Genetica最新文献_第4页

Insulin and circadian rhythm genes of the Nile rat (Arvicanthis niloticus) are conserved and orthologous to those in the rat, mouse and human 尼罗河大鼠（Arvicanthis niloticus）的胰岛素基因和昼夜节律基因与大鼠、小鼠和人类的胰岛素基因和昼夜节律基因是一致和直向的

IF 1.5 4区生物学

Genetica Pub Date : 2023-12-15 DOI: 10.1007/s10709-023-00202-z

Soon-Sen Leow, Jia-Shiun Khoo, Siuk-Mun Ng, Wei-Kang Lee, Chee-Choong Hoh, Syed Fairus, Ravigadevi Sambanthamurthi, K. C. Hayes

{"title":"Insulin and circadian rhythm genes of the Nile rat (Arvicanthis niloticus) are conserved and orthologous to those in the rat, mouse and human","authors":"Soon-Sen Leow, Jia-Shiun Khoo, Siuk-Mun Ng, Wei-Kang Lee, Chee-Choong Hoh, Syed Fairus, Ravigadevi Sambanthamurthi, K. C. Hayes","doi":"10.1007/s10709-023-00202-z","DOIUrl":"https://doi.org/10.1007/s10709-023-00202-z","url":null,"abstract":"The African grass or Nile rat (NR) (Arvicanthis niloticus) is a herbivorous diurnal rodent which is used as a biological model for research on type 2 diabetes mellitus (T2DM) and the circadian rhythm. Similar to humans, male NRs develop T2DM with high-carbohydrate diets. The NR thus provides a unique opportunity to identify the nutritional and underlying genetic factors that characterise human T2DM, as well as the effects of potential anti-diabetic phytochemicals such as Water-Soluble Palm Fruit Extract. Whole genome sequencing (WGS) could help identify possible genetic causes why NRs spontaneously develop T2DM in captivity. In this study, we performed WGS on a hepatic deoxyribonucleic acid (DNA) sample isolated from a male NR using PacBio high-fidelity long-read sequencing. The WGS data obtained were then de novo assembled and annotated using PacBio HiFi isoform sequencing (Iso-Seq) data as well as previous Illumina RNA sequencing (RNA-Seq) data. Genes related to insulin and circadian rhythm pathways were present in the NR genome, similar to orthologues in the rat, mouse and human genomes. T2DM development in the NR is thus most likely not attributable to structural differences in these genes when compared to other biological models. Further studies are warranted to gain additional insights on the genetic-environmental factors which underlie the genetic permissiveness of NRs to develop T2DM.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"85 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138686274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Methods for two nonstandard problems arising from the Luria-Delbrück experiment. luria - delbr<e:1> ck实验中出现的两个非标准问题的方法。

IF 1.5 4区生物学

Genetica Pub Date : 2023-12-01 Epub Date: 2023-11-27 DOI: 10.1007/s10709-023-00200-1

Qi Zheng

引用次数: 0

Forecasting effects of climate changes on the population genetic structure of Anacardium occidentale in the Cerrado biome, Brazil. 气候变化对巴西塞拉多生物群落西洋Anacardium occidentale种群遗传结构的影响预测。

IF 1.5 4区生物学

Genetica Pub Date : 2023-12-01 Epub Date: 2023-11-03 DOI: 10.1007/s10709-023-00199-5

Jacqueline Souza Lima, Rosane Garcia Collevatti, Leciane Kárita de Oliveira, Lázaro José Chaves, Ronaldo Veloso Naves, Thannya Nascimento Soares, José Alexandre Felizola Diniz Filho, Mariana Pires de Campos Telles

