Genetica最新文献_第8页

The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba. 对古巴濒临灭绝的西印度海牛的遗传多样性和结构的首次评估。

IF 1.5 4区生物学

Genetica Pub Date : 2022-12-01 Epub Date: 2022-10-22 DOI: 10.1007/s10709-022-00172-8

Anmari Alvarez-Aleman, Margaret E Hunter, Thomas K Frazer, James A Powell, Eddy Garcia Alfonso, James D Austin

{"title":"The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba.","authors":"Anmari Alvarez-Aleman, Margaret E Hunter, Thomas K Frazer, James A Powell, Eddy Garcia Alfonso, James D Austin","doi":"10.1007/s10709-022-00172-8","DOIUrl":"https://doi.org/10.1007/s10709-022-00172-8","url":null,"abstract":"The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites HE = 0.44, and SNP HE = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite FIS = 0.12, SNP FIS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all Ne < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"327-341"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40651500","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

Characterization of the complete mitochondrial genome of Miamiensis avidus causing flatfish scuticociliatosis. 引起比目鱼scucoiliosis的Miamiensis avidus线粒体全基因组的鉴定。

IF 1.5 4区生物学

Genetica Pub Date : 2022-12-01 Epub Date: 2022-10-21 DOI: 10.1007/s10709-022-00167-5

Na Young Kim, Sang Jung Ahn, Jung Soo Seo, Eun Ji Jeon, Mi Young Cho, Hye Sung Choi

{"title":"Characterization of the complete mitochondrial genome of Miamiensis avidus causing flatfish scuticociliatosis.","authors":"Na Young Kim, Sang Jung Ahn, Jung Soo Seo, Eun Ji Jeon, Mi Young Cho, Hye Sung Choi","doi":"10.1007/s10709-022-00167-5","DOIUrl":"https://doi.org/10.1007/s10709-022-00167-5","url":null,"abstract":"Miamiensis avidus is a parasitic pathogen that causes the disease scuticociliatosis in teleost fish species. It is a ciliate and a free-living marine protozoan belonging to the order Philasterida, subclass Scuticociliatida, class Oligohymenophorea, and phylum Ciliophora. The complete mt-genome of M. avidus was linear and 38,695 bp in length with 47 genes, including 40 protein-coding genes, two ribosomal RNA (rRNA) genes, and five transfer RNA (tRNA) genes. Of these, 20 genes typically belong to the clusters of orthologous groups, playing roles in energy production and conversion, translation, ribosomal structure and biogenesis, and defense mechanisms. This is the first report of sequencing and characterization of the mt-genome of M. avidus, which was observed to be linear and possessing the typical ciliate mitochondrial genome organization and phylogenetic relationships. Remarkable differences were observed between M. avidus and other ciliates in the mitochondrially encoded rRNAs, extensive gene loss in ribosomal genes and tRNAs, terminal repeat sequences, and stop codon usage. A comparative and phylogenetic analysis of M. avidus and Uronema marinum of the order Hymenostomatida, which is most closely related to the order Philasterida, signified the promise of the mitogenome data of M. avidus as a valuable genetic marker in species detection and taxonomic research. The present study has potential applications in epidemiological studies and host-parasite interaction investigations facilitating disease control.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"407-420"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40648965","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

Genetic structure of Enyalius capetinga (Squamata, Leiosauridae) in Central Cerrado and transitional areas between the Cerrado and the Atlantic forest, with updated geographic distribution. 塞拉多中部及塞拉多与大西洋森林之间过渡地区的长尾叶蝉遗传结构及其地理分布的更新。

IF 1.5 4区生物学

Genetica Pub Date : 2022-12-01 Epub Date: 2022-10-13 DOI: 10.1007/s10709-022-00170-w

