Genetica最新文献_第8页

Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map. 利用表型可塑性了解基因型-表型图谱的结构和进化。

IF 1.5 4区生物学

Genetica Pub Date : 2022-08-01 Epub Date: 2021-10-06 DOI: 10.1007/s10709-021-00135-5

Luis-Miguel Chevin, Christelle Leung, Arnaud Le Rouzic, Tobias Uller

{"title":"Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map.","authors":"Luis-Miguel Chevin, Christelle Leung, Arnaud Le Rouzic, Tobias Uller","doi":"10.1007/s10709-021-00135-5","DOIUrl":"https://doi.org/10.1007/s10709-021-00135-5","url":null,"abstract":"Deciphering the genotype-phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype-phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype-environment-phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 3-4","pages":"209-221"},"PeriodicalIF":1.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39492513","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: 18

Correction to: What is a phenotype? History and new developments of the concept. 更正:什么是表现型?历史和新发展的概念。

IF 1.5 4区生物学

Genetica Pub Date : 2022-08-01 DOI: 10.1007/s10709-021-00144-4

Dominique de Vienne

引用次数: 0

Chromosomal distribution of major rDNA and genome size variation in Belostoma angustum Lauck, B. nessimiani Ribeiro & Alecrim, and B. sanctulum Montandon (Insecta, Heteroptera, Belostomatidae) Belostoma angustum Lauck、B. nessimiani Ribeiro & Alecrim和B. sanctulum Montandon主要rDNA的染色体分布及基因组大小差异(昆虫科，异翅目，Belostomatidae)

IF 1.5 4区生物学

Genetica Pub Date : 2022-05-11 DOI: 10.1007/s10709-022-00156-8

Cassiane Furlan Lopes, Alice Lemos Costa, J. F. Dionísio, Andres Delgado Cañedo, R. da Rosa, Analía Del Valle Garnero, José Ricardo Inacio Ribeiro, R. J. Gunski

引用次数: 1

Identification of a 5-gene-risk score model for predicting luminal A-invasive lobular breast cancer survival 预测腔a浸润性小叶乳腺癌症生存率的5基因风险评分模型的确定

IF 1.5 4区生物学

Genetica Pub Date : 2022-05-10 DOI: 10.1007/s10709-022-00157-7

Yi-Huan Chen, Taofeng Zhang, Yiyuan Liu, Jiehua Zheng, Weixun Lin, Yaokun Chen, Jiehui Cai, Juan Zou, Zhiyang Li

引用次数: 2

The species of Oxytropis DC. of section Gloeocephala Bunge (Fabaceae) from Northeast Asia: genetic diversity and relationships based on sequencing of the intergenic spacers of cpDNA and ITS nrDNA. 棘豆属植物。基于cpDNA和ITS - nrDNA基因间间隔序列的遗传多样性和亲缘关系。

IF 1.5 4区生物学

Genetica Pub Date : 2022-04-01 Epub Date: 2022-02-25 DOI: 10.1007/s10709-022-00152-y

Alla Kholina, Marina Kozyrenko, Elena Artyukova, Valentin Yakubov, Mariya Khoreva, Elena Andrianova, Olga Mochalova, Denis Sandanov

{"title":"The species of Oxytropis DC. of section Gloeocephala Bunge (Fabaceae) from Northeast Asia: genetic diversity and relationships based on sequencing of the intergenic spacers of cpDNA and ITS nrDNA.","authors":"Alla Kholina, Marina Kozyrenko, Elena Artyukova, Valentin Yakubov, Mariya Khoreva, Elena Andrianova, Olga Mochalova, Denis Sandanov","doi":"10.1007/s10709-022-00152-y","DOIUrl":"https://doi.org/10.1007/s10709-022-00152-y","url":null,"abstract":"Phylogenetic relationships within Oxytropis DC. sect. Gloeocephala Bunge from Northeast Asia were studied using plastid intergenic spacers (psbA-trnH + trnL-trnF + trnS-trnG) and ITS nrDNA. Populations of O. anadyrensis Vass., O. borealis DC., O. middendorffii Trautv., O. trautvetteri Meinsh., and O. vasskovskyi Jurtz. were monomorphic or characterised by a low level of chloroplast genetic diversity (h varied from 0.143 to 0.692, and π from 0.0001 to 0.0005). Presumably, the low genetic diversity was a result of the severe bottlenecks during Pleistocene glaciation-interglacial cycles. Twenty chlorotypes were identified; species studied had no shared chlorotypes. Chlorotypes of O. anadyrensis, O. borealis, and O. middendorffii formed two lineages each, while the chlorotypes of O. trautvetteri and O. vasskovskyi formed one separate lineage each in the phylogenetic network. There were specific diagnostic markers of cpDNA in each lineage, excluding O. vasskovskyi. The presence of a species-specific diagnostic marker in O. trautvetteri and specific markers in two lineages of O. anadyrensis support circumscribing these taxa as independent species. Regarding ITS nrDNA polymorphism, five ribotypes were detected. The differences revealed in plastid and nuclear genomes of Oxytropis sect. Gloeocephala confirmed that the Asian sector of Megaberingia was the main centre of diversification of arctic legumes.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 2","pages":"117-128"},"PeriodicalIF":1.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39960648","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: 2

