IF 3.1 3区生物学

Genome Pub Date : 2023-01-01 DOI: 10.1139/gen-2021-0111

Shaocheng Bai, Shuaishuai Hu, Yingying Dai, Rongshuai Jin, Chen Zhang, Fan Yao, Qiaoqin Weng, Pin Zhai, Bohao Zhao, Xinsheng Wu, Yang Chen

{"title":"NRAS promotes the proliferation of melanocytes to increase melanin deposition in Rex rabbits.","authors":"Shaocheng Bai, Shuaishuai Hu, Yingying Dai, Rongshuai Jin, Chen Zhang, Fan Yao, Qiaoqin Weng, Pin Zhai, Bohao Zhao, Xinsheng Wu, Yang Chen","doi":"10.1139/gen-2021-0111","DOIUrl":"https://doi.org/10.1139/gen-2021-0111","url":null,"abstract":"Melanocytes play a major role in the formation of mammalian fur color and are regulated by several genes. Despite playing the pivotal role in the study of melanoma, the mechanistic role of NRAS (neuroblastoma RAS viral oncogene homolog) in the formation of mammalian epidermal color is still elusive. First of all, the expression levels of NRAS mRNA and protein in the dorsal skin of different colored Rex rabbits were detected by qRT-PCR and Western blot. Then, the subcellular localization of NRAS was identified in melanocytes by indirect immunofluorescence. Next, the expression of NRAS was overexpressed and knocked down in melanocytes, and its efficiency was verified by qRT-PCR and Western blot. Subsequently, NaOH, CCK-8, and Annexin V-FITC were used to verify the changes in melanin content, proliferation, and apoptosis in melanocytes. Finally, we analyzed the regulation of NRAS on other genes (MITF, TYR, DCT, PMEL, and CREB) that affect melanin production. In silico studies showed NRAS as a stable and hydrophilic protein, and it is localized in the cytoplasm and nucleus of melanocytes. The mRNA and protein expression levels of NRAS were significantly different in skin of different colored Rex rabbits, and the highest level was found in black skin (P < 0.01). Moreover, the NRAS demonstrated impact on the proliferation, apoptosis, and melanin production of melanocytes (P < 0.05), and the strong correlation of NRAS with melanin-related genes was evidently observed (P < 0.05). Our results suggested that NRAS can be used as a gene that regulates melanin production and controls melanocyte proliferation and apoptosis, providing a new theoretical basis for studying the mechanism of mammalian fur color formation.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10547991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosomes in the African frog genus Tomopterna (Pyxicephalidae) and probing the origin of tetraploid Tomopterna tandyi. 非洲平尾蛙属(Pyxicephalidae)的染色体与四倍体Tomopterna tandyi起源的探讨。

IF 3.1 3区生物学

Genome Pub Date : 2022-12-01 Epub Date: 2022-10-12 DOI: 10.1139/gen-2022-0053

James P Bogart, Abeda Dawood, François S Becker, Alan Channing

{"title":"Chromosomes in the African frog genus Tomopterna (Pyxicephalidae) and probing the origin of tetraploid Tomopterna tandyi.","authors":"James P Bogart, Abeda Dawood, François S Becker, Alan Channing","doi":"10.1139/gen-2022-0053","DOIUrl":"https://doi.org/10.1139/gen-2022-0053","url":null,"abstract":"Speciation by polyploidization has been documented to have independently occurred in 12 families of anuran amphibians. Tomopterna tandyi was described as a South African allotetraploid species of sand frogs in the family Pyxicephalidae. Recent taxonomic revisions and new species descriptions in the genus present problems with respect to the evolution of this tetraploid species. Chromosomes, mitochondrial and nuclear gene sequences, isozymes, and male mating calls were examined for T. tandyi and for diploid species of Tomopterna. Mitochondrial sequences confirmed the diploid species, T. adiastola, to be the maternal ancestor that gave rise to the tetraploid about 5 mya. Nuclear sequences and isozymes reveal a complex reticulation of paternal ancestry that may be explained by occasional hybridization of T. tandyi with diploid species of Tompoterna at various times in sympatric populations. Interspecific diploid to tetraploid gene introgression is suspected to have also occurred in Australian and North American tetraploid species of frogs. Diploid to tetraploid introgression is facilitated through triploid hybrids that are more viable than diploid hybrids and produce unreduced triploid eggs.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33501701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Autophagy in cell fate decisions: knowledge gained from Drosophila. 细胞命运决定中的自噬:从果蝇那里获得的知识。