M A Ishihara, F M C B Domingos, S C Gomides, I A Novelli, G R Colli, S M Vargas

{"title":"Genetic structure of Enyalius capetinga (Squamata, Leiosauridae) in Central Cerrado and transitional areas between the Cerrado and the Atlantic forest, with updated geographic distribution.","authors":"M A Ishihara, F M C B Domingos, S C Gomides, I A Novelli, G R Colli, S M Vargas","doi":"10.1007/s10709-022-00170-w","DOIUrl":"https://doi.org/10.1007/s10709-022-00170-w","url":null,"abstract":"The Brazilian Cerrado is considered a biodiversity hotspot highly threatened by human activities. Recently, many studies have demonstrated how underestimated is Cerrado's biodiversity considering squamate species, and the identification of divergent and cryptic lineages is essential for the formulation of effective conservation strategies. The transition areas between the Cerrado and the Atlantic Forest are even less known and, consequently, often dismissed in conservation policies. As previous studies suggested the presence of cryptic diversity within E. capetinga, we investigated patterns and processes in the geographic distribution of its genealogical lineages. We used DNA sequences from individuals collected in six localities and sequences publicly available from three mitochondrial markers (CYT-B, 16S and ND4) and one nuclear marker (C-Mos). We tested if the core and ecotone regions of the Cerrado show differences in biotic and abiotic characteristics that could promote genetic structure and divergence among lineages within E. capetinga. We found evidence for divergent lineages within the species, but not congruent with our hypothesis. Similar divergent patterns were observed in other Cerrado lizards, including interspecific divergences within the Enyalius genus. Molecular characterization of field-collected individuals (previously identified as E. bilineatus), allowed us to update the geographic distribution of the species to include the ecotone between the Cerrado and the Atlantic Forest, an area where species distribution overlap.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 6","pages":"367-377"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33506365","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

Long-term evolution of quantitative traits in the Drosophila melanogaster species subgroup. 黑腹果蝇亚群数量性状的长期进化。

IF 1.5 4区生物学

Genetica Pub Date : 2022-12-01 Epub Date: 2022-10-15 DOI: 10.1007/s10709-022-00171-9

Amir Yassin, Nelly Gidaszewski, Vincent Debat, Jean R David

{"title":"Long-term evolution of quantitative traits in the Drosophila melanogaster species subgroup.","authors":"Amir Yassin, Nelly Gidaszewski, Vincent Debat, Jean R David","doi":"10.1007/s10709-022-00171-9","DOIUrl":"https://doi.org/10.1007/s10709-022-00171-9","url":null,"abstract":"Quantitative genetics aims at untangling the genetic and environmental effects on phenotypic variation. Trait heritability, which summarizes the relative importance of genetic effects, is estimated at the intraspecific level, but theory predicts that heritability could influence long-term evolution of quantitative traits. The phylogenetic signal concept bears resemblance to heritability and it has often been called species-level heritability. Under certain conditions, such as trait neutrality or contribution to phylogenesis, within-species heritability and between-species phylogenetic signal should be correlated. Here, we investigate the potential relationship between these two concepts by examining the evolution of multiple morphological traits for which heritability has been estimated in Drosophila melanogaster. Specifically, we analysed 42 morphological traits in both sexes on a phylogeny inferred from 22 nuclear genes for nine species of the melanogaster subgroup. We used Pagel's λ as a measurement of phylogenetic signal because it is the least influenced by the number of analysed taxa. Pigmentation traits showed the strongest concordance with the phylogeny, but no correlation was found between phylogenetic signal and heritability estimates mined from the literature. We obtained data for multiple climatic variables inferred from the geographical distribution of each species. Phylogenetic regression of quantitative traits on climatic variables showed a significantly positive correlation with heritability. Convergent selection, the response to which depends on the trait heritability, may have led to the null association between phylogenetic signal and heritability for morphological traits in Drosophila. We discuss the possible causes of discrepancy between both statistics and caution against their confusion in evolutionary biology.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 6","pages":"343-353"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33512044","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

Comparative analysis of microsatellites in coding regions provides insights into the adaptability of the giant panda, polar bear and brown bear 编码区微卫星的比较分析为大熊猫、北极熊和棕熊的适应性提供了见解

IF 1.5 4区生物学

Genetica Pub Date : 2022-10-26 DOI: 10.1007/s10709-022-00173-7

Meiling Cheng, Daxin Xie, Megan Price, Chuang Zhou, Xiuyue Zhang

引用次数: 0

Molecular phylogeny of Japanese marine Tanytarsini chironomids (Chironomidae: Chironominae). 文章标题日本海生手摇星虱的分子系统发育(手摇蝇科:手摇蝇科)。

IF 1.5 4区生物学

Genetica Pub Date : 2022-10-01 Epub Date: 2022-08-13 DOI: 10.1007/s10709-022-00163-9

