scholarly journals Recurrent single-gene duplication drives the expansion and expression diversification of the ADH gene family in pear and other Rosaceae species

2019 ◽  
Author(s):  
Shaoling Zhang ◽  
Weiwei Zeng ◽  
Xin Qiao ◽  
Qionghou Li ◽  
Chunxin Liu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Aromatic Compounds ◽  
Gene Evolution ◽  
Single Gene ◽  
Gene Clusters ◽  
Fruit Species ◽  
Rosaceae Species ◽  
Adh Genes ◽  
Adh Gene

Abstract Background Alcohol dehydrogenases (ADHs) are essential to plant growth and the formation of aromatic compounds in fruits. However, the evolutionary history and characteristics of ADH gene expression remain largely unclear in Chinese white pear ( Pyrus bretschneideri ) and other fruit species from the family Rosaceae.Results In this study, 464 ADH genes were identified in eight Rosaceae fruit species and 68 of the genes were from pear. Based on the analyses of phylogeny and conserved motifs, the pear ADH genes were classified into four subgroups (I, II, III, and IV). The chromosomal distribution of the genes was found to be uneven and numerous clusters of physically linked ADH genes were detected. Frequent single-gene duplication events were found to have contributed to the formation of ADH gene clusters and the expansion of the ADH gene family in these eight Rosaceae species. Purifying selection was the major force in ADH gene evolution. The younger genes derived from tandem and proximal duplications had evolved faster than those that derived from other types of duplication. RNA-sequencing and quantitative-real time-PCR analysis revealed that the expression levels of three ADH genes were closely correlated with the content of aromatic compounds that are found during fruit development.Conclusion Comprehensive analyses were conducted in eight Rosaceae species and 464 ADH genes were identified. The results of this study provide new insights into the evolution and expression characteristics of ADH family genes in pear and other Rosaceae species.

scholarly journals Genome-wide identification and comparative analysis of the ADH gene family in Chinese white pear (Pyrus bretschneideri) and other Rosaceae species

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 3484-3496
Author(s):  
Weiwei Zeng ◽  
Xin Qiao ◽  
Qionghou Li ◽  
Chunxin Liu ◽  
Jun Wu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Gene Family ◽  
Rosaceae Species ◽  
Chinese White ◽  
Genome Wide ◽  
Adh Gene

scholarly journals Genome-Wide Identification and Comparative Analysis of the ASR Gene Family in the Rosaceae and Expression Analysis of PbrASRs During Fruit Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Biying Zhao ◽  
Xianrong Yi ◽  
Xin Qiao ◽  
Yan Tang ◽  
Zhimei Xu ◽  
...  
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Gene Evolution ◽  
Structural Characteristics ◽  
Abiotic Stress Tolerance ◽  
Purifying Selection ◽  
Fruit Species ◽  
Organ Specific ◽  
Specific Proteins ◽  
Plant Families

The members of the Abscisic Acid (ABA) Stress and Ripening gene family (ASR) encode a class of plant-specific proteins with ABA/WDS domains that play important roles in fruit ripening, abiotic stress tolerance and biotic stress resistance in plants. The ASR gene family has been widely investigated in the monocotyledons and dicotyledons. Although the genome sequence is already available for eight fruit species of the Rosaceae, there is far less information about the evolutionary characteristics and the function of the ASR genes in the Rosaceae than in other plant families. Twenty-seven ASR genes were identified from species in the Rosaceae and divided into four subfamilies (I, II, III, and IV) on the basis of structural characteristics and phylogenetic analysis. Purifying selection was the primary force for ASR family gene evolution in eight Rosaceae species. qPCR experiments showed that the expression pattern of PbrASR genes from Pyrus bretschneideri was organ-specific, being mainly expressed in flower, fruit, leaf, and root. During fruit development, the mRNA abundance levels of different PbrASR genes were either down- or up-regulated, and were also induced by exogenous ABA. Furthermore, subcellular localization results showed that PbrASR proteins were mainly located in the nucleus and cytoplasm. These results provide a theoretical foundation for investigation of the evolution, expression, and functions of the ASR gene family in commercial fruit species of the Rosaceae family.

scholarly journals Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

2014 ◽  
Vol 112 (5) ◽  
pp. 1493-1498 ◽  
Author(s):  
Fabio Cortesi ◽  
Zuzana Musilová ◽  
Sara M. Stieb ◽  
Nathan S. Hart ◽  
Ulrike E. Siebeck ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Evolution ◽  
Single Gene ◽  
Gene Family Evolution ◽  
Raw Material ◽  
Opsin Gene ◽  
Evolutionary Mechanisms ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
History Of

