Genetica最新文献

{"title":"Comparative analysis of cold-responsive genes under short-term cold stimulation and cold-adaptive genes under long-term heterogeneous environments reveals a cold adaptation mechanism in weeping forsythia.","authors":"Yong Li,&nbsp;Shu-Chen Wang,&nbsp;Qian Li,&nbsp;Ming-Wan Li,&nbsp;Run-Li Mao,&nbsp;He-Chen Zhang,&nbsp;Wang-Jun Yuan,&nbsp;Jine Quan","doi":"10.1007/s10709-022-00176-4","DOIUrl":"https://doi.org/10.1007/s10709-022-00176-4","url":null,"abstract":"<p><p>Identifying cold-related genes can provide insights into the cold adaptation mechanism of weeping forsythia. In this study, we compared the changes in gene expressions and physiological and biochemical indices under short-term cold stimulation with the changes in gene sequences under a long-term heterogeneous environment to investigate the cold adaptation mechanism in weeping forsythia. The data of adaptive gene sequence changes, e.g., single nucleotide polymorphisms, were obtained from previous landscape genomics studies. The physiological and biochemical indicators and transcriptome results showed that weeping forsythia initiated a series of programs, including increasing cell osmotic pressures, scavenging ROS, activating the defense mechanism that crosses with pathogen infection, and upregulating CBF/DREB1 transcription factor 1, to cope with short-term cold stress. A reanalysis of landscape genomic data suggested that weeping forsythia responded to long-term heterogeneous cold stress by the differentiation of genes related to synthesis of aromatic substances and adenosine triphosphate. Our results supported the hypothesis that the adaptation mechanisms of species to short-term environmental stimulation and long-term stress in heterogeneous environments are different. The differences in cold tolerance among populations are not necessarily obtained by changing cold-responsive gene sequences. This study provides new insights into the cold adaptation mechanisms of plants.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"151 1","pages":"47-59"},"PeriodicalIF":1.5,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9190467","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}

{"title":"Identification, molecular characterization, and in silico structural analysis of larval salivary glands Netrin-A as a potent biomarker from Lucilia sericata (Diptera: Calliphoridae).","authors":"Masoumeh Bagheri,&nbsp;Hamzeh Alipour,&nbsp;Tahereh Karamzadeh,&nbsp;Marzieh Shahriari-Namadi,&nbsp;Abbasali Raz,&nbsp;Kourosh Azizi,&nbsp;Javad Dadgar Pakdel,&nbsp;Mohammad Djaefar Moemenbellah-Fard","doi":"10.1007/s10709-022-00164-8","DOIUrl":"https://doi.org/10.1007/s10709-022-00164-8","url":null,"abstract":"<p><p>The greenbottle blowfly Lucilia sericata (L. sericata) is increasingly used in larval therapy of chronic wounds. Netrins as bifunctional proteins are in the superfamily of Laminins secreted from larval salivary glands. The Netrin protein has a significant instructive role in axon guidance, causing neuronal outgrowth, angiogenesis, and cell migration. It seems to be crucial in wound healing and acts as a potential biomarker in diagnosing some clinical diseases. This survey aimed to identify molecular features and analyze in silico structural configuration of Netrin-A in L. sericata larvae. The larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericata Netrin-A (LSN-A) was then identified using rapid amplification of circular DNA ends (RACE) and rapid amplification of genomic ends (RAGE). Parts of the Netrin-A gene, including the middle, 3'-, and 5'-ends, were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its estimated molecular weight was 78.6 kDa. Sequencing of this fragment and its BLAST analysis revealed laminin-based high (95%) similarity with the mRNA sequence of Lucilia cuprina Netrin-A. The 3-D structure of Netrin-A drawn by SWISS-MODEL exhibited its partial resemblance to the reference molecule Netrin-1 of Homo sapiens. This study supports the molecular and structural analyses of LSN-A protein, which could lead to wound treatment. Ultimately, it can be an effective candidate to ameliorate injury. Our next attempt is to produce LSN-A recombinant protein for use in biomedical sciences.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 6","pages":"379-394"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33469985","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}

{"title":"The complete chloroplast genome of two Firmiana species and comparative analysis with other related species.","authors":"Qifeng Lu,&nbsp;Wenhua Luo","doi":"10.1007/s10709-022-00169-3","DOIUrl":"https://doi.org/10.1007/s10709-022-00169-3","url":null,"abstract":"<p><p>Firmiana is a small genus within the subfamily Sterculioideae of the Malvaceae. There are nine Firmiana species distributed in South and South-west China, most of which are endangered. Due to the shortage of plastid genomes data, the phylogenetic relationships and the evolutionary history of this genus remain unclear. Therefore, the complete chloroplast genomes of F. calcarean and F. hainanensis were sequenced using high-throughput sequencing and then compared with the chloroplast genomes of other reported Firmiana species. The genome size of F. calcarean and F. hainanensis is 161,263 and 160,031 bp long, respectively, containing a total of 131 genes (including 85 protein coding genes, 37 tRNAs, 8 rRNAs, and one pseudogene). Comparative analysis revealed that the genome structure, GC content, gene content and order, as well as the RNA editing sites within the chloroplast genomes of F. calcarean and F. hainanensis were similar to previously reported Firmiana species. ML phylogenetic analysis revealed that F. danxiaensis, F. hainanensis, F. calcarean, F. simplex, and F. major form a sister group to F. colorata, F. pulcherrima, and F. kwangsiensis. The SSRs, long repeats, and 21 highly divergent regions (Pi > 0.01) identified in this study might provide potential DNA markers for further population genetics and phylogenetic studies of Firmiana. Our findings can help design new species-specific molecular markers and the general framework to further explore the evolutionary history of Firmiana and to address their conservation challenges.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"395-405"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40662428","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}