{"title":"Forecasting effects of climate changes on the population genetic structure of Anacardium occidentale in the Cerrado biome, Brazil.","authors":"Jacqueline Souza Lima, Rosane Garcia Collevatti, Leciane Kárita de Oliveira, Lázaro José Chaves, Ronaldo Veloso Naves, Thannya Nascimento Soares, José Alexandre Felizola Diniz Filho, Mariana Pires de Campos Telles","doi":"10.1007/s10709-023-00199-5","DOIUrl":"10.1007/s10709-023-00199-5","url":null,"abstract":"There has been a continuous interest in understanding the patterns of genetic diversity in natural populations because of the role of intraspecific genetic diversity as the basis of all evolutionary change and thus, its potential effects on population persistence when facing environmental changes. Here, we provided the first description of genetic diversity distribution and population structure of Anacardium occidentale L. (cashew) from the Brazilian Cerrado, one of the most economically important tropical crops in the world. We applied Bayesian clustering approaches (STRUCTURE and POPS) that allow predicting the effects of future climatic changes on the population genetic structure of A. occidentale. We identified distinct genetic groups corresponding to the southwestern, central, and northern regions of the species' range. The characterized genetic clusters will disappear under future climate change scenarios, leading to a homogenization of genetic variability across the landscape. Our findings suggest a high likelihood for the loss of genetic diversity, which in turn will reduce the evolutionary potential of the species to cope with predicted future climatic changes. Results from this study may help develop management strategies to conserve the genetic diversity and structure of natural cashew populations.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"357-367"},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71434930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Approaches to increase the validity of gene family identification using manual homology search tools. 使用手动同源性搜索工具提高基因家族鉴定有效性的方法。

IF 1.5 4区生物学

Genetica Pub Date : 2023-12-01 Epub Date: 2023-10-10 DOI: 10.1007/s10709-023-00196-8

Benjamin J Nestor, Philipp E Bayer, Cassandria G Tay Fernandez, David Edwards, Patrick M Finnegan

{"title":"Approaches to increase the validity of gene family identification using manual homology search tools.","authors":"Benjamin J Nestor, Philipp E Bayer, Cassandria G Tay Fernandez, David Edwards, Patrick M Finnegan","doi":"10.1007/s10709-023-00196-8","DOIUrl":"10.1007/s10709-023-00196-8","url":null,"abstract":"Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"325-338"},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10692271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The misregulation of mitochondria-associated genes caused by GAGA-factor lack promotes autophagic germ cell death in Drosophila testes. GAGA因子缺乏引起的线粒体相关基因的失调促进了果蝇睾丸中自噬生殖细胞的死亡。

IF 1.5 4区生物学

Genetica Pub Date : 2023-12-01 Epub Date: 2023-10-11 DOI: 10.1007/s10709-023-00197-7

Natalia V Dorogova, Svetlana A Fedorova, Elena U Bolobolova, Elina M Baricheva

{"title":"The misregulation of mitochondria-associated genes caused by GAGA-factor lack promotes autophagic germ cell death in Drosophila testes.","authors":"Natalia V Dorogova, Svetlana A Fedorova, Elena U Bolobolova, Elina M Baricheva","doi":"10.1007/s10709-023-00197-7","DOIUrl":"10.1007/s10709-023-00197-7","url":null,"abstract":"The Drosophila GAGA-factor encoded by the Trithorax-like (Trl) gene is DNA-binding protein with unusually wide range of applications in diverse cell contexts. In Drosophila spermatogenesis, reduced GAGA expression caused by Trl mutations induces mass autophagy leading to germ cell death. In this work, we investigated the contribution of mitochondrial abnormalities to autophagic germ cell death in Trl gene mutants. Using a cytological approach, in combination with an analysis of high-throughput RNA sequencing (RNA-seq) data, we demonstrated that the GAGA deficiency led to considerable defects in mitochondrial ultrastructure, by causing misregulation of GAGA target genes encoding essential components of mitochondrial molecular machinery. Mitochondrial anomalies induced excessive production of reactive oxygen species and their release into the cytoplasm, thereby provoking oxidative stress. Changes in transcription levels of some GAGA-independent genes in the Trl mutants indicated that testis cells experience ATP deficiency and metabolic aberrations, that may trigger extensive autophagy progressing to cell death.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"349-355"},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 transcriptome analysis of eyes reveals the adaptive mechanism of mantis shrimp (oratosquilla oratoria) induced by a dark environment. 对眼睛的比较转录组分析揭示了螳螂虾在黑暗环境中的适应机制。

