GenomePub Date : 2023-05-01DOI: 10.1139/gen-2022-0100
Kawalpreet Kaur, Swati Megha, Zhengping Wang, Nat N V Kav, Habibur Rahman
{"title":"Identification and expression analysis of C2H2-zinc finger protein genes reveals their role in stress tolerance in <i>Brassica napus</i>.","authors":"Kawalpreet Kaur, Swati Megha, Zhengping Wang, Nat N V Kav, Habibur Rahman","doi":"10.1139/gen-2022-0100","DOIUrl":"https://doi.org/10.1139/gen-2022-0100","url":null,"abstract":"<p><p>C2H2-zinc finger (C2H2-ZF) genes are involved in various biological processes in plants including stress response; however, they lack characterization in <i>Brassica napus</i>. We identified 267 C2H2-ZF genes in <i>B. napus</i> and deciphered their physiological properties, subcellular localization, structure, synteny, and phylogeny and investigated the expression of 20 genes in response to different stresses and phytohormone treatments. The 267 genes were distributed on 19 chromosomes; phylogenetic analysis categorized them into five clades. They varied from 0.41 to 9.2 kb in length, had stress-responsive <i>cis</i>-acting elements in promoter regions, and their protein length varied from 9 to 1366 amino acids. About 42% of the genes had one exon, and 88% genes had orthologs in <i>Arabidopsis thaliana</i>. About 97% of the genes were located in nucleus and 3% in cytoplasmic organelles. qRT-PCR analysis showed a different expression pattern of these genes in response to biotic stresses (<i>Plasmodiophora brassicae</i> and <i>Sclerotinia sclerotiorum</i>) and abiotic stresses (cold, drought, and salinity) and hormonal treatments. Differential expression of the same gene was observed under multiple stress conditions, and a few genes showed similar expression in response to more than one phytohormones. Our results suggest that the C2H2-ZF genes can be targeted for the improvement of stress tolerance in canola.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9438684","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}
GenomePub Date : 2023-05-01DOI: 10.1139/gen-2022-0086
Sabrina A Attéré, Cynthia Gagné-Thivierge, Valérie E Paquet, Gabrielle R Leduc, Antony T Vincent, Steve J Charette
{"title":"<i>Aeromonas salmonicida</i> isolates from Canada demonstrate wide distribution and clustering among mesophilic strains.","authors":"Sabrina A Attéré, Cynthia Gagné-Thivierge, Valérie E Paquet, Gabrielle R Leduc, Antony T Vincent, Steve J Charette","doi":"10.1139/gen-2022-0086","DOIUrl":"https://doi.org/10.1139/gen-2022-0086","url":null,"abstract":"<p><p>All the 36 known species to date of the genus <i>Aeromonas</i> are mesophilic except the species <i>Aeromonas salmonicida</i>, which includes both psychrophilic and mesophilic subspecies. For 20 years, more and more mesophilic <i>A. salmonicida</i> strains have been discovered. Only <i>A. salmonicida</i> subsp. <i>pectinolytica</i> has officially been classified as a mesophilic subspecies. Most mesophiles have been isolated in hot countries. We present, for the first time, the characterization of two new mesophilic isolates from Quebec (Canada). Phenotypic and genomic characterizations were carried out on these strains, isolated from dead fish from a fish farm. Isolates 19-K304 and 19-K308 are clearly mesophiles, virulent to the amoeba <i>Dictyostelium discoideum</i>, a surrogate host, and close to strain Y577, isolated in India. To our knowledge, this is the first time that mesophilic strains isolated from different countries are so similar. The major difference between the isolates is the presence of plasmid pY47-3, a cryptic plasmid that sometimes presents in mesophilic strains. More importantly, our extensive phylogenetic analysis reveals two well-defined clades of mesophilic strains with psychrophiles associated with one of these clades. This helps to have a better understanding of the evolution of this species and the apparition of psychrophilic subspecies.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9735227","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}
GenomePub Date : 2023-04-01DOI: 10.1139/gen-2022-0087
Zhen-Ni Xie, Jia Lao, Hao Liu, Wan-Xiang Zhang, Wei He, Can Zhong, Jing Xie, Shui-Han Zhang, Jian Jin