IF 3.1 3区生物学

Genome Pub Date : 2022-12-01 Epub Date: 2022-10-14 DOI: 10.1139/gen-2022-0069

Camille Lacarrière-Keïta, Sonya Nassari, Steve Jean

引用次数: 0

Fine mapping of a major QTL qPA7-1 for low hydrocyanic acid content in sorghum-sudangrass hybrid. 高粱-苏丹草杂种低氢氰酸主要QTL qPA7-1的精细定位。

IF 3.1 3区生物学

Genome Pub Date : 2022-12-01 Epub Date: 2022-09-15 DOI: 10.1139/gen-2021-0114

Guofang Wu, Xiaoxia Yu, Zhuo Yu, Qianqian Lu, Dongsheng Yang, Yue Shi, Jiaqi Li, Jingwei Li

{"title":"Fine mapping of a major QTL qPA7-1 for low hydrocyanic acid content in sorghum-sudangrass hybrid.","authors":"Guofang Wu, Xiaoxia Yu, Zhuo Yu, Qianqian Lu, Dongsheng Yang, Yue Shi, Jiaqi Li, Jingwei Li","doi":"10.1139/gen-2021-0114","DOIUrl":"https://doi.org/10.1139/gen-2021-0114","url":null,"abstract":"The purpose of this study was to study the genetic mechanism of low hydrocyanic acid (HCN) content. The segregation of HCN content trait in fresh stems and leaves was determined in the sorghum (Sorghum bicolor (L.) Moench)-sudangrass (Sorghum sudanense (Piper) Stapf) hybrid F2 population (N = 1200), also used to detect a quantitative trait locus (QTL) for HCN content. Our hypothesis was that the additive effect of QTL was negative, showing that QTL was associated with low HCN. In the present research, a total of 11 simple sequence repeats (SSR) polymorphic primers were screened, and four SSR markers associated with low HCN content were developed based on the bulked segregant analysis method. A high-resolution genetic linkage group of the previously known qPA7-1 locus of the low HCN trait was constructed by analyzing different populations, families, and recombinants. Then, the QTL qPA7-1 of sorghum-sudangrass hybrid was fine-mapped to a 203.6 kb region between markers SORBI4G4-120 and SORBI4G4-680, and seven candidate genes for low HCN were predicted in this region based on sequence comparison with the sorghum reference genome. According to gene annotation, the candidate genes related to low HCN content may be different from those involved in the known regulation mode of sorghum dhurrin biosynthesis and metabolism.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40358015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

miR-181a-5p is a potential candidate epigenetic biomarker in multiple sclerosis. miR-181a-5p是多发性硬化症的潜在候选表观遗传生物标志物。

IF 3.1 3区生物学

Genome Pub Date : 2022-11-01 Epub Date: 2022-09-14 DOI: 10.1139/gen-2022-0040

Tuba Gökdoğan Edgünlü, Şenay Görücü Yılmaz, Ufuk Emre, Bahar Taşdelen, Oktay Kuru, Gülnihal Kutlu, Mehmet Emin Erdal

{"title":"miR-181a-5p is a potential candidate epigenetic biomarker in multiple sclerosis.","authors":"Tuba Gökdoğan Edgünlü, Şenay Görücü Yılmaz, Ufuk Emre, Bahar Taşdelen, Oktay Kuru, Gülnihal Kutlu, Mehmet Emin Erdal","doi":"10.1139/gen-2022-0040","DOIUrl":"https://doi.org/10.1139/gen-2022-0040","url":null,"abstract":"Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by demyelination and axonal degeneration. Abnormal expression of microRNAs (miRNAs) plays an important role in MS pathology. In this cohort study, differential expression of the four miRNAs (hsa-miR-155-5p, hsa-miR-9-5p, hsa-miR-181a-5p, and hsa-miR-125b-5p) was investigated in 69 individuals, including 39 MS patients (relapsing-remitting MS (RRMS), n = 27; secondary progressive MS (SPMS), n = 12) and 30 healthy controls. In silico analyses revealed possible genes and pathways specific to miRNAs. Peripheral blood miRNA expressions were detected by quantitative real-time PCR (qPCR). hsa-miR-181a-5p was downregulated and associated with increased MS risk (P = 0.012). The other three miRNAs were upregulated and not associated with MS (P < 0.05). The area under the curve (AUC) is 0.779. In silico analyses showed that hsa-miR-181a-5p may participate in MS pathology by targeting MAP2K1, CREB1, ATXN1, and ATXN3 genes in inflammation and neurodegeneration pathways. The circulatory hsa-miR-181a-5p can regulate target genes, reversing the mechanisms involved in MS pathologies such as protein uptake and processing, cell proliferation and survival, inflammation, and neurodegeneration. Thus, this miRNA could be used as an epigenomic-guided diagnostic tool and for therapeutic purpose.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40356582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Using telomeric length measurements and methylation to understand the karyotype diversification of Ctenomys minutus (a small fossorial mammal). 使用端粒长度测量和甲基化来了解分钟栉水母(一种小型化石哺乳动物)的核型多样化。

