IF 3.1 3区生物学

Genome Pub Date : 2024-01-01 Epub Date: 2023-09-25 DOI: 10.1139/gen-2023-0044

Kenta Nakashima, Mashiro Yuhazu, Shun Mikuriya, Megumi Kasai, Jun Abe, Akito Taneda, Akira Kanazawa

{"title":"Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location.","authors":"Kenta Nakashima, Mashiro Yuhazu, Shun Mikuriya, Megumi Kasai, Jun Abe, Akito Taneda, Akira Kanazawa","doi":"10.1139/gen-2023-0044","DOIUrl":"10.1139/gen-2023-0044","url":null,"abstract":"Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon SORE-1. We analyzed SORE-1, inserted in exon 1 of the GmphyA2 gene, one of the newest insertions in this family so far identified. Cytosine methylation was detected in this element but was barely present in the adjacent regions. These results were correlated, respectively, with the presence and absence of the production of short interfering RNAs. Cytosine methylation profiles of 74 SORE-1 elements in the Williams 82 reference genome indicated that methylation frequency in the adjacent regions of SORE-1 was profoundly higher in pericentromeric regions than in euchromatic chromosome arms and was only weakly correlated with the length of time after insertion into the genome. Notably, the higher level of methylation in the 5' adjacent regions of SORE-1 coincided with the presence of repetitive elements in pericentromeric regions. Together, these results suggest that epigenetic influence of SORE-1 on the adjacent regions is influenced by its location on the chromosome.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":3.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41117856","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

Note of appreciation. 感谢信

IF 3.1 3区生物学

Genome Pub Date : 2024-01-01 DOI: 10.1139/gen-2023-0092

引用次数: 0

Genomic analysis of the MLST population structure and antimicrobial resistance genes associated with Salmonella enterica in Mexico. 墨西哥肠炎沙门氏菌MLST群体结构和耐药基因的基因组分析。

IF 3.1 3区生物学

Genome Pub Date : 2023-12-01 Epub Date: 2023-07-21 DOI: 10.1139/gen-2023-0007

Adrián Gómez-Baltazar, Angélica Godínez-Oviedo, Gerardo Vázquez-Marrufo, Ma Soledad Vázquez-Garcidueñas, Montserrat Hernández-Iturriaga

{"title":"Genomic analysis of the MLST population structure and antimicrobial resistance genes associated with Salmonella enterica in Mexico.","authors":"Adrián Gómez-Baltazar, Angélica Godínez-Oviedo, Gerardo Vázquez-Marrufo, Ma Soledad Vázquez-Garcidueñas, Montserrat Hernández-Iturriaga","doi":"10.1139/gen-2023-0007","DOIUrl":"10.1139/gen-2023-0007","url":null,"abstract":"Salmonella enterica is one of the most commonly reported foodborne pathogens by public health agencies worldwide. In this study, the multilocus sequence typing (MLST) population structure and frequency of antimicrobial resistance (AMR) genes were evaluated in S. enterica strains from Mexico (n = 2561). The most common sources of isolation were food (44.28%), environment (27.41%), animal-related (24.83%), and human (3.48%). The most prevalent serovars were Newport (8.51%), Oranienburg (7.03%), Anatum (5.78%), Typhimurium (5.12%), and Infantis (4.57%). As determined by the 7-gene MLST scheme, the most frequent sequence types were ST23, ST64, and ST32. The core genome MLST scheme identified 132 HC2000 and 195 HC900 hierarchical clusters, with the HC2000_2 cluster being the most prevalent in Mexico (n = 256). A total of 78 different AMR genes belonging to 13 antimicrobial classes were detected in 638 genomic assemblies of S. enterica. The most frequent class was aminoglycosides (31.76%), followed by tetracyclines (12.53%) and sulfonamides (11.91%). These results can help public health agencies in Mexico prioritize their efforts and resources to increase the genomic sequencing of circulating Salmonella strains. Additionally, they provide valuable information for local and global public health efforts to reduce the impact of foodborne diseases and AMR.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"319-332"},"PeriodicalIF":3.1,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10069175","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

