scholarly journals Evolutionary patterns of chimeric retrogenes in Oryza species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yanli Zhou ◽  
Chengjun Zhang
Keyword(s):  
Positive Selection ◽  
Genome Evolution ◽  
Rice Genome ◽  
Chimeric Gene ◽  
Oryza Species ◽  
Evolutionary Patterns ◽  
Plant Genomes ◽  
Parental Gene ◽  
Flanking Sequences ◽  
Substitution Ratio

AbstractChimeric retroposition is a process by which RNA is reverse transcribed and the resulting cDNA is integrated into the genome along with flanking sequences. This process plays essential roles and drives genome evolution. Although the origination rates of chimeric retrogenes are high in plant genomes, the evolutionary patterns of the retrogenes and their parental genes are relatively uncharacterised in the rice genome. In this study, we evaluated the substitution ratio of 24 retrogenes and their parental genes to clarify their evolutionary patterns. The results indicated that seven gene pairs were under positive selection. Additionally, soon after new chimeric retrogenes were formed, they rapidly evolved. However, an unexpected pattern was also revealed. Specifically, after an undefined period following the formation of new chimeric retrogenes, the parental genes, rather than the new chimeric retrogenes, rapidly evolved under positive selection. We also observed that one retro chimeric gene (RCG3) was highly expressed in infected calli, whereas its parental gene was not. Finally, a comparison of our Ka/Ks analysis with that of other species indicated that the proportion of genes under positive selection is greater for chimeric retrogenes than for non-chimeric retrogenes in the rice genome.

scholarly journals Evolutionary patterns of the chimerical retrogenes in Oryza

2019 ◽  
Author(s):  
Yanli Zhou ◽  
Huazhi Song ◽  
Jinghua Xiao ◽  
Qifa Zhang ◽  
Manyuan Long ◽  
...  
Keyword(s):  
Positive Selection ◽  
Rice Genome ◽  
Rapid Evolution ◽  
Plant Genome ◽  
Likelihood Method ◽  
Flanking Sequence ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Parental Gene ◽  
Substitution Ratio

AbstractChimerical retroposition delineate a process by which RNA reverse transcribed integration into genome accompanied with recruiting flanking sequence, which is asserted to play essential roles and drive genome evolution. Although chimerical retrogenes hold high origination rate in plant genome, the evolutionary pattern of retrogenes and their parental genes are not well understood in rice genome. In this study, using maximum likelihood method, we evaluated the substitution ratio along lineages of 24 retrogenes and parental gene pairs to retrospect the evolutionary patterns. The results indicate that some specific lineages in 7 pairs underwent positive selection. Besides the rapid evolution in the initial stage of new chimerical retrogene evolution, an unexpected pattern was revealed: soon or some uncertain period after the origination of new chimerical retrogenes, their parental genes evolved rapidly under positive selection, rather than the rapid evolution of the new chimerical retrogenes themselves. This result lend support to the hypothesis that the new copy assistant the function evolution among parental gene and retrogene. Transcriptionally, we also found that one retrogene (RCG3) have a high expression at the period of calli infection which supported by chip data while its parental gene doesn’t have. Finally, by calibration to Ka/Ks analysis results in other species including Apis mellifera, we concluded that chimerical retrogenes are higher proportionally positive selected than the regular genes in the rice genome.

scholarly journals The MHC Class Ia Genes in Chenfu’s Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Animals ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 34
Author(s):  
Hu Chen ◽  
Siqi Huang ◽  
Ye Jiang ◽  
Fuyao Han ◽  
Qingyong Ni ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Positive Selection ◽  
Phylogenetic Relationships ◽  
Molecular Mechanisms ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Evolutionary Patterns ◽  
Mhc Genes ◽  
Mhc Class Ia ◽  
Related Proteins

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.

Sequence rearrangement in the AT-rich minisatellite of the novel rice transposable element Basho

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 493-502 ◽  
Author(s):  
Tsuyoshi Inukai ◽  
Yoshio Sano
Keyword(s):  
Repeat Unit ◽  
Rice Genome ◽  
Single Strand ◽  
Homology Search ◽  
Matrix Attachment Region ◽  
Site Preference ◽  
The Matrix ◽  
Attachment Region ◽  
Flanking Sequences ◽  
Direct Amplification