{"title":"Characterization of the chloroplast genome of medicinal herb <i>Polygonatum cyrtonema</i> and identification of molecular markers by comparative analysis.","authors":"Zhen-Ni Xie, Jia Lao, Hao Liu, Wan-Xiang Zhang, Wei He, Can Zhong, Jing Xie, Shui-Han Zhang, Jian Jin","doi":"10.1139/gen-2022-0087","DOIUrl":"https://doi.org/10.1139/gen-2022-0087","url":null,"abstract":"<p><p><i>Polygonatum cyrtonema</i> Hua is a traditional Chinese herb medicine, and it is widely distributed in China. The intrageneric taxonomy and phylogenetic relationships within <i>Polygonatum</i> have long been controversial due to their morphological similarity and lacking special DNA barcodes. In this paper, the complete chloroplast genome is a relatively conserved quadripartite structure including a large single copy region of 84 711 bp, a small single copy region of 18 210 bp, and a pair of inverted repeats region of 26 142 bp. A total of 342 simple sequence repeats were identified, and most of them were found to be composed of A/T, including 126 mono-nucleotides and 179 di-nucleotides. Nucleotide diversity was analyzed and eight highly variable regions (psbl∼trnT-CGU, atpF∼atpH, trnT-GGU∼psbD, psaJ∼rps20, trnL-UAG∼ndhD, ndhG∼ndhl, ndhA, and rpl32∼ccsA) were identified as potential molecular markers. Phylogenetic analysis based on the whole chloroplast genome showed that <i>P. cyrtonema</i>, within the family Asparagaceae, is closely related to <i>Polygonatum sibiricum</i> and <i>Polygonatum kingianum</i>. The sequence matK, trnT-GGU & ccsA, and ndhG∼ndhA were identified as three DNA barcodes. The assembly and comparative analysis of <i>P. cyrtonema</i> complete chloroplast genome will provide essential molecular information about the evolution and molecular biology for further study.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9238094","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}
GenomePub Date : 2023-04-01DOI: 10.1139/gen-2022-0008
R J Corbett, L M Ford, N E Raney, J M Grabowski, C W Ernst
{"title":"Pig fetal skeletal muscle development is associated with genome-wide DNA hypomethylation and corresponding alterations in transcript and microRNA expression.","authors":"R J Corbett, L M Ford, N E Raney, J M Grabowski, C W Ernst","doi":"10.1139/gen-2022-0008","DOIUrl":"https://doi.org/10.1139/gen-2022-0008","url":null,"abstract":"<p><p>Fetal myogenesis represents a critical period of porcine skeletal muscle development and requires coordinated expression of thousands of genes. Epigenetic mechanisms, including DNA methylation, drive transcriptional regulation during development; however, these processes are understudied in developing porcine tissues. We performed bisulfite sequencing to assess DNA methylation in pig <i>longissimus dorsi</i> muscle at 41- and 70-days gestation (dg), as well as RNA- and small RNA-sequencing to identify coordinated changes in methylation and expression between myogenic stages. We identified 45 739 differentially methylated regions (DMRs) between stages, and the majority (<i>N</i> = 34 232) were hypomethylated at 70 versus 41 dg. Integration of methylation and transcriptomic data revealed strong associations between differential gene methylation and expression. Differential miRNA methylation was significantly negatively correlated with abundance, and dynamic expression of assayed miRNAs persisted postnatally. Motif analysis revealed significant enrichment of myogenic regulatory factor motifs among hypomethylated regions, suggesting that DNA hypomethylation may function to increase accessibility of muscle-specific transcription factors. We show that developmental DMRs are enriched for GWAS SNPs for muscle- and meat-related traits, demonstrating the potential for epigenetic processes to influence phenotypic diversity. Our results enhance understanding of DNA methylation dynamics of porcine myogenesis and reveal putative <i>cis</i>-regulatory elements governed by epigenetic processes.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9592806","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}
GenomePub Date : 2023-03-01DOI: 10.1139/gen-2022-0026
Simon Orozco-Arias, Mathilde Dupeyron, David Gutierrez-Duque, Reinel Tabares-Soto, Romain Guyot