Glycolate oxidase gene family identification and functional analyses in cotton resistance to Verticillium wilt. 棉花抗黄萎病乙醇酸氧化酶基因家族鉴定及功能分析。

IF 3.1 3区生物学

Genome Pub Date : 2023-12-01 Epub Date: 2023-07-20 DOI: 10.1139/gen-2023-0002

Lijun Dong, Xue Zhang, Meng Wang, Xiaohong Fu, Guixia Liu, Shuling Zhang

{"title":"Glycolate oxidase gene family identification and functional analyses in cotton resistance to Verticillium wilt.","authors":"Lijun Dong, Xue Zhang, Meng Wang, Xiaohong Fu, Guixia Liu, Shuling Zhang","doi":"10.1139/gen-2023-0002","DOIUrl":"10.1139/gen-2023-0002","url":null,"abstract":"Glycolate oxidase (GOX) plays an important role in the regulation of photorespiration and photosynthesis in plants. However, as one of the main enzymes to produce the second messenger hydrogen peroxide (H2O2), its functions in response to pathogens are still poorly understood. In this study, we carried out genome-wide identification, and 14 GOX genes were identified in Gossypium hirsutum. These GOX genes are located on 10 chromosomes and divided into hydroxyacid-oxidases (HAOX) and GOX groups. After infection with Verticillium dahliae Kleb., six GOX gene expression levels were changed. Moreover, H2O2, salicylic acid (SA), and the content and activity of GOX increased in cotton. GhHAOX2-D-silenced plants showed more wilting than control plants after infection with V. dahliae. Additionally, H2O2 accumulation and SA content were reduced in GhHAOX2-D-silenced plants. The expression levels of GhPAL, GhPAD4, and GhPR1 and the lignin content of the silenced plants were significantly lower than those of the control plants. These results indicate that GhHAOX2-D is a positive regulator of Verticillium wilt tolerance in cotton and may promote H2O2 accumulation via the synergistic effects of GOX genes and SA. Collectively, GOX genes play an important role in cotton resistance to Verticillium wilt.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"305-318"},"PeriodicalIF":3.1,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10101225","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

Half-chromatid mutation as a possible cause of mosaic males and females in Hymenoptera and rare fertile male tortoiseshell cats. 半染色单体突变是膜翅目和稀有可育雄性龟壳猫中雄性和雌性马赛克的可能原因。

IF 3.1 3区生物学

Genome Pub Date : 2023-11-01 Epub Date: 2023-06-12 DOI: 10.1139/gen-2023-0006

Robin E Owen

{"title":"Half-chromatid mutation as a possible cause of mosaic males and females in Hymenoptera and rare fertile male tortoiseshell cats.","authors":"Robin E Owen","doi":"10.1139/gen-2023-0006","DOIUrl":"10.1139/gen-2023-0006","url":null,"abstract":"Half-chromatid mutations occur when a single base change in a gamete is transmitted to the zygote, which, after DNA replication and cleavage, will result in a mosaic individual. These mutations will be passed on through the germ plasm and also may be expressed somatically. Half-chromatid mutation has been suggested to account for the observed lower frequency of males than expected for lethal X-linked recessive disorders in humans, such as Lesch-Nyhan syndrome, incontinentia pigmenti, and Duchene muscular dystrophy. Although attention has been paid to half-chromatid mutation in humans, it otherwise has been ignored. Here I show that half-chromatid mutation in haplodiploid organisms, such as Hymenoptera, has some interesting and important consequences: (i) since all genes follow the X-linked pattern of inheritance, half-chromatid mutations should be relatively easier to detect; (ii) recessive mutations of all viabilities may be expected; (iii) mosaics of both sexes are expected in haplodiploids with half-chromatid mutation; (iv) gynandromorphs could result from half-chromatid mutation at the sex-determination locus, in species with single-locus complementary sex-determination. Finally, half-chromatid mutation can account for the rare fertile male tortoiseshell phenotype observed in the domestic cat, Felis catus, and which still has not been fully accounted for by other mechanisms.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"295-304"},"PeriodicalIF":3.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10385581","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

