scholarly journals Genome-Wide Analysis of Carboxylesterases (COEs) in the Whitefly, Bemisia tabaci (Gennadius)

2019 ◽  
Vol 20 (20) ◽  
pp. 4973
Author(s):  
Jixing Xia ◽  
Haifeng Xu ◽  
Zezhong Yang ◽  
Huipeng Pan ◽  
Xin Yang ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Expression Patterns ◽  
Invasive Pest ◽  
Neighbor Joining ◽  
Functional Categories ◽  
Genome Database ◽  
Genome Wide ◽  
A Genome ◽  
Multifunctional Enzymes ◽  
Insight Into

The whitefly (Bemisia tabaci), an important invasive pest that causes severe damage to crops worldwide, has developed resistance to a variety of insecticides. Carboxylesterases (COEs) are important multifunctional enzymes involved in the growth, development, and xenobiotic metabolism of insects. However, systematic studies on the COEs of B. tabaci are scarce. Here, 42 putative COEs in different functional categories were identified in the Mediterranean species of B. tabaci (B. tabaci MED) based on a genome database and neighbor-joining phylogeny. The expression patterns of the COEs were affected by the development of B. tabaci. The expression levels of six COEs were positively correlated with the concentration of imidacloprid to which B. tabaci adults were exposed. The mortality of B. tabaci MED adults fed dsBTbe5 (67.5%) and dsBTjhe2 (58.4%) was significantly higher than the adults fed dsEGFP (41.1%) when treated with imidacloprid. Our results provide a basis for functional research on COEs in B. tabaci and provide new insight into the imidacloprid resistance of B. tabaci.

scholarly journals SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

2022 ◽  
Author(s):  
Tiago da Silva Ribeiro ◽  
José A Galván ◽  
John E Pool
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Genetic Variant ◽  
Real Data ◽  
Selective Sweeps ◽  
Functional Categories ◽  
Genome Scans ◽  
Genome Wide ◽  
A Genome ◽  
Local Selection

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

scholarly journals Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets

2016 ◽  
Author(s):  
Bony De Kumar ◽  
Hugo J. Parker ◽  
Ariel Paulson ◽  
Mark E. Parrish ◽  
Irina Pushel ◽  
...  
Keyword(s):  
Es Cells ◽  
Hox Proteins ◽  
Binding Motifs ◽  
Functional Roles ◽  
Regulatory Interactions ◽  
Mouse Es Cells ◽  
Genome Wide ◽  
A Genome ◽  
Combinatorial Interactions ◽  
Insight Into

AbstractHoxa1 has diverse functional roles in differentiation and development. We have identified and characterized properties of regions bound by Hoxa1 on a genome-wide basis in differentiating mouse ES cells. Hoxa1 bound regions are enriched for clusters of consensus binding motifs for Hox, Pbx and Meis and many display co-occupancy of Pbx and Meis. Pbx and Meis are members of the TALE family and genome-wide analysis of multiple TALE members (Pbx, Meis, TGIF, Prep1 and Prep2) show that nearly all Hoxa1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins defines distinct classes of Hoxa1 targets and indicates a role as cofactors in modulating the specificity of Hox proteins. We also discovered extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes. This study provides new insight into a regulatory network involving combinatorial interactions between Hoxa1 and TALE proteins.

scholarly journals Big fish, little fish: a multi-omics investigation of growth traits in silver trevally (Pseudocaranx georgianus – araara)

2021 ◽  
Author(s):  
◽  
Noémie Valenza-Troubat
Keyword(s):  
New Zealand ◽  
Linkage Mapping ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Growth Traits ◽  
Expression Patterns ◽  
Linkage Groups ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome

<p><b>Understanding the relationship between DNA sequence variation and the diversity of observable traits across the tree of life is a central research theme in biology. In all organisms, most traits vary continuously between individuals. Explaining the genetic basis of this quantitative variation requires disentangling genetic from non-genetic factors, as well as their interactions. The identification of causal genetic variants yields fundamental insights into how evolution creates diversity across the tree of life. Ultimately, this information can be used for medical, environmental and agricultural applications. Aquaculture is an industry that is experiencing significant global growth and is benefiting from the advances of genomic research. Genomic information helps to improve complex commercial phenotypes such as growth traits, which are easily quantified visually, but influenced by polygenes and multiple environmental factors, such as temperature. In the context of a global food crisis and environmental change, there is an urgent need not only to understand which genetic variants are potential candidates for selection gains, but also how the architecture of these traits are composed (e.g. monogenes, polygenes) and how they are influenced by and interact with the environment. The overall goal of this thesis research was to generate a genome-wide multi-omics dataset matched with exhaustive phenotypic information derived from a F0-F1 pedigree to investigate the quantitative genetic basis of growth in the New Zealand silver trevally (Pseudocaranx georgianus). These data were used to identify genomic regions that co-segregate with growth traits, and to describe the regulation of the genes involved in response to temperature fluctuations. The findings of this research helped gain fundamental insights into the genotype–phenotype map in an important teleost species and understand its ability to dynamically respond to temperature variations. This will ultimately support the establishment of a genomics-informed New Zealand aquaculture breeding programme. </b></p> <p>Chapter 1 of this thesis provides an overview of how genes interact with the environment to produce various growth phenotypes and how an understanding of this is important in aquaculture. This first chapter provides the deeper context for the research in subsequent data chapters. </p> <p>Chapter 2 describes the study population, the collection of phenotypic and genotypic data, and a first description of the genetic parameters of growth traits in trevally. A combination of Whole Genome Sequencing (WGS) and Genotyping-By-Sequencing (GBS) techniques were used to generate 60 thousand Single Nucleotide Polymorphism (SNP) markers for individuals in a two-generation pedigree. Together with phenotypic data, the genotyping data were used to reconstruct the pedigree, measure inbreeding levels, and estimate heritability for 10 growth traits. Parents were identified for 63% of the offspring and successful pedigree reconstruction indicated highly uneven contributions of each parent, and between the sexes, to the subsequent generation. The average inbreeding levels did not change between generations, but were significantly different between families. Growth patterns were found to be similar to that of other carangids and subject to seasonal variations. Heritability as well as genetic and phenotypic correlations were estimated using both a pedigree and a genomic relatedness matrix. All growth trait heritability estimates and correlations were found to be consistently high and positively correlated to each other. </p> <p>In Chapter 3, genotypic and phenotypic data were used to carry out linkage mapping and a genome-wide association study (GWAS) to map quantitative trait loci (QTLs) associated with growth differences in the F1 population. A linkage map was generated using the largest family, which allowed to scan for rare variants associated with the traits. The linkage map reported in this thesis is the first one for the Pseudocaranx genus and one of the densest for the carangid family. It included 19,861 SNPs contained in 24 linkage groups, which correspond to the 24 trevally chromosomes. Eight significant QTLs associated with height, length and weight were discovered on three linkage groups. Using GWAS, 113 SNPs associated with nine traits were identified and 29 genetic growth hot spots were uncovered. Two of the GWAS markers co-located with the QTLs discovered with the linkage mapping analysis. This demonstrates that combining QTL mapping and GWAS represents a powerful approach for the identification and validation of loci controlling complex phenotypes, such as growth, and provides important insights into the genetic architecture of these traits. </p> <p>Chapter 4, the last data chapter, investigates plasticity in gene expression patterns and growth of juvenile trevally, in response to different temperatures. Temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and the gene expression patterns of the pituitary gland and the liver were compared across treatments in a subset of 100 individuals, using RNA sequencing. Results showed that growth increased 50% more in the warmer compared with the colder condition, suggesting that temperature has a large impact on the metabolic activity associated with growth. We were able to annotate 27,887 gene models and found 39 differentially expressed genes (DEGs) in the pituitary, and 238 in the liver. Of these, 6 DEGs showed a common expression pattern between the tissues. Annotated blast matches of all DEGs revealed genes linked to major pathways affecting metabolism and reproduction. Our results indicate that native New Zealand trevally exhibit predictable plastic regulatory responses to temperature stress and the genes identified provide excellent for selective breeding objectives and studied how populations may adapt to increasing temperatures.</p> <p>Finally, Chapter 5 discusses the implications, future directions, and application of this research for trevally and other breeding programmes. It more broadly highlights the insights that were gained on the genetic architecture of growth, and the role of temperature in interacting and modulating genes involved in plastic growth responses.</p>

