IF 2.3 3区生物学

Genome Pub Date : 2024-06-01 Epub Date: 2024-02-27 DOI: 10.1139/gen-2023-0135

Yina Her, Danielle M Pascual, Zoe Goldstone-Joubert, Paul C Marcogliese

引用次数: 0

Should I shrink or should I grow: cell size changes in tissue morphogenesis. 我应该缩小还是生长：组织形态发生过程中的细胞大小变化

IF 3.1 3区生物学

Genome Pub Date : 2024-05-01 Epub Date: 2024-01-10 DOI: 10.1139/gen-2023-0091

Gordana Scepanovic, Rodrigo Fernandez-Gonzalez

引用次数: 0

Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus. 黄曲霉菌株的有丝分裂基因组进化：为了更好地理解区分菌属。

IF 3.1 3区生物学

Genome Pub Date : 2024-05-01 Epub Date: 2023-12-20 DOI: 10.1139/gen-2022-0092

Evrim Özkale, Özgül Doğan, Mahir Budak, Ertan Mahir Korkmaz

{"title":"Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus.","authors":"Evrim Özkale, Özgül Doğan, Mahir Budak, Ertan Mahir Korkmaz","doi":"10.1139/gen-2022-0092","DOIUrl":"10.1139/gen-2022-0092","url":null,"abstract":"Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"139-150"},"PeriodicalIF":3.1,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138829302","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

Conventional cytogenetics and microsatellite chromosomal distribution in social wasp Mischocyttarus cassununga (Ihering, 1903) (Vespidae, Polistinae, Mischocyttarini). 社会黄蜂 Mischocyttarus cassununga (Ihering, 1903) （蝶形目，波利斯蝶科，Mischocyttarini）的常规细胞遗传学和微卫星染色体分布。

IF 3.1 3区生物学

Genome Pub Date : 2024-05-01 Epub Date: 2024-01-23 DOI: 10.1139/gen-2023-0026

Camila Moura Novaes, Gisele Amaro Teixeira, Eydyeliana Month Juris, Denilce Meneses Lopes

{"title":"Conventional cytogenetics and microsatellite chromosomal distribution in social wasp Mischocyttarus cassununga (Ihering, 1903) (Vespidae, Polistinae, Mischocyttarini).","authors":"Camila Moura Novaes, Gisele Amaro Teixeira, Eydyeliana Month Juris, Denilce Meneses Lopes","doi":"10.1139/gen-2023-0026","DOIUrl":"10.1139/gen-2023-0026","url":null,"abstract":"Cytogenetics has allowed the investigation of chromosomal diversity and repetitive genomic content in wasps. In this study, we characterized the karyotype of the social wasp Mischocyttarus cassununga using conventional cytogenetics and chromosomal mapping of repetitive sequences. This study was undertaken to extend our understanding of the genomic organization of repetitive DNA in social wasps and is the first molecular cytogenetic insight into the genus Mischocyttarus. The karyotype of M. cassununga had a chromosome number of 2n = 64 for females and n = 32 for males. Constitutive heterochromatin exhibited three distribution patterns: centromeric and pericentromeric regions along the smaller arms and extending almost the entire chromosome. The major ribosomal DNA sites were located on chromosome pair in females and one chromosome in males. Positive signals for the microsatellite probes (GA)n and (GAG)n were observed in the euchromatic regions of all chromosomes. The microsatellites, (CGG)n, (TAT)n, (TTAGG)n, and (TCAGG)n were not observed in any region of the chromosomes. Our results contrast with those previously obtained for Polybia fastidiosuscula, which showed that the microsatellites (GAG)n, (CGG)n, (TAT)n, (TTAGG)n, and (TCAGG)n are located predominantly in constitutive heterochromatin. This suggests variations in the diversity and chromosomal organization of repetitive sequences in the genomes of social wasps.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"151-157"},"PeriodicalIF":3.1,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542167","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

Development of EST-SSR markers in Bergenia ciliata using de novo transcriptome sequencing. 利用全新转录组测序技术开发纤毛虫 EST-SSR 标记。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-01 Epub Date: 2023-12-13 DOI: 10.1139/gen-2023-0059

Harish Chandra Singh, Vandana Tiwari, Avinash Tiwari, Tikam S Rana

{"title":"Development of EST-SSR markers in Bergenia ciliata using de novo transcriptome sequencing.","authors":"Harish Chandra Singh, Vandana Tiwari, Avinash Tiwari, Tikam S Rana","doi":"10.1139/gen-2023-0059","DOIUrl":"10.1139/gen-2023-0059","url":null,"abstract":"Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in the Indian Himalayan Region. It is widely used in medicines, healthcare systems, cosmetics, fodder, and ornamental purposes. The Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers. A total of 18 226 simple sequence repeats (SSRs) were identified wherein di-nucleotides were found to be abundant (47.88%), followed by mono-nucleotide (35.03%) and tri-nucleotide (15.88%) repeats. A total of 11 839 EST-SSR primers were designed, of which 96 primer pairs were commercially synthesized. Finally, 17 primer pairs revealed clear, distinct polymorphic bands, and these primers were validated with 40 diverse B. ciliata accessions. The present study revealed moderate level of genetic diversity (Ho = 0.389, He = 0.542, and PIC = 0.513). Furthermore, the transcriptome data and EST-SSR markers generated during the present investigation could be an important genetic resource for functional genomics, population studies, and conservation genetics of the genus Bergenia.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"119-124"},"PeriodicalIF":3.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138802843","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