Comparative plastomes of species from Phrymaceae and Mazaceae: insights into adaptive evolution, codon usage bias, and phylogenetic relationships. Phrymaceae和Mazaceae物种的比较质体：对适应性进化、密码子使用偏差和系统发育关系的见解。

IF 3.1 3区生物学

Genome Pub Date : 2023-11-01 Epub Date: 2023-05-09 DOI: 10.1139/gen-2023-0014

Xiaofeng Chi, Ronglian Chen, Faqi Zhang, Shilong Chen

引用次数: 0

Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. 辣椒染色体远端重复DNA序列的丰富性。

IF 3.1 3区生物学

Genome Pub Date : 2023-10-01 Epub Date: 2023-06-26 DOI: 10.1139/gen-2022-0083

Rafael de Assis, Leandro S A Gonçalves, Romain Guyot, André Laforga Vanzela

{"title":"Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes.","authors":"Rafael de Assis, Leandro S A Gonçalves, Romain Guyot, André Laforga Vanzela","doi":"10.1139/gen-2022-0083","DOIUrl":"10.1139/gen-2022-0083","url":null,"abstract":"Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition, and genomic distribution has been provided. Here, we exploited the noncoding repetitive fraction, represented by satellite sequences, that tends to accumulate in blocks along chromosomes, especially near the chromosome ends of peppers. Two satellite DNA sequences were identified (CDR-1 and CDR-2), characterized and mapped in silico in three Capsicum genomes (C. annuum, C. chinense, and C. baccatum) using data from the published high-coverage sequencing and repeats finding bioinformatic tools. Localization using FISH in the chromosomes of these species and in two others (C. frutescens and C. chacoense), totaling five species, showed signals adjacent to the rDNA sites. A sequence comparison with existing Solanaceae repeats showed that CDR-1 and CDR-2 have different origins but without homology to rDNA sequences. Satellites occupied subterminal chromosomal regions, sometimes collocated with or adjacent to 35S rDNA sequences. Our results expand knowledge about the diversity of subterminal regions of Capsicum chromosomes, showing different amounts and distributions within and between karyotypes. In addition, these sequences may be useful for future phylogenetic studies.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"269-280"},"PeriodicalIF":3.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9946603","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

Identification of alternative splicing and RNA-binding proteins involved in myocardial ischemia-reperfusion injury. 心肌缺血再灌注损伤中选择性剪接和RNA结合蛋白的鉴定。

IF 3.1 3区生物学

Genome Pub Date : 2023-10-01 Epub Date: 2023-07-19 DOI: 10.1139/gen-2022-0102

Li Feng, Min Guo, Chunrong Jin

{"title":"Identification of alternative splicing and RNA-binding proteins involved in myocardial ischemia-reperfusion injury.","authors":"Li Feng, Min Guo, Chunrong Jin","doi":"10.1139/gen-2022-0102","DOIUrl":"10.1139/gen-2022-0102","url":null,"abstract":"Alternative splicing (AS) and RNA-binding proteins (RBPs) have been implicated in various cardiovascular diseases. Yet, a comprehensive understanding of their role in myocardial ischemia-reperfusion injury (MIRI) remains elusive. We aimed to identify potential therapeutic targets for MIRI by studying genome-wide changes in AS events and RBPs. We analyzed RNA-seq data from ischemia-reperfusion mouse models and the control group from the GSE130217 data set using Splicing Site Usage Variation Analysis software. We identified 28 regulated alternative splicing events (RASEs) and 47 differentially expressed RBP (DE-RBP) genes in MIRI. Most variable splicing events were involved in cassette exon, alternative 5' splice, alternative 3' splice, and retained intron types. Gene Ontology and Kyoto Encyclopedia of Genes (KOBAS 2.0 server) and Genomes pathway enrichment analyses showed that the differentially expressed variable splicing and RBP genes were mainly enriched in pathways related to myocardial function. The RBP-RASE network demonstrated a common variance relationship between DE-RBPs and RASEs, indicating that RBPs regulate variable shear events in MIRI. This study systematically identified important alterations in RASEs and RBPs in MIRI, expanding our understanding of the underlying pathogenesis of MIRI.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"261-268"},"PeriodicalIF":3.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9834768","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