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

scholarly journals Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

2019 ◽  
Vol 20 (21) ◽  
pp. 5419 ◽  
Author(s):  
Gao-Feng Zhou ◽  
Li-Ping Zhang ◽  
Bi-Xian Li ◽  
Ou Sheng ◽  
Qing-Jiang Wei ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plant Hormones ◽  
Target Genes ◽  
Expression Patterns ◽  
Poncirus Trifoliata ◽  
Differentially Expressed ◽  
Boron Deficiency ◽  
Trifoliate Orange ◽  
Genome Wide ◽  
A Genome

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

scholarly journals Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

2015 ◽  
Vol 67 (2) ◽  
pp. 373-383
Author(s):  
Bo Wang ◽  
Su Yingjuan ◽  
Ting Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Genome Wide ◽  
A Genome ◽  
Rbcs Gene ◽  
Rbcs Genes ◽  
Selaginella Moellendorffii ◽  
Insight Into ◽  
Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

scholarly journals A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

2019 ◽  
Vol 11 (8) ◽  
pp. 2078-2098 ◽  
Author(s):  
Shu-Ye Jiang ◽  
Jingjing Jin ◽  
Rajani Sarojam ◽  
Srinivasan Ramachandran
Keyword(s):  
Gene Family ◽  
Large Scale ◽  
Family Members ◽  
Terpene Synthase ◽  
Limited Information ◽  
Terpene Synthases ◽  
Genome Wide ◽  
A Genome ◽  
Family Expansion ◽  
Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

scholarly journals Admixture into and within sub-Saharan Africa

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
George BJ Busby ◽  
Gavin Band ◽  
Quang Si Le ◽  
Muminatou Jallow ◽  
Edith Bougama ◽  
...  
Keyword(s):  
Gene Flow ◽  
Geographic Region ◽  
Sub Saharan Africa ◽  
Genome Wide ◽  
A Genome ◽  
Depth Analysis ◽  
Shared Ancestry ◽  
Sub Saharan ◽  
Linguistic Groups ◽  
Insight Into

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

Identification and expression analysis of chloroplast ribonucleoproteins (cpRNPs) in Arabidopsis and rice

Genome ◽  
2020 ◽  
Author(s):  
Jiawen Wu ◽  
Huimin Liu ◽  
Shan Lu ◽  
Jian Hua ◽  
Baohong Zou
Keyword(s):  
Expression Analysis ◽  
Stress Responses ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Stability Control ◽  
Rna Recognition Motif ◽  
Chloroplast Targeting ◽  
Genome Wide ◽  
A Genome ◽  
Targeting Signal

Chloroplast ribonucleoproteins (cpRNPs) are implicated in splicing, editing and stability control of chloroplast RNAs as well as in regulating development and stress tolerance. To facilitate a comprehensive understanding of their functions, we carried out a genome-wide identification, curation, and phylogenetic analysis of cpRNP genes in Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Ten cpRNP genes were identified in each of Arabidopsis and rice genomes based on the presence of two RRM (RNA recognition motif) domains and an N-terminal chloroplast targeting signal peptide in the predicted proteins. These proteins are localized to chloroplasts. Gene expression analysis revealed that cpRNPs have differential tissue expression patterns and some cpRNPs are induced by abiotic stresses such as cold, heat and drought. Taken together, our study provides a comprehensive annotation of the cpRNP gene family and their expression patterns in Arabidopsis and rice which will facilitate further studies on their roles in plant growth and stress responses.

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