IF 1.5 4区生物学

Genetica Pub Date : 2023-12-01 Epub Date: 2023-10-13 DOI: 10.1007/s10709-023-00198-6

Xiaoli Sun, Ling He, Bujin Ayi, Yuyang Qiu, Jiayue Xu, Wei Yu, Tinghao Yan, Ge Ding, Boping Tang, Gang Wang, Daizhen Zhang

{"title":"Comparative transcriptome analysis of eyes reveals the adaptive mechanism of mantis shrimp (oratosquilla oratoria) induced by a dark environment.","authors":"Xiaoli Sun, Ling He, Bujin Ayi, Yuyang Qiu, Jiayue Xu, Wei Yu, Tinghao Yan, Ge Ding, Boping Tang, Gang Wang, Daizhen Zhang","doi":"10.1007/s10709-023-00198-6","DOIUrl":"10.1007/s10709-023-00198-6","url":null,"abstract":"The light-dark cycle significantly impacts the growth and development of animals. Mantis shrimps (Oratosquilla oratoria) receive light through their complex photoreceptors. To reveal the adaptive expression mechanism of the mantis shrimp induced in a dark environment, we performed comparative transcriptome analysis with O. oratoria cultured in a light environment (Oo-L) as the control group and O. oratoria cultured in a dark environment (Oo-D) as the experimental group. In the screening of differentially expressed genes (DEGs) between the Oo-L and Oo-D groups, a total of 88 DEGs with |log2FC| > 1 and FDR < 0.05 were identified, of which 78 were upregulated and 10 were downregulated. Then, FBP1 and Pepck were downregulated in the gluconeogenesis pathway, and MKNK2 was upregulated in the MAPK classical pathway, which promoted cell proliferation and differentiation, indicating that the activity of mantis shrimp was slowed and the metabolic rate decreases in the dark environment. As a result, the energy was saved for its growth and development. At the same time, we performed gene set enrichment analysis (GSEA) on all DEGs. In the KEGG pathway analysis, each metabolic pathway in the dark environment showed a slowing trend. GO was enriched in biological processes such as eye development, sensory perception and sensory organ development. The study showed that mantis shrimp slowed down metabolism in the dark, while the role of sensory organs prominent. It provides important information for further understanding the energy metabolism and has great significance to study the physiology of mantis shrimp in dark environment.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"339-348"},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Genome-wide analysis of glutamate receptor gene family in allopolyploid Brassica napus and its diploid progenitors. 异源多倍体甘蓝型油菜及其二倍体祖先谷氨酸受体基因家族的全基因组分析。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 Epub Date: 2023-08-25 DOI: 10.1007/s10709-023-00192-y