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata 酒藤及其伴生病原菌黑花霉和互花霉密码子使用模式的综合分析

IF 1.5 4区生物学

Genetica Pub Date : 2022-04-01 DOI: 10.1007/s10709-022-00154-w

J. Chandan, Suruchi Gupta, V. Babu, Deepika Singh, Ravail Singh

引用次数: 8

Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses 人类密码子使用偏向性基因与甲型流感病毒非结构蛋白1基因相似，共同参与甲型流感病毒的感染发病过程

IF 1.5 4区生物学

Genetica Pub Date : 2022-04-01 DOI: 10.1007/s10709-022-00155-9

Komi Nambou, Manawa Anakpa, Yin Tong

引用次数: 1

Mitochondrial DNA (CA)_n dinucleotide repeat variations in Sinhalese and Vedda populations in Sri Lanka. 斯里兰卡僧伽罗人和维达人的线粒体DNA (CA)二核苷酸重复变异。

IF 1.5 4区生物学

Genetica Pub Date : 2022-04-01 Epub Date: 2022-02-10 DOI: 10.1007/s10709-022-00150-0

Anjana H J Welikala, Ruwandi Ranasinghe, Kamani H Tennekoon, Joanne T Kotelawala, Punsisi R Weerasooriya

{"title":"Mitochondrial DNA (CA)n dinucleotide repeat variations in Sinhalese and Vedda populations in Sri Lanka.","authors":"Anjana H J Welikala, Ruwandi Ranasinghe, Kamani H Tennekoon, Joanne T Kotelawala, Punsisi R Weerasooriya","doi":"10.1007/s10709-022-00150-0","DOIUrl":"https://doi.org/10.1007/s10709-022-00150-0","url":null,"abstract":"Sinhalese and Vedda people are respectively the major ethnic group and the descendants of the probably earliest inhabitants of Sri Lanka, both believed to have a long history of settlement on the island. However, very little information is available on the origin and possible migration patterns of the two populations. Some studies have focused on (CA) dinucleotide repeat variations located in the mitochondrial hypervariable region 3 (HVS3) (base pairs 514-524) as a useful biomarker to understand migration patterns of different populations. Hence, here we analyze these repeat variations in these two ethnic groups to understand their historical roots and possible patterns of gene flow. Blood samples were collected from healthy, maternally unrelated individuals (N = 109) and mitochondrial D-loop was amplified and sequenced. The (CA)4 dinucleotide repeat in hypervariable region 3 was detected in the majority of Vedda samples while the remaining samples were defined by a (CA)5 cluster. In contrast, the (CA)5 repeat was the most frequent among Sinhalese followed by (CA)4 and (CA)7 repeats. Haplogroup diversity of (CA)4 variation indicated that the majority of Sinhalese individuals grouped into the M30 haplogroup while Vedda clustered into the R5a2b and U7a2 haplogroups. No significant differences in diversity measures were observed among the two populations. However, Multidimensional Scaling indicated a separate clustering for aboriginal Vedda and contemporary Sinhalese populations. Results from this study can be used together with mitochondrial DNA information from hypervariable regions 1 and 2 to perform anthropological and forensic investigations in the two populations studied.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 2","pages":"145-150"},"PeriodicalIF":1.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39767411","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: 2