Atsuya Kodama, Rion Maruta, Hidetoshi Saito, Koichiro Kawai

引用次数: 0

Genetics of yield component traits under salt stress at flowering stage and selection of salt tolerant pre-breeding lines for rice improvement. 开花期盐胁迫下产量组成性状的遗传及水稻耐盐预育种选育。

IF 1.5 4区生物学

Genetica Pub Date : 2022-10-01 Epub Date: 2022-07-15 DOI: 10.1007/s10709-022-00160-y

Rajat Pruthi, Venkata Ramana Rao Puram, John Ontoy, Prasant K Subudhi

{"title":"Genetics of yield component traits under salt stress at flowering stage and selection of salt tolerant pre-breeding lines for rice improvement.","authors":"Rajat Pruthi, Venkata Ramana Rao Puram, John Ontoy, Prasant K Subudhi","doi":"10.1007/s10709-022-00160-y","DOIUrl":"https://doi.org/10.1007/s10709-022-00160-y","url":null,"abstract":"Rice is highly vulnerable to salt stress at both seedling and flowering stage. While research efforts largely focused on seedling stage salinity tolerance, flowering stage salt tolerance studies are limited. Development of rice cultivars with salt tolerance at both stages will enhance rice productivity in salt affected farmlands. In the present study, two introgression line (IL) populations of a salt-tolerant landrace 'Nona Bokra (N)' were developed in the genetic backgrounds of two U.S. cultivars 'Cheniere (C)' and 'Jupiter (J)' and were evaluated for elucidation of the genetic basis of agronomically important traits at flowering stage and development of salt tolerant pre-breeding lines. Evaluation of both sets of ILs (JN-ILs and CN-ILs) under saline (EC = 8 dSm-1) environment led to identification of a total of 33 QTLs for seven different yield and yield component traits impacted by salt stress. Majority of large-effect QTLs for traits such as panicle length (qPL1.1JN), spikelet sterility (qSS1.1JN), thousand-grain weight (qTGW1.1JN), days to flowering (qDFF1.1CN), and plant height (qPH1.1CN) were located on chromosome 1. Some candidate genes present within the major effect QTL regions include potassium channel OsKAT1, NAC domain-containing protein, potassium transporters, and photosensitive leaf rolling 1. Comparison of the results with earlier reports on seedling stage suggested a different set of genes controlling salt tolerance at both stages. In addition, pre-breeding lines with improved flowering stage salinity tolerance were identified. These pre-breeding rice lines will accelerate fine mapping, map-based cloning, and pyramiding of desirable alleles for both flowering and seedling stage salt tolerance through marker assisted selection.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"273-288"},"PeriodicalIF":1.5,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40606455","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

Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia). 刺珊瑚(Cnidaria, Hexacorallia)的物种和种群基因组分化。

IF 1.5 4区生物学

Genetica Pub Date : 2022-10-01 Epub Date: 2022-09-09 DOI: 10.1007/s10709-022-00165-7

Didier Aurelle, Marine Pratlong, Nicolas Oury, Anne Haguenauer, Pauline Gélin, Hélène Magalon, Mehdi Adjeroud, Pascal Romans, Jeremie Vidal-Dupiol, Michel Claereboudt, Camille Noûs, Lauric Reynes, Eve Toulza, François Bonhomme, Guillaume Mitta, Pierre Pontarotti

{"title":"Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia).","authors":"Didier Aurelle, Marine Pratlong, Nicolas Oury, Anne Haguenauer, Pauline Gélin, Hélène Magalon, Mehdi Adjeroud, Pascal Romans, Jeremie Vidal-Dupiol, Michel Claereboudt, Camille Noûs, Lauric Reynes, Eve Toulza, François Bonhomme, Guillaume Mitta, Pierre Pontarotti","doi":"10.1007/s10709-022-00165-7","DOIUrl":"https://doi.org/10.1007/s10709-022-00165-7","url":null,"abstract":"Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 5","pages":"247-262"},"PeriodicalIF":1.5,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33455552","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

Recognition of functional genetic polymorphism using ESE motif definition: a conservative evolutionary approach to CYP2D6/CYP2C19 gene variants. 使用ESE基序定义识别功能性遗传多态性:CYP2D6/CYP2C19基因变异的保守进化方法