Bidhan Chandra Roy, Nikita Shukla, Ratan Gachhui, Ashutosh Mukherjee

{"title":"Genome-wide analysis of glutamate receptor gene family in allopolyploid Brassica napus and its diploid progenitors.","authors":"Bidhan Chandra Roy, Nikita Shukla, Ratan Gachhui, Ashutosh Mukherjee","doi":"10.1007/s10709-023-00192-y","DOIUrl":"10.1007/s10709-023-00192-y","url":null,"abstract":"Ionotropic glutamate receptors are ligand-gated nonselective cation channels that mediate neurotransmission in the central nervous system of animals. Plants possess homologous proteins called glutamate receptor-like channels (GLRs) which are involved in vital physiological processes including seed germination, long-distance signaling, chemotaxis, Ca2+ signaling etc. Till now, a comprehensive genome-wide analysis of the GLR gene family members in different economically important species of Brassica is missing. Considering the origin of allotetraploid Brassica napus from the hybridization between the diploid Brassica oleracea and Brassica rapa, we have identified 11, 27 and 65 GLR genes in B. oleracea, B. rapa and B. napus, respectively showing an expansion of this gene family in B. napus. Chromosomal locations revealed several tandemly duplicated GLR genes in all the three species. Moreover, the gene family expanded in B. napus after allopolyploidization. The phylogenetic analysis showed that the 103 GLRs are classified into three main groups. The exon-intron structures of these genes are not very conserved and showed wide variation in intron numbers. However, protein sequences are much conserved as shown by the presence of ten short amino acid sequence motifs. Predicted cis-acting elements in 1 kb promoters of GLR genes are mainly involved in light, stress and hormone responses. RNA-seq analysis showed that in B. oleracea and B. rapa, some GLRs are more tissue specific than others. In B. napus, some GLRs are downregulated under cold stress, while others are upregulated. In summary, this bioinformatic study of the GLR gene family of the three Brassica species provides evidence for the expansion of this gene family in B. napus and also provided useful information for in-depth studies of their biological functions in Brassica.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"293-310"},"PeriodicalIF":1.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10069863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America. 中美洲猩红金刚鹦鹉亚种间的细胞核不一致和分化模式。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 Epub Date: 2023-08-23 DOI: 10.1007/s10709-023-00193-x

Matthew L Aardema, Kari L Schmidt, George Amato

{"title":"Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America.","authors":"Matthew L Aardema, Kari L Schmidt, George Amato","doi":"10.1007/s10709-023-00193-x","DOIUrl":"10.1007/s10709-023-00193-x","url":null,"abstract":"The scarlet macaw, Ara macao, is a neotropical parrot that contains two described subspecies with broadly discrete geographical distributions. One subspecies, A. m. macao, is found from South America north into southwestern Costa Rica, while the second subspecies, A. m. cyanoptera, is found from eastern Costa Rica north into central Mexico. Our previous research using mitochondrial data to examine phylogeographical divergence across the collective range of these two subspecies concluded that they represent distinct evolutionary entities, with minimal contemporary hybridization between them. Here we further examine phylogenetic relationships and patterns of genetic variation between these two subspecies using a dataset of genetic markers derived from their nuclear genomes. Our analyses show clear nuclear divergence between A. m. macao and A. m. cyanoptera in Central America. Collectively however, samples from this region appear genetically more similar to one another than they do to the examined South American (Brazilian) A. m. macao sample. This observation contradicts our previous assessments based on mitochondrial DNA analyses that A. m. macao in Central and South America represent a single phylogeographical group that is evolutionarily distinct from Central American A. m. cyanoptera. Nonetheless, in agreement with our previous findings, ongoing genetic exchange between the two subspecies appears limited. Rather, our analyses indicate that incomplete lineage sorting is the best supported explanation for cytonuclear discordance within these parrots. High-altitude regions in Central America may act as a reproductive barrier, limiting contemporary hybridization between A. m. macao and A. m. cyanoptera. The phylogeographic complexities of scarlet macaw taxa in this region highlight the need for additional evolutionary examinations of these populations.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"281-292"},"PeriodicalIF":1.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10654179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10060369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification. 新热带细尾蛇科鱼类（Ostariophysi，Characiformes）多样化的核型变化的宏观进化后果。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 Epub Date: 2023-08-11 DOI: 10.1007/s10709-023-00191-z

Uedson Pereira Jacobina, Alany Itala Pontes, Lucas Costa, Gustavo Souza

{"title":"Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification.","authors":"Uedson Pereira Jacobina, Alany Itala Pontes, Lucas Costa, Gustavo Souza","doi":"10.1007/s10709-023-00191-z","DOIUrl":"10.1007/s10709-023-00191-z","url":null,"abstract":"In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"311-321"},"PeriodicalIF":1.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10199706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Correction to: Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification. 更正：新热带Serrasalmidae鱼类（Ostariophysi，Characiformes）多样化的核型变化的宏观进化后果。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 DOI: 10.1007/s10709-023-00195-9

Uedson Pereira Jacobina, Alany Itala Pontes, Lucas Costa, Gustavo Souza

引用次数: 0