{"title":"The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba.","authors":"Anmari Alvarez-Aleman,&nbsp;Margaret E Hunter,&nbsp;Thomas K Frazer,&nbsp;James A Powell,&nbsp;Eddy Garcia Alfonso,&nbsp;James D Austin","doi":"10.1007/s10709-022-00172-8","DOIUrl":"https://doi.org/10.1007/s10709-022-00172-8","url":null,"abstract":"<p><p>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 H_E = 0.44, and SNP H_E = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite F_IS = 0.12, SNP F_IS = 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 N_e < 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.</p>","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}

{"title":"Characterization of the complete mitochondrial genome of Miamiensis avidus causing flatfish scuticociliatosis.","authors":"Na Young Kim,&nbsp;Sang Jung Ahn,&nbsp;Jung Soo Seo,&nbsp;Eun Ji Jeon,&nbsp;Mi Young Cho,&nbsp;Hye Sung Choi","doi":"10.1007/s10709-022-00167-5","DOIUrl":"https://doi.org/10.1007/s10709-022-00167-5","url":null,"abstract":"<p><p>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.</p>","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}

{"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,&nbsp;F M C B Domingos,&nbsp;S C Gomides,&nbsp;I A Novelli,&nbsp;G R Colli,&nbsp;S M Vargas","doi":"10.1007/s10709-022-00170-w","DOIUrl":"https://doi.org/10.1007/s10709-022-00170-w","url":null,"abstract":"<p><p>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.</p>","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}

{"title":"Long-term evolution of quantitative traits in the Drosophila melanogaster species subgroup.","authors":"Amir Yassin,&nbsp;Nelly Gidaszewski,&nbsp;Vincent Debat,&nbsp;Jean R David","doi":"10.1007/s10709-022-00171-9","DOIUrl":"https://doi.org/10.1007/s10709-022-00171-9","url":null,"abstract":"<p><p>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.</p>","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}

{"title":"Comparative analysis of microsatellites in coding regions provides insights into the adaptability of the giant panda, polar bear and brown bear","authors":"Meiling Cheng, Daxin Xie, Megan Price, Chuang Zhou, Xiuyue Zhang","doi":"10.1007/s10709-022-00173-7","DOIUrl":"https://doi.org/10.1007/s10709-022-00173-7","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 1","pages":"355 - 366"},"PeriodicalIF":1.5,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48797236","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}

{"title":"Molecular phylogeny of Japanese marine Tanytarsini chironomids (Chironomidae: Chironominae).","authors":"Atsuya Kodama,&nbsp;Rion Maruta,&nbsp;Hidetoshi Saito,&nbsp;Koichiro Kawai","doi":"10.1007/s10709-022-00163-9","DOIUrl":"https://doi.org/10.1007/s10709-022-00163-9","url":null,"abstract":"<p><p>Tanytarsini is a large tribe of Chironomidae with at least 11 recorded marine species grouped in three genera. In this study, we performed a phylogenic analysis using molecular data from 13 Tanytarsini genera, including all Japanese marine species in a large tribe of Chironominae, to estimate their phylogenetic positions and evolutionary history. The phylogenetic reconstruction grouped the marine species in two clades. One clade was composed of five marine Tanytarsus and two marine Pontomyia species within a larger clade of Tanytarsus. Pontomyia is considered to have morphologically specialized and adapted to marine environments by rapid evolution, although it formed a clade with Tanytarsus. The only one species of Tanytarsus, T. pelagicus, clustered as a member of the second clade, which was mainly composed by species of the genus Paratanytarsus. Thus, we redescribe T. pelagicus as Paratanytarsus pelagicus.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"263-272"},"PeriodicalIF":1.5,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40695393","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}

{"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,&nbsp;Venkata Ramana Rao Puram,&nbsp;John Ontoy,&nbsp;Prasant K Subudhi","doi":"10.1007/s10709-022-00160-y","DOIUrl":"https://doi.org/10.1007/s10709-022-00160-y","url":null,"abstract":"<p><p>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 (qPL1.1^JN), spikelet sterility (qSS1.1^JN), thousand-grain weight (qTGW1.1^JN), days to flowering (qDFF1.1^CN), and plant height (qPH1.1^CN) 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.</p>","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}