{"title":"High nucleotide similarity of three <i>Copia</i> lineage LTR retrotransposons among plant genomes.","authors":"Simon Orozco-Arias, Mathilde Dupeyron, David Gutierrez-Duque, Reinel Tabares-Soto, Romain Guyot","doi":"10.1139/gen-2022-0026","DOIUrl":"https://doi.org/10.1139/gen-2022-0026","url":null,"abstract":"<p><p>Transposable elements (TEs) are mobile elements found in the majority of eukaryotic genomes. TEs deeply impact the structure and evolution of chromosomes and can induce mutations affecting coding genes. In plants, the major group of TEs is long terminal repeat retrotransposons (LTR-RTs). They are classified into superfamilies (<i>Gypsy</i>, <i>Copia</i>) and subclassified into lineages. Horizontal transfer (HT), defined as the nonsexual transmission of genetic material between species, is a process allowing LTR-RTs to invade a new genome. Although this phenomenon was considered rare, recent studies demonstrate numerous transfers of LTR-RTs. This study aims to determine which LTR-RT lineages are shared with high similarity among 69 plant genomes. We identified and classified 88 450 LTR-RTs and determined 143 cases of high similarities between pairs of genomes. Most of them involved three <i>Copia</i> lineages (<i>Oryco</i>/<i>Ivana</i>, <i>Retrofit</i>/<i>Ale</i>, and <i>Tork</i>/<i>Tar</i>/<i>Ikeros</i>). A detailed analysis of three cases of high similarities involving <i>Tork</i>/<i>Tar</i>/<i>Ikeros</i> group shows an uneven distribution in the phylogeny of the elements and incongruence with between phylogenetic trees topologies, indicating they could be originated from HTs. Overall, our results suggest that LTR-RT <i>Copia</i> lineages share outstanding similarity between distant species and may likely be involved in HT mechanisms more frequent than initially estimated.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9361134","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}
GenomePub Date : 2023-03-01DOI: 10.1139/gen-2022-0095
Mara Garcia Tavares, Gisele Amaro Teixeira
{"title":"Cytogenetic characterization of solitary wasp <i>Ancistrocerus flavomarginatus</i> (Brèthes, 1906) (Hymenoptera, Vespidae) with insights into the chromosomal evolution in the genus.","authors":"Mara Garcia Tavares, Gisele Amaro Teixeira","doi":"10.1139/gen-2022-0095","DOIUrl":"https://doi.org/10.1139/gen-2022-0095","url":null,"abstract":"<p><p>Cytogenetic studies have enabled the characterization of the chromosomal macrostructure and microstructure and have contributed to the understanding of the evolution of wasp karyotypes. However, studies on Eumeninae solitary wasps are scarce. In this study, we characterized the karyotype of <i>Ancistrocerus flavomarginatus</i> (Brèthes<i>,</i> 1906) and compared it with previous data from other <i>Ancistrocerus</i> (Wesmael, 1836) species to shed light on the chromosomal diversity of the genus. A chromosome number of 2<i>n</i> = 24 in females and <i>n</i> = 12 in males was observed. Comparing the <i>A. flavomarginatus</i> karyotype with that of another <i>Ancistrocerus</i> species showed variations in the morphology of some chromosomal pairs. The presence of two larger chromosome pairs, almost entirely heterochromatic, and the predominance of subtelocentric chromosomes with heterochromatic short arms in <i>A. flavomarginatus</i> support the occurrence of fissions in <i>Ancistrocerus</i>. A single site of ribosomal genes was observed in <i>A. flavomarginatus</i>, in addition to a size polymorphism of these rDNA clusters between the homologues of some analyzed females. This polymorphism may originate from duplications/deletions due to unequal crossing-over or amplification via transposable elements. The (GA)<sub>15</sub> microsatellite is located exclusively in euchromatic regions. Our data show that different rearrangements seem to shape chromosomal evolution in <i>Ancistrocerus</i> species.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9377555","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}
GenomePub Date : 2023-02-01DOI: 10.1139/gen-2022-0050
Tianze Wu, Gang Deng, Qinggang Yin, Shilin Chen, Yongping Zhang, Bo Wang, Li Xiang, Xia Liu
{"title":"Characterization and molecular evolution analysis of <i>Periploca forrestii</i> inferred from its complete chloroplast genome sequence.","authors":"Tianze Wu, Gang Deng, Qinggang Yin, Shilin Chen, Yongping Zhang, Bo Wang, Li Xiang, Xia Liu","doi":"10.1139/gen-2022-0050","DOIUrl":"https://doi.org/10.1139/gen-2022-0050","url":null,"abstract":"<p><p><i>Periploca forrestii</i>, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of <i>P. forrestii</i> based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724 bp in length and had four subregions. Moreover, an 84 433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on <i>P. forrestii</i>. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the <i>psaI</i> and <i>ycf2</i> genes, which might reflect specific adaptions to the <i>P. forrestii</i> particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important <i>P. forrestii</i> genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10631174","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}