The Hedgehog pathway in penaeid shrimp: developmental expression and evolution of splice junctions in Pancrustacea. 对虾的Hedgehog通路:平壳类动物剪接连接的发育表达和进化。

IF 1.5 4区生物学

Genetica Pub Date : 2022-04-01 Epub Date: 2022-02-07 DOI: 10.1007/s10709-022-00151-z

Philip L Hertzler, Emma J Devries, Rachel A DeBoer

{"title":"The Hedgehog pathway in penaeid shrimp: developmental expression and evolution of splice junctions in Pancrustacea.","authors":"Philip L Hertzler, Emma J Devries, Rachel A DeBoer","doi":"10.1007/s10709-022-00151-z","DOIUrl":"https://doi.org/10.1007/s10709-022-00151-z","url":null,"abstract":"Penaeid shrimp embryos undergo holoblastic division, gastrulation by invagination, and hatching as a nauplius larva. Posterior segments form and differentiate during larval development. Hedgehog (Hh) pathway genes from penaeid shrimp and other pancrustaceans were identified by in silico analysis of genomes and transcriptomes, and mapped onto a recent pancrustacean phylogeny to determine patterns of intron gains and losses. Penaeus vannamei, P. japonicus, and P. monodon Hh proteins were encoded by four exons. Amphipod, isopod, and ostracod hh were also encoded by four exons, but hh from other arthropod groups contained three conserved exons. The novel hh intron is hypothesized to have arisen independently in the malacostracan ancestor and Ostracoda by a transposon insertion. Shared patterns of ptc, smo, and ci exon structure were found for Malacostraca, Branchiopoda + Hexapoda, Hexanauplia (Thecostraca + Copepoda), Multicrustacea (Thecostraca + Copepoda + Malacostraca), and Pancrustacea minus Oligostraca. mRNA expression of P. vannamei of hh, ptc, and ci from developmental transcriptomes of zygotes through postlarvae showed low expression from zygote to gastrula, which increased at limb bud, peaked at unhatched nauplius, and declined in nauplius and later larval stages. smo expression was found in zygotes, peaked in gastrula, and declined in limb bud and later stages. These results are consistent with a role for Hh signaling during segmentation in penaeid shrimp.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 2","pages":"87-96"},"PeriodicalIF":1.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39896328","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: 2

Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG. LGG竞争内源性RNA网络中作用的LncRNA、MiRNA和MRNA的综合分析。

IF 1.5 4区生物学

Genetica Pub Date : 2022-02-01 Epub Date: 2022-01-07 DOI: 10.1007/s10709-021-00145-3

Yiming Ding, Hanjie Liu, Chuanbao Zhang, Zhaoshi Bao, Shuqing Yu

{"title":"Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG.","authors":"Yiming Ding, Hanjie Liu, Chuanbao Zhang, Zhaoshi Bao, Shuqing Yu","doi":"10.1007/s10709-021-00145-3","DOIUrl":"https://doi.org/10.1007/s10709-021-00145-3","url":null,"abstract":"Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computational method to analyse the relationships among the mRNAs, lncRNAs, and miRNAs in these samples. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to predict the biological processes (BPs) and pathways associated with these genes. Kaplan-Meier survival analysis was used to evaluate the association between the expression levels of specific mRNAs, lncRNAs, and miRNAs and overall survival. Finally, we created a ceRNA network describing the relationships among these mRNAs, lncRNAs, and miRNAs using Cytoscape 3.5.1. A total of 2555 differentially expressed (DE) mRNAs, 218 DElncRNAs, and 192 DEmiRNAs were identified using R. In addition, GO and KEGG pathway analysis of the mRNAs and lncRNAs in the ceRNA network identified 10 BPs, 10 cell components, 10 molecular functions, and 48 KEGG pathways as selectively enriched. A total of 55 lncRNAs, 50 miRNAs, and 10 mRNAs from this network were shown to be closely associated with overall survival in LGG. Finally, 59 miRNAs, 235 mRNAs, and 17 lncRNAs were used to develop a ceRNA network comprising 313 nodes and 1046 edges. This study helps expand our understanding of ceRNA networks and serves to clarify the underlying pathogenesis mechanism of LGG.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 1","pages":"41-50"},"PeriodicalIF":1.5,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39905845","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: 1