and computational cost in sequencing genomes. However, de novo whole-genome assembly still presents significant challenges related to the quality of the results. Pursuing de novo whole-genome assembly remains a formidable challenge, underscored by intricate considerations surrounding computational demands and result quality. As sequencing accuracy and throughput steadily advance, a continuous stream of innovative assembly tools floods the field. Navigating this dynamic landscape necessitates a reasonable choice of sequencing platform, depth, and assembly tools to orchestrate high-quality genome reconstructions. This comprehensive review delves into the intricate interplay between cutting-edge long read sequencing technologies, assembly methodologies, and the ever-evolving field of genomics. With a focus on addressing the pivotal challenges and harnessing the opportunities presented by these advancements, we provide an in-depth exploration of the crucial factors influencing the selection of optimal strategies for achieving robust and insightful genome assemblies.
{"title":"Advancements in long-read genome sequencing technologies and algorithms","authors":"Elena Espinosa , Rocio Bautista , Rafael Larrosa , Oscar Plata","doi":"10.1016/j.ygeno.2024.110842","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110842","url":null,"abstract":"<div><p>The recent advent of long read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), have led to substantial improvements in accuracy and computational cost in sequencing genomes. However, <em>de novo</em> whole-genome assembly still presents significant challenges related to the quality of the results. Pursuing <em>de novo</em> whole-genome assembly remains a formidable challenge, underscored by intricate considerations surrounding computational demands and result quality. As sequencing accuracy and throughput steadily advance, a continuous stream of innovative assembly tools floods the field. Navigating this dynamic landscape necessitates a reasonable choice of sequencing platform, depth, and assembly tools to orchestrate high-quality genome reconstructions. This comprehensive review delves into the intricate interplay between cutting-edge long read sequencing technologies, assembly methodologies, and the ever-evolving field of genomics. With a focus on addressing the pivotal challenges and harnessing the opportunities presented by these advancements, we provide an in-depth exploration of the crucial factors influencing the selection of optimal strategies for achieving robust and insightful genome assemblies.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000636/pdfft?md5=603d081d81256facebeb344b90f2edff&pid=1-s2.0-S0888754324000636-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140551364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-11DOI: 10.1016/j.ygeno.2024.110845
Qing Lu , Qin Tian , Wei Gu , Chen-Xuan Yang , Ding-Jie Wang , Ting-Shuang Yi
Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.
{"title":"Comparative genomics on chloroplasts of Rubus (Rosaceae)","authors":"Qing Lu , Qin Tian , Wei Gu , Chen-Xuan Yang , Ding-Jie Wang , Ting-Shuang Yi","doi":"10.1016/j.ygeno.2024.110845","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110845","url":null,"abstract":"<div><p><em>Rubus</em>, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple <em>Rubus</em> species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of <em>Rubus</em>, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of <em>Rubus</em> exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the <em>Rubus</em> plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of <em>Rubus</em> was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of <em>Rubus</em>, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000661/pdfft?md5=bbaf540cbe213064572298c478656801&pid=1-s2.0-S0888754324000661-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140618539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}