Gene regulation supporting sociality shared across lineages and variation in complexity. 支持跨血统社会性的基因调控和复杂性差异。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-01 Epub Date: 2023-12-14 DOI: 10.1139/gen-2023-0054

Benjamin C Pyenson, Sandra M Rehan

{"title":"Gene regulation supporting sociality shared across lineages and variation in complexity.","authors":"Benjamin C Pyenson, Sandra M Rehan","doi":"10.1139/gen-2023-0054","DOIUrl":"10.1139/gen-2023-0054","url":null,"abstract":"Across evolutionary lineages, insects vary in social complexity, from those that exhibit extended parental care to those with elaborate divisions of labor. Here, we synthesize the sociogenomic resources from hundreds of species to describe common gene regulatory mechanisms in insects that regulate social organization across phylogeny and levels of social complexity. Different social phenotypes expressed by insects can be linked to the organization of co-expressing gene networks and features of the epigenetic landscape. Insect sociality also stems from processes like the emergence of parental care and the decoupling of ancestral genetic programs. One underexplored avenue is how variation in a group's social environment affects the gene expression of individuals. Additionally, an experimental reduction of gene expression would demonstrate how the activity of specific genes contributes to insect social phenotypes. While tissue specificity provides greater localization of the gene expression underlying social complexity, emerging transcriptomic analysis of insect brains at the cellular level provides even greater resolution to understand the molecular basis of social insect evolution.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"99-108"},"PeriodicalIF":3.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138802844","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

Satellite DNAs, heterochromatin, and sex chromosomes of the wattled jacana (Charadriiformes; Jacanidae): a species with highly rearranged karyotype. 疣鼻鸦（Charadriiformes; Jacanidae）的卫星 DNA、异染色质和性染色体：一种核型高度重排的物种。

IF 3.1 3区生物学

Genome Pub Date : 2024-04-01 Epub Date: 2024-02-05 DOI: 10.1139/gen-2023-0082

Alan Moura de Oliveira, Guilherme Mota Souza, Gustavo Akira Toma, Natalia Dos Santos, Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, Geize Aparecida Deon, Princia Grejo Setti, Fábio Porto-Foresti, Ricardo Utsunomia, Ricardo José Gunski, Analía Del Valle Garnero, Edivaldo Herculano Correa de Oliveira, Rafael Kretschmer, Marcelo de Bello Cioffi

{"title":"Satellite DNAs, heterochromatin, and sex chromosomes of the wattled jacana (Charadriiformes; Jacanidae): a species with highly rearranged karyotype.","authors":"Alan Moura de Oliveira, Guilherme Mota Souza, Gustavo Akira Toma, Natalia Dos Santos, Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, Geize Aparecida Deon, Princia Grejo Setti, Fábio Porto-Foresti, Ricardo Utsunomia, Ricardo José Gunski, Analía Del Valle Garnero, Edivaldo Herculano Correa de Oliveira, Rafael Kretschmer, Marcelo de Bello Cioffi","doi":"10.1139/gen-2023-0082","DOIUrl":"10.1139/gen-2023-0082","url":null,"abstract":"Charadriiformes, which comprises shorebirds and their relatives, is one of the most diverse avian orders, with over 390 species showing a wide range of karyotypes. Here, we isolated and characterized the whole collection of satellite DNAs (satDNAs) at both molecular and cytogenetic levels of one of its representative species, named the wattled jacana (Jacana jacana), a species that contains a typical ZZ/ZW sex chromosome system and a highly rearranged karyotype. In addition, we also investigate the in situ location of telomeric and microsatellite repeats. A small catalog of 11 satDNAs was identified that typically accumulated on microchromosomes and on the W chromosome. The latter also showed a significant accumulation of telomeric signals, being (GA)10 the only microsatellite with positive hybridization signals among all the 16 tested ones. These current findings contribute to our understanding of the genomic organization of repetitive DNAs in a bird species with high degree of chromosomal reorganization contrary to the majority of bird species that have stable karyotypes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"109-118"},"PeriodicalIF":3.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691652","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

Investigating the expression of fertility-regulating LncRNAs in multiparous and uniparous Shal ewe's ovaries. 研究多胎和单胎雌羊卵巢中生育调节lncrna的表达。