IF 3.1 3区生物学

Genome Pub Date : 2022-11-01 Epub Date: 2022-08-31 DOI: 10.1139/gen-2022-0018

C A Matzenbacher, J Da Silva, A L H Garcia, R Kretschmer, M Cappetta, E H C de Oliveira, T R O de Freitas

{"title":"Using telomeric length measurements and methylation to understand the karyotype diversification of Ctenomys minutus (a small fossorial mammal).","authors":"C A Matzenbacher, J Da Silva, A L H Garcia, R Kretschmer, M Cappetta, E H C de Oliveira, T R O de Freitas","doi":"10.1139/gen-2022-0018","DOIUrl":"https://doi.org/10.1139/gen-2022-0018","url":null,"abstract":"The genus Ctenomys has been widely used in karyotype evolution studies due to the variation in their diploid numbers. Ctenomys minutus is characterized by intraspecific variation in diploid number (2n = 42, 46, 48, and 50), which makes it an interesting model to investigate genomic rearrangements mechanisms that could lead to different cytotypes in this species. Thereupon, it has been already shown that DNA methylation may participate in chromosome structure. Therefore, we aimed to investigate whether telomeres and global DNA methylation had a role in the genome rearrangements that led to this variation in C. minutus. We also realized an analysis for the presence of intrachromosomal telomeric repeats (ITRs) by fluorescence in situ hybridization. Our study demonstrated that neither telomere length nor DNA methylation had significant differences among the cytotypes. However, if only females were considered, there were significant differences for telomere length and methylation. Young individuals, regardless of their cytotypes, had the most methylated DNA. Regarding the ITRs, we found a signal on chromosome 1 in 2n = 50b. No evidence was found that telomere length or methylation could have influenced chromosomal rearrangements, although new cytotypes seem to have emerged within the distribution of parental cytotypes by the accumulation of different chromosomal rearrangements.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40334923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of the 12-oxophytoeienoic acid reductase (OPR) gene family in pepper (Capsicum annuum L.) and functional characterization of CaOPR6 in pepper fruit development and stress response. 辣椒(Capsicum annuum L.) 12-氧植物烯酸还原酶(OPR)基因家族的鉴定及CaOPR6在辣椒果实发育和胁迫响应中的功能表征

IF 3.1 3区生物学

Genome Pub Date : 2022-11-01 Epub Date: 2022-08-09 DOI: 10.1139/gen-2022-0037

Wen-Feng Nie, Yue Chen, Junjie Tao, Yu Li, Jianping Liu, Yong Zhou, Youxin Yang

{"title":"Identification of the 12-oxophytoeienoic acid reductase (OPR) gene family in pepper (Capsicum annuum L.) and functional characterization of CaOPR6 in pepper fruit development and stress response.","authors":"Wen-Feng Nie, Yue Chen, Junjie Tao, Yu Li, Jianping Liu, Yong Zhou, Youxin Yang","doi":"10.1139/gen-2022-0037","DOIUrl":"https://doi.org/10.1139/gen-2022-0037","url":null,"abstract":"The 12-oxophytoeienoic acid reductase (OPR) is a kind of enzyme in the octadecanoid biosynthesis pathway that determines the biosynthesis of jasmonic acid. Although the roles of OPRs have been extensively studied in several crop plants, little is known about the biological functions of OPR-encoding genes in Capsicum annuum plants. In this study, seven OPR family genes (CaOPR1-7) were identified from the C. annuum genome. The physical and chemical properties of CaOPR1-7 were further analyzed, including gene expression patterns, promoter elements, and chromosomal locations. The results showed that the seven CaOPR homologues could be divided into two subgroups, and CaOPR6 was highly similar to AtOPR3 in Arabidopsis. The expression of CaOPR6 was significantly induced by various stresses such as cold, salt, and pathogen infection, indicating that CaOPR6 plays important roles in response to abiotic and biotic stresses. Overall, these findings improve the understanding of the biological functions of CaOPR6 in the development of pepper fruit and stress response of pepper plants, and facilitate further studies on the molecular biology of OPR proteins in Solanaceae vegetables.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40693140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Zebrafish optineurin: genomic organization and transcription regulation. 斑马鱼优神经蛋白:基因组组织和转录调控。