In the process of characterizing a rice wx deletion mutant, an AT-rich minisatellite sequence that consisted of units of ~80 bp was detected about 2.3 kb downstream of the wx gene. This AT-rich minisatellite was a multiple-copy element (1 × 103 to 2 × 103 copies per haploid genome) and interspersed in the rice genome. By BLAST homology search it was indicated that not only the tandem repeat but also both flanking sequences were conserved among copies. According to the characteristics of the termini (5'-CHH ...CTAG-3') and a target site preference for T, this AT-rich minisatellite accompanying the flanking sequences was classified into a novel transposon, Basho. The results of direct amplification of Basho showed that relatively large variation in size existed in the Basho family. We estimate the variation to be generated by not only alteration of the number of units in the minisatellite but also by duplications of larger blocks including the conserved flanking sequences caused by single-strand mispairing (SSM) at noncontiguous repeats. Because the AT-rich minisatellite contained in Basho possessed several motifs of the matrix attachment region (MAR) in its repeat unit, the functional role as MAR in the rice genome was discussed.Key words: Oryza sativa, minisatellite, Basho, single strand mispairing (SSM).

scholarly journals Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection

2021 ◽  
Author(s):  
Yuan Huang ◽  
Jiahui Chen ◽  
Chuan Dong ◽  
Dylan Sosa ◽  
Shengqian Xia ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Duplication ◽  
Positive Selection ◽  
Specific Gene ◽  
Phenotypic Evolution ◽  
New Genes ◽  
Parental Gene ◽  
New Gene ◽  
Species Specific ◽  
Partial Gene Duplication

Abstract Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-seq analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana.

scholarly journals Comparative Genome and Transcriptome Analysis Reveals Gene Selection Patterns Along with the Paleo-Climate Change in the Populus Phylogeny

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 163
Author(s):  
You-jie Zhao ◽  
Chang-zhi Han ◽  
Yong Cao ◽  
Hua Zhou
Keyword(s):  
Positive Selection ◽  
Transcriptome Analysis ◽  
Middle Miocene ◽  
Gene Selection ◽  
Ice Age ◽  
Divergence Times ◽  
Evolutionary Patterns ◽  
Stress Genes ◽  
Paleoclimate Change ◽  
Climate Transition

Poplars are widely distributed in the northern hemisphere and have good adaptability to different living environments. The accumulation of genome and transcriptome data provides a chance to conduct comparative genomics and transcriptomics analyses to elucidate the evolutionary patterns of Populus phylogeny. Transcript sequences of eight Salicaceae species were downloaded from public databases. All of the pairwise orthologues were identified by comparative transcriptome analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of divergence. The divergence times of the phylogenetic clades were mainly estimated during the Middle Miocene Climate Transition (MMCT) to Quaternary Ice Age. We also identified all of the fast-evolving sequences of positive selection and found some resistance genes that were related to environmental factors. Our results suggest that drought-, H2O2- and cold-stress genes are involved in positive selection along with the paleoclimate change. These data are useful in elucidating the evolutionary patterns and causes of speciation in the Populus lineage.

scholarly journals Structure and expression of the human gene encoding major heat shock protein HSP70.

1985 ◽  
Vol 5 (2) ◽  
pp. 330-341 ◽  
Author(s):  
B Wu ◽  
C Hunt ◽  
R Morimoto
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Genomic Library ◽  
Human Gene ◽  
Chimeric Gene ◽  
Hsp70 Gene ◽  
Gene Encoding ◽  
Hsp70 Mrna ◽  
Flanking Sequences ◽  
Heat Shock Protein Hsp70

We have cloned a human gene encoding the 70,000-dalton heat shock protein (HSP70) from a human genomic library, using the Drosophila HSP70 gene as a heterologous hybridization probe. The human recombinant clone hybridized to a 2.6-kilobase polyadenylated mRNA from HeLa cells exposed to 43 degrees C for 2 h. The 2.6-kilobase mRNA was shown to direct the translation in vitro of a 70,000-dalton protein similar in electrophoretic mobility to the HSP70 synthesized in vivo. From the analysis of S1 nuclease-resistant mRNA-DNA hybrids, the HSP70 gene appears to be transcribed as an uninterrupted mRNA of 2.3 kilobases. We show that the cloned HSP70 gene contains the sequences necessary for heat shock-induced expression by two criteria. First, hamster cells transfected with a subclone containing the HSP70 gene and flanking sequences synthesized a HSP70-like protein upon heat shock. Second, human cells transfected with a chimeric gene containing the 5' flanking sequences of the HSP70 gene and the coding sequences of the bacterial chloramphenicol acetyltransferase gene transcribed the chimeric gene upon heat shock. We show that the HSP70 mRNA transcribed in an adenovirus 5 transformed human cell line (293 cells) is identical to the HSP70 mRNA induced by heat shock.

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