IF 1.5 4区生物学

Genetica Pub Date : 2022-10-01 Epub Date: 2022-08-01 DOI: 10.1007/s10709-022-00161-x

Mitra Samadi, Laleh Beigi, Fatemeh Yadegari, Alireza Madjid Ansari, Keivan Majidzadeh-A, Maryam Eskordi, Leila Farahmand

{"title":"Recognition of functional genetic polymorphism using ESE motif definition: a conservative evolutionary approach to CYP2D6/CYP2C19 gene variants.","authors":"Mitra Samadi, Laleh Beigi, Fatemeh Yadegari, Alireza Madjid Ansari, Keivan Majidzadeh-A, Maryam Eskordi, Leila Farahmand","doi":"10.1007/s10709-022-00161-x","DOIUrl":"https://doi.org/10.1007/s10709-022-00161-x","url":null,"abstract":"Although predicting the effects of variants near intron-exon boundaries is relatively straightforward, predicting the functional Exon Splicing Enhancers (ESEs) and the possible effects of variants within ESEs remains a challenge. Considering the essential role of CYP2D6/CYP2C19 genes in drug metabolism, we attempted to identify variants that are most likely to disrupt splicing through their effect on these ESEs. ESEs were predicted in these two genes using ESEfinder 3.0, incorporating a series of filters (increased threshold and evolutionary conservation). Finally, reported mutations were evaluated for their potential to disrupt splicing by affecting these ESEs. Initially, 169 and 243 ESEs were predicted for CYP2C19/CYP2D6, respectively. However, applying the filters, the number of predicted ESEs was reduced to 26 and 19 in CYP2C19/CYP2D6, respectively. Comparing prioritized predicted ESEs with known sequence variants in CYP2C19/CYP2D6 genes highlights 18 variations within conserved ESEs for each gene. We found good agreement in cases where such predictions could be compared to experimental evidence. In total, we prioritized a subset of mutational changes in CYP2C19/CYP2D6 genes that may affect the function of these genes and lead to altered drug responses. Clinical studies and functional analysis for investigating detailed functional consequences of the mentioned mutations and their phenotypic outcomes is mostly recommended.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"289-297"},"PeriodicalIF":1.5,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40591971","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

The complete mitochondrial genome of Talpa martinorum (Mammalia: Talpidae), a mole species endemic to Thrace: genome content and phylogenetic considerations. 色雷斯特有的鼹鼠物种Talpa martinorum(哺乳动物:Talpidae)的完整线粒体基因组:基因组内容和系统发育的考虑。

IF 1.5 4区生物学

Genetica Pub Date : 2022-10-01 Epub Date: 2022-08-27 DOI: 10.1007/s10709-022-00162-w

Sadık Demirtaş, Mahir Budak, Ertan M Korkmaz, Jeremy B Searle, David T Bilton, İslam Gündüz

{"title":"The complete mitochondrial genome of Talpa martinorum (Mammalia: Talpidae), a mole species endemic to Thrace: genome content and phylogenetic considerations.","authors":"Sadık Demirtaş, Mahir Budak, Ertan M Korkmaz, Jeremy B Searle, David T Bilton, İslam Gündüz","doi":"10.1007/s10709-022-00162-w","DOIUrl":"https://doi.org/10.1007/s10709-022-00162-w","url":null,"abstract":"The complete mitogenome sequence of Talpa martinorum, a recently described Balkan endemic mole, was assembled from next generation sequence data. The mitogenome is similar to that of the three other Talpa species sequenced to date, being 16,835 bp in length, and containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication, and a control region or D-loop. Compared to other Talpa mitogenomes sequenced to date, that of T. martinorum differs in the length of D-loop and stop codon usage. TAG and T-- are the stop codons for the ND1 and ATP8 genes, respectively, in T. martinorum, whilst TAA acts as a stop codon for both ND1 and ATP8 in the other three Talpa species sequenced. Phylogeny reconstructions based on Maximum Likelihood and Bayesian inference analyses yielded phylogenies with similar topologies, demonstrating that T. martinorum nests within the western lineage of the genus, being closely related to T. aquitania and T. occidentalis.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"317-325"},"PeriodicalIF":1.5,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40660433","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