scholarly journals Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay

2018 ◽  
Vol 115 (5) ◽  
pp. 968-973 ◽  
Author(s):  
Bronwyn A. Lucas ◽  
Eitan Lavi ◽  
Lily Shiue ◽  
Hana Cho ◽  
Sol Katzman ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Regulatory Networks ◽  
Parallel Evolution ◽  
Orthologous Gene ◽  
Control Networks ◽  
Short Interspersed Elements ◽  
Gene Pairs ◽  
Sine Insertion ◽  
Rapid Divergence ◽  
Species Specific

Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3′-untranslated regions (3′-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3′-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3′-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20–25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

Molecular evidence from short interspersed elements (SINEs) that Oncorhynchus masou (cherry salmon) is monophyletic

1998 ◽  
Vol 55 (8) ◽  
pp. 1864-1870 ◽  
Author(s):  
Shigenori Murata ◽  
Nobuyoshi Takasaki ◽  
Toshio Okazaki ◽  
Takanori Kobayashi ◽  
Ken-ichi Numachi ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Evidence ◽  
Oncorhynchus Masou ◽  
Chain Reaction ◽  
Short Interspersed Elements ◽  
Local Populations ◽  
Specific Manner ◽  
Sine Insertion ◽  
Polymerase Chain ◽  
Species Specific

The genome of salmonid species contains numerous short interspersed repetitive elements (SINEs), which are known as members of the Hpa I family of SINEs. We have isolated and characterized eight loci at which Hpa I SINEs have been inserted in a species-specific manner in the genome of Oncorhynchus masou (cherry salmon). All of these SINE units were fixed in each of the local populations examined. This observation suggests that the SINE insertion events must have occurred in the genome of the single ancestral species of all the subspecies of O. masou and that the SINEs must have spread throughout the various populations before the divergence of subspecies. This provides unequivocal evidence that O. masou is monophyletic. These species-specific SINE units provide a very convenient and reliable tool for identification of O. masou by the polymerase chain reaction.

scholarly journals Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome

2020 ◽  
Vol 12 (3) ◽  
pp. 1-17
Author(s):  
Nicolai K H Barth ◽  
Lifei Li ◽  
Leila Taher
Keyword(s):  
Convergent Evolution ◽  
Regulatory Networks ◽  
Tissue Specificity ◽  
Target Genes ◽  
Mouse Genome ◽  
Intrinsic Property ◽  
Mammalian Genome ◽  
Fine Tuning ◽  
Evolutionary Advantage ◽  
Species Specific

Abstract Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: Redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become nonfunctional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue specificity as compared with other genes. Finally, we found that although enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.

scholarly journals Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jifang Zhang ◽  
Jian Zhao ◽  
Qunyun Tan ◽  
Xiaojun Qiu ◽  
Shiyong Mei
Keyword(s):  
Transcription Factors ◽  
Raphanus Sativus ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Key Genes ◽  
Transcript Profiles ◽  
Species Specific ◽  
Anthocyanin Biosynthetic Genes

AbstractRadish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

ScFT6: A Putative Candidate for Sugarcane Floral Inducer

2021 ◽  
Author(s):  
Manoel Viana Linhares-Neto ◽  
Pedro Vitor Schumacher ◽  
Thales Henrique Cherubino Ribeiro ◽  
Carlos Henrique Cardon ◽  
Pâmela Marinho Resende ◽  
...  
Keyword(s):  
Flowering Time ◽  
Regulatory Networks ◽  
Floral Induction ◽  
Orthologous Gene ◽  
Time Behavior ◽  
Variable Expression ◽  
Binding Protein Gene ◽  
Sugarcane Productivity ◽  
Phosphatidylethanolamine Binding Protein

Abstract One of the factors that can decrease sugarcane productivity is the flowering, because it affects the quantity and quality of feedstock, due to sucrose consumption from the stem during inflorescence emission. Photoperiodicity is the main environmental factor involved in sugarcane floral induction, which occurs by the integration of gene regulatory networks in response to environmental and endogenous stimuli. One of the genes involved in those regulatory networks is the FLOWERING LOCUS T (FT), which is considered a phloem-mobile signal that stimulates floral induction in the shoot apical meristem. This work aimed to identify and characterize homologs of the FT gene in sugarcane, as well as to determine the putative function of these genes during floral induction. From this perspective, we have conducted in silico analyses of putative FT orthologs in sugarcane, as well as the expression levels in different photoperiodic conditions in a 24-hours-day-cycle of ScFT6 in different plant tissues in contrasting cultivars in terms of flowering time. Three new possible FT orthologs were found with high similarity to FT homologs in other species. Among three genes identified, we highlighted ScFT6, which has a conserved domain and amino acids at characteristic positions for the flowering inducer phosphatidylethanolamine-binding protein gene family. Additionally, its expression occurs according to coincidental model, possibly being controlled by the circadian clock. Cultivars with distinct flowering time behavior display variable expression for the ScFT6 gene, suggesting a possible genotypic relationship for its expression. Therefore, sugarcane has at least one putative orthologous gene in relation to FT that promotes floral induction.

scholarly journals Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils

2018 ◽  
Author(s):  
Veronica Preite ◽  
Christian Sailer ◽  
Lara Syllwasschy ◽  
Sian Bray ◽  
Ute Krämer ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Arabidopsis Halleri ◽  
Individual Genome ◽  
Genetic Changes ◽  
Association Analyses ◽  
Systematic Testing ◽  
Related Plant ◽  
Arabidopsis Arenosa ◽  
Species Specific ◽  
Degree Of Convergence

AbstractIt is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from 8 populations on metalliferous and non-metalliferous soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical SNPs in several A. halleri genes at two independently colonized metalliferous sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine metalliferous soils involves convergent evolution, which will likely be more pervasive across sites purposely chosen for maximal similarity in soil composition.

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

scholarly journals Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea

2020 ◽  
Vol 2020 ◽  
pp. 1-19
Author(s):  
Chenyang Liu ◽  
Dongliang Yuan ◽  
Tong Liu ◽  
Mengge Xing ◽  
Wenying Xu ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Cultivated Species ◽  
Arachis Duranensis ◽  
Gene Structures ◽  
Wild Peanut

RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated their evolution relationships. The RWP-RK proteins were classified into two groups, RWP-RK domain proteins and NODULE-INCEPTION-like proteins. Chromosomal distributions, gene structures, and conserved motifs of RWP-RK genes were compared among wild and cultivated peanuts. In addition, we identified 12 orthologous gene pairs from the two wild peanut species, 13 from A. duranensis and A. hypogaea, and 13 from A. ipaensis and A. hypogaea. One, one, and seventeen duplicated gene pairs were identified within the A. duranensis, A. ipaensis, and A. hypogaea genomes, respectively. Moreover, different numbers of cis-acting elements in the RWP-RK promoters were found in wild and cultivated species (87 in A. duranensis, 89 in A. ipaensis, and 92 in A. hypogaea), and as a result, many RWP-RK genes showed distinct expression patterns in different tissues. Our study will provide useful information for further functional and evolutionary analysis of the RWP-RK genes.

scholarly journals Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 310 ◽  
Author(s):  
Junying Liu ◽  
Huiyan Fan ◽  
Ying Wang ◽  
Chenggui Han ◽  
Xianbing Wang ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Regulatory Networks ◽  
Target Genes ◽  
Tobacco Rattle Virus ◽  
Yellow Vein ◽  
Differentially Expressed ◽  
Virus Induced Gene Silencing ◽  
Developmental Defects ◽  
Differentially Expressed Mirnas ◽  
Species Specific

Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.

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