A species-specific digital PCR assay for the endangered blue racer (Coluber constrictor foxii) in Canada. 濒危的加拿大蓝尾蛇(哥伦比亚蟒蛇foxii)的种特异性数字PCR分析。

IF 3.1 3区生物学

Genome Pub Date : 2023-09-01 DOI: 10.1139/gen-2023-0008

Orianne Tournayre, Ryan Wolfe, Hannah McCurdy-Adams, Amy A Chabot, Stephen C Lougheed

{"title":"A species-specific digital PCR assay for the endangered blue racer (Coluber constrictor foxii) in Canada.","authors":"Orianne Tournayre, Ryan Wolfe, Hannah McCurdy-Adams, Amy A Chabot, Stephen C Lougheed","doi":"10.1139/gen-2023-0008","DOIUrl":"https://doi.org/10.1139/gen-2023-0008","url":null,"abstract":"The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 9","pages":"251-260"},"PeriodicalIF":3.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10139605","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

Phylogenomics of transcriptionally active AP2/ERF and bHLH transcription factors and study of their promoter regions in Nothapodytes nimmoniana (J.Graham) Mabb. Nothapodytes nimmonana转录活性AP2/ERF和bHLH转录因子的系统基因组学及其启动子区研究(J.Graham) mab。

IF 3.1 3区生物学

Genome Pub Date : 2023-09-01 DOI: 10.1139/gen-2023-0009

Rucha C Godbole, Swapnil B Kadam, Anupama A Pable, Sudhir Singh, Vitthal T Barvkar

{"title":"Phylogenomics of transcriptionally active AP2/ERF and bHLH transcription factors and study of their promoter regions in Nothapodytes nimmoniana (J.Graham) Mabb.","authors":"Rucha C Godbole, Swapnil B Kadam, Anupama A Pable, Sudhir Singh, Vitthal T Barvkar","doi":"10.1139/gen-2023-0009","DOIUrl":"https://doi.org/10.1139/gen-2023-0009","url":null,"abstract":"Nothapodytes nimmoniana is a medicinally important plant producing anticancer monoterpene indole alkaloid (MIA), camptothecin (CPT). The CPT is synthesised through the strictosidine intermediate following the MIA pathway; however, transcriptional regulation of CPT pathway is still elusive in N. nimmoniana. Biosynthesis of MIA is regulated by various transcription factors (TFs) belonging to AP2/ERF, bHLH, MYB, and WRKY families. The present study identified transcriptionally active full-length 105 AP2/ERF and 68 bHLH family TFs from the N. nimmoniana. AP2/ERF TFs were divided into three subfamilies along with a soloist, while bHLH TFs were divided into 10 subfamilies according to their phylogenetic similarities. Three group IXa ERFs, Nn-ERF22, Nn-ERF29, and Nn-ERF41, one subfamily IVa TF Nn-bHLH7, and three subfamilies IIIe Nn-bHLH33, Nn-bHLH51, and Nn-bHLH52 clustered with the TFs regulating alkaloid biosynthesis in Catharanthus roseus, tomato, tobacco, and Artemisia annua. Expression of these TFs in N. nimmoniana was higher in roots, which is a primary CPT accumulating tissue. Moreover, genome skimming approach was used to reconstruct the promoter regions of candidate ERF genes to identify the cis-regulatory elements. The presence of G-boxes and other jasmonic acid-responsive elements in the promoter suggests the regulation of ERFs by bHLHs. The present study effectively generated and used genomics resource for characterisation of regulatory TFs from non-model medicinal plant.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 9","pages":"235-250"},"PeriodicalIF":3.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10132974","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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