IF 3.1 3区生物学

Genome Pub Date : 2024-03-01 Epub Date: 2023-11-20 DOI: 10.1139/gen-2023-0055

Shahram Hosseinzadeh, Ali Akbar Masoudi

{"title":"Investigating the expression of fertility-regulating LncRNAs in multiparous and uniparous Shal ewe's ovaries.","authors":"Shahram Hosseinzadeh, Ali Akbar Masoudi","doi":"10.1139/gen-2023-0055","DOIUrl":"10.1139/gen-2023-0055","url":null,"abstract":"Sheep is the primary source of animal protein in Iran. Birth type is one of the significant features that determine total meat output. Little is known about how long non-coding RNAs (LncRNAs) affect litter size. The purpose of this research is to investigate the DE-LncRNAs in ovarian tissue between multiparous and uniparous Shal ewes. Through bioinformatics analyses, LncRNAs with variable expression levels between ewes were discovered. Target genes were annotated using the DAVID database, and STRING and Cytoscape software were used to evaluate their interactions. The expression levels of 148 LncRNAs were different in the multiparous and uniparous ewe groups (false discovery rate (FDR) < 0.05). Eight biological process terms, nine cellular component terms, 10 molecular function terms, and 38 KEGG pathways were significant (FDR < 0.05) in the GO analysis. One of the most significant processes impacting fertility is mitogen-activated protein kinase (MAPK) signaling pathway, followed by oocyte meiosis, gonadotropin-releasing hormone signaling pathway, progesterone-mediated oocyte maturation, oxytocin signaling pathway, and cAMP signaling pathway. ENSOARG00000025710, ENSOARG00000025667, ENSOARG00000026034, and ENSOARG00000026632 are LncRNAs that may affect litter size and fertility. The most crucial hub genes include MAPK1, BRD2, GAK, RAP1B, FGF2, RAP1B, and RAP1B. We hope that this study will encourage researchers to further investigate the effect of LncRNAs on fertility.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"78-89"},"PeriodicalIF":3.1,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138175995","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 chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes. 应用寡核苷酸探针荧光原位杂交技术鉴定陆地棉染色体。

IF 3.1 3区生物学

Genome Pub Date : 2024-03-01 Epub Date: 2023-11-03 DOI: 10.1139/gen-2023-0051

Min Xu, Haiyue Guo, Yingying Wang, Baoliang Zhou

{"title":"Identification of chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes.","authors":"Min Xu, Haiyue Guo, Yingying Wang, Baoliang Zhou","doi":"10.1139/gen-2023-0051","DOIUrl":"10.1139/gen-2023-0051","url":null,"abstract":"Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved. Here, we developed 16 oligonucleotide probes for rapid and accurate identification of chromosomes in Gossypium hirsutum: 9 probes, of which each is able to distinguish individually one pair of chromosomes, and seven probes, of which each distinguishes multiple pairs of chromosomes. Besides the identification of Chrs. A09 and D09, we first find Chr. D08, which carries both 45S and 5S rDNA sequences. Interestingly, we also find Chr. A07 has a small 45S rDNA size, suggesting that the size of this site on Chr. A07 may have reduced during evolution. By the combination of 45S and 5S rDNA sequences and oligonucleotide probes developed, 10 chromosomes (Chrs. 3-7, and 9-13) in A subgenome and 7 (Chrs. 1-2, 4-5, and 7-9) in D subgenome of cotton are able to be recognized. This study establishes cotton oligonucleotide fluorescence in situ hybridization technology for discrimination of chromosomes, which supports and guides for sequence assembling, particularly, for tandem repeat sequences in cotton.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"64-77"},"PeriodicalIF":3.1,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71434217","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

The complete chloroplast genome of Aristolochia fangchi provided insights into the phylogeny and species identification of Aristolochia. 马兜铃科植物芳奇的完整叶绿体基因组为马兜铃科植物的系统发育和物种鉴定提供了见解。

IF 3.1 3区生物学

Genome Pub Date : 2024-03-01 Epub Date: 2023-12-13 DOI: 10.1139/gen-2023-0068

Qingqun Cai, Shiyin Feng, Xiasheng Zheng

{"title":"The complete chloroplast genome of Aristolochia fangchi provided insights into the phylogeny and species identification of Aristolochia.","authors":"Qingqun Cai, Shiyin Feng, Xiasheng Zheng","doi":"10.1139/gen-2023-0068","DOIUrl":"10.1139/gen-2023-0068","url":null,"abstract":"Aristolochia fangchi is an important species within the family Aristolochiaceae, most of which contain nephrotoxic aristolochic acid. The inadvertent use of Aristolochiaceae plants as raw ingredients in the manufacturing of patent medicine poses a significant risk warranting considerable attention. In this study, we assembled and analyzed the complete chloroplast genome of Aristolochia fangchi, which is a 159 867 bp long circular molecule. Functional annotation of the A. fangchi plastome unveiled a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Subsequently, a series of genome structure and characteristic evaluations were conducted against the A. fangchi plastome. Further phylogenetic analysis suggested that a plausible phylogenetic relationship among Aristolochiaceae derived from the concatenated sequences of shared conserved genes rather than from the entire chloroplast genome with one IR copy. Finally, a DNA polymorphism assessment against a dozen Aristolochia plastomes yielded multiple potential regions for biomarker designation. Six pairs of primers were generated and underwent both in silico and actual PCR validations. In conclusion, this study identified the unique characteristics of the A. fangchi plastome, providing invaluable insights for further investigations on species identification and the phylogeny evolution between A. fangchi and its related species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"90-98"},"PeriodicalIF":3.1,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138802845","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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