GenomePub Date : 2023-02-01DOI: 10.1139/gen-2022-0063
Hiu-Lam Ngai, Bobby Lim-Ho Kong, David Tai-Wai Lau, P C Shaw
{"title":"Differentiation of Lingxiaohua and Yangjinhua by chloroplast genome sequencing and DNA barcoding markers.","authors":"Hiu-Lam Ngai, Bobby Lim-Ho Kong, David Tai-Wai Lau, P C Shaw","doi":"10.1139/gen-2022-0063","DOIUrl":"https://doi.org/10.1139/gen-2022-0063","url":null,"abstract":"<p><p>Lingxiaohua (Campsis Flos, <i>Campsis grandiflora</i> (Thunb.) K. Schum) is a medicinal herb used for promoting diuresis and treating blood-related disorders by the promotion of blood circulation. It also possesses anti-inflammatory and antioxidative properties. This non-poisonous plant is frequently confused with poisonous Yangjinhua (Daturae Metelis Flos, <i>Datura metel</i> Linnaeus) in the market, resulting in serious anticholinergic poisoning. The confusion of these two herbs is due to the similarity in their appearances. In our study, we compared the complete chloroplast genomes of the two plants and found that they are very different in terms of their gene content and gene arrangement. There were also significant differences in the number and repeating motifs of microsatellites and complex repeats. We used universal primers for the amplification of <i>rbcL, matK, psbA-trnH</i>, and <i>ITS2</i> regions and successfully differentiated the two plants. Furthermore, we designed two pairs of primers based on the nucleotide differences in chloroplast genomes at the <i>rps14</i> and <i>rpoC1</i> regions to provide additional authentication markers. The universal primers and specific primers when used together can accurately discriminate Lingxiaohua and Yangjinhua.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10631172","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}
GenomePub Date : 2023-01-01DOI: 10.1139/gen-2022-0104
{"title":"Note of appreciation.","authors":"","doi":"10.1139/gen-2022-0104","DOIUrl":"https://doi.org/10.1139/gen-2022-0104","url":null,"abstract":"","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":"10574031","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}
{"title":"Complete genome analysis of <i>Pseudomonas furukawaii</i> ZS1 isolated from grass carp (<i>Ctenopharyngodon idellus</i>) culture water.","authors":"Shuhui Niu, Wangbao Gong, Zhifei Li, Kai Zhang, Guangjun Wang, Ermeng Yu, Yun Xia, Jingjing Tian, Hongyan Li, Jiajia Ni, Jun Xie","doi":"10.1139/gen-2022-0055","DOIUrl":"https://doi.org/10.1139/gen-2022-0055","url":null,"abstract":"<p><p><i>Pseudomonas furukawaii</i> ZS1, isolated from grass carp (<i>Ctenopharyngodon idellus</i>) culture water, exhibits efficient aerobic nitrate reduction without nitrite accumulation; however, the molecular pathway underlying this aerobic nitrate reduction remains unclear. In this study, we constructed a complete genome map of <i>P. furukawaii</i> ZS1 and performed a comparative genomic analysis with a reference strain. The results showed that <i>P. furukawaii</i> ZS1 genome was 6 026 050 bp in size and contained 5427 predicted protein-coding sequences. The genome contained all the necessary genes for the dissimilatory nitrate reduction to ammonia pathway but lacked those for the assimilatory nitrate reduction pathway; additionally, genes that convert ammonia to organic nitrogen were also identified. The presence of putative genes associated with the nitrogen and oxidative phosphorylation pathways implied that ZS1 can perform respiration and nitrate reduction simultaneously under aerobic conditions, so that nitrite is rapidly consumed for detoxication by denitrification. The aim of this study is to indicate the great potential of strain ZS1 for future full-scale applications in aquaculture. This work provided insights at the molecular level on the nitrogen metabolic pathways in <i>Pseudomonas</i> species. The understanding of nitrogen metabolic pathways also provides significant molecular information for further <i>Pseudomonas</i> species modification and development.</p>","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":"10509037","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}