IF 3.1 3区生物学

Genome Pub Date : 2022-10-01 Epub Date: 2022-08-29 DOI: 10.1139/gen-2022-0019

Iris A L Silva, Débora Varela, M Leonor Cancela, Natércia Conceição

{"title":"Zebrafish optineurin: genomic organization and transcription regulation.","authors":"Iris A L Silva, Débora Varela, M Leonor Cancela, Natércia Conceição","doi":"10.1139/gen-2022-0019","DOIUrl":"https://doi.org/10.1139/gen-2022-0019","url":null,"abstract":"Optineurin (OPTN) is involved in a variety of mechanisms, such as autophagy, vesicle trafficking, and nuclear factor kappa-B (NF-κB) signaling. Mutations in the OPTN gene have been associated with different pathologies, including glaucoma, amyotrophic lateral sclerosis, and Paget's disease of bone. Since the relationship between fish and mammalian OPTN is not well understood, the objective of the present work was to characterize the zebrafish optn gene and protein structure and to investigate its transcriptional regulation. Through a comparative in silico analysis, we observed that zebrafish optn presents genomic features similar to those of its human counterpart, including its neighboring genes and structure. A comparison of OPTN protein from different species revealed a high degree of conservation in its functional domains and three-dimensional structure. Furthermore, our in vitro transient-reporter analysis identified a functional promoter in the upstream region of the zebrafish optn gene, along with a region important for its transcription regulation. Site-directed mutagenesis revealed that the NF-κB motif is responsible for the activation of this region. In conclusion, with this study, we characterize zebrafish optn and our results indicate that zebrafish can be considered as an alternative model to study OPTN's biological role in bone-related diseases.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33445757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of novel candidate of brown planthopper resistance gene Bph44 in rice (Oryza sativa L.). 水稻抗褐飞虱新候选基因Bph44的鉴定。

IF 3.1 3区生物学

Genome Pub Date : 2022-10-01 Epub Date: 2022-07-21 DOI: 10.1139/gen-2022-0020

Iwan Kiswanto, Lita Soetopo, Afifuddin Latif Adiredjo

引用次数: 3

Karyotype conservation and genomic organization of repetitive sequences in the leaf-cutting ant Atta cephalotes (Linnaeus, 1758) (Formicidae: Myrmicinae). 切叶蚁Atta cephalotes (Linnaeus, 1758)(蚁科:蚁科)重复序列的核型保存和基因组组织。

IF 3.1 3区生物学

Genome Pub Date : 2022-10-01 Epub Date: 2022-08-16 DOI: 10.1139/gen-2021-0129

Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Linda Inês Silveira, Jérôme Orivel, Denilce Meneses Lopes, Hilton Jeferson Alves Cardoso de Aguiar

{"title":"Karyotype conservation and genomic organization of repetitive sequences in the leaf-cutting ant Atta cephalotes (Linnaeus, 1758) (Formicidae: Myrmicinae).","authors":"Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Linda Inês Silveira, Jérôme Orivel, Denilce Meneses Lopes, Hilton Jeferson Alves Cardoso de Aguiar","doi":"10.1139/gen-2021-0129","DOIUrl":"https://doi.org/10.1139/gen-2021-0129","url":null,"abstract":"Leaf-cutting ants are among the New World's most conspicuous and studied ant species due to their notable ecological and economic roles. Cytogenetic studies carried out in Atta show remarkable karyotype conservation among the species. We performed classical cytogenetics and physical mapping of repetitive sequences in the leaf-cutting ant Atta cephalotes (Linnaeus, 1758), the type species of the genus. Our goal was to test the karyotype conservation in Atta and to understand the genomic organization and diversity regarding repetitive sequences in leaf-cutting ants. Atta cephalotes showed 2n = 22 (18m + 2sm + 2st) chromosomes. The heterochromatin followed a centromeric pattern, and the GC-rich regions and 18S rDNA clusters were co-located interstitially in the 4th metacentric pair. These cytogenetic characteristics were observed in other Atta species that had previously been studied, confirming the karyotype conservation in Atta. Evolutionary implications regarding the conservation of the chromosome number in leaf-cutting ants are discussed. Telomeric motif (TTAGG)n was detected in A. cephalotes as observed in other ants. Five out of the 11 microsatellites showed a scattered distribution exclusively on euchromatic areas of the chromosomes. Repetitive sequences mapped on the chromosomes of A. cephalotes are the first insights into genomic organization and diversity in leaf-cutting ants, useful in further comparative studies.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40615782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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