Single-gene and whole-genome duplications are important evolutionary mechanisms that contribute to biological diversification by launching new genetic raw material. For example, the evolution of animal vision is tightly linked to the expansion of the opsin gene family encoding light-absorbing visual pigments. In teleost fishes, the most species-rich vertebrate group, opsins are particularly diverse and key to the successful colonization of habitats ranging from the bioluminescence-biased but basically dark deep sea to clear mountain streams. In this study, we report a previously unnoticed duplication of the violet-blue short wavelength-sensitive 2 (SWS2) opsin, which coincides with the radiation of highly diverse percomorph fishes, permitting us to reinterpret the evolution of this gene family. The inspection of close to 100 fish genomes revealed that, triggered by frequent gene conversion between duplicates, the evolutionary history of SWS2 is rather complex and difficult to predict. Coincidentally, we also report potential cases of gene resurrection in vertebrate opsins, whereby pseudogenized genes were found to convert with their functional paralogs. We then identify multiple novel amino acid substitutions that are likely to have contributed to the adaptive differentiation between SWS2 copies. Finally, using the dusky dottyback Pseudochromis fuscus, we show that the newly discovered SWS2A duplicates can contribute to visual adaptation in two ways: by gaining sensitivities to different wavelengths of light and by being differentially expressed between ontogenetic stages. Thus, our study highlights the importance of comparative approaches in gaining a comprehensive view of the dynamics underlying gene family evolution and ultimately, animal diversification.

Evolution of cow nonstomach lysozyme genes

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1082-1090 ◽  
Author(s):  
David M Irwin
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Gene Family ◽  
Adaptive Evolution ◽  
Concerted Evolution ◽  
Gene Evolution ◽  
Gene Duplications ◽  
Cdna Sequences ◽  
Defence Enzymes ◽  
And Function

Expansion of the lysozyme gene family is associated with the evolution of the ruminant lifestyle in ruminant artiodactyls such as the cow. Gene duplications allowed recombination between stomach lysozyme genes that may have assisted in the evolution of an enzyme adapted to survive and function in the stomach environment. Despite amplification of lysozyme genes, cow tears, milk, and blood are considered to be lysozyme deficient. Here we have identified 2 new cow lysozyme cDNA sequences and show that at least 4 different lysozymes are expressed in cows in nonstomach tissues and probably function as antibacterial defence enzymes. These 4 lysozyme genes are in addition to the 4 digestive lysozyme genes expressed in the stomach, yielding a number of expressed lysozyme genes in the cow larger than that found in most nonlysozyme-deficient mammals. In contrast to expectations, evidence for recombination between stomach and nonstomach lysozyme genes was found. Recombination, through concerted evolution, may have allowed some lysozymes to acquire the ability to survive in occasional acidic environments.Key words: molecular evolution, adaptive evolution, lysozyme, ruminants, gene duplication, gene evolution.

scholarly journals Comparative analysis of bHLH transcription factors in five Rosaceae species, and expression analysis of PbbHLHs in response to drought stress in pear

2020 ◽  
Author(s):  
Xiaobing Kou ◽  
Changlong Xiong ◽  
Danqi Wang ◽  
Yangyang Sun ◽  
Peng Wang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gene Family ◽  
Expression Analysis ◽  
Tissue Expression ◽  
Evolutionary Pattern ◽  
Helix Loop Helix ◽  
Tissue Expression Analysis ◽  
Fruit Species ◽  
Rosaceae Species ◽  
Duplication Events

Abstract Background The bHLH (basic helix-loop-helix) transcription factor family plays important roles in regulating plant growth and development. However, informations about bHLH in rosaceous fruit species are still limited. Results In this study, a total of 198 PbbHLH genes were identified in the pear, with 188 bHLH genes in apple, 129 bHLH genes in peach, 112 in strawberry and 122 in Chinese plum. These Rosaceae bHLH genes, plus the 150 Arabidopsis thaliana bHLH genes, were divided into 34 groups, which included one Rosaceae-specific group. Evolutionary pattern analysis showed that whole-genome duplication (WGD) and segmental duplication played critical roles in expansion of the PbbHLH gene family. Ks value indicated that the two WGD duplication events (a recent WGD and an ancient WGD event) lead to the expansion of bHLH gene family. Tissue expression analysis shows that PbbHLHs may have diversity functions in different tissues. Furthermore, eight up-regulated and seven down-regulated PbbHLH genes were identified as the candidate genes in response to drought stress. Conclusion A comprehensive analysis of bHLH genes was performed in five Rosaceae species. The phylogenetic, evolution and expression analyses of the bHLH gene family in pear will be meaningful for investigating the biological roles of PbbHLH genes.

Structure, expression, chromosomal location and product of the gene encoding Adh2 in Petunia.

Genetics ◽  
1993 ◽  
Vol 133 (4) ◽  
pp. 999-1007
Author(s):  
R G Gregerson ◽  
L Cameron ◽  
M McLean ◽  
P Dennis ◽  
J Strommer
Keyword(s):  
Chromosomal Location ◽  
Higher Plants ◽  
Gene Encoding ◽  
Genomic Libraries ◽  
Regulatory Strategy ◽  
Adh1 Gene ◽  
Adh Genes ◽  
Genes Encoding ◽  
Adh Gene ◽  
Polymerase Chain

Abstract In most higher plants the genes encoding alcohol dehydrogenase comprise a small gene family, usually with two members. The Adh1 gene of Petunia has been cloned and analyzed, but a second identifiable gene was not recovered from any of three genomic libraries. We have therefore employed the polymerase chain reaction to obtain the major portion of a second Adh gene. From sequence, mapping and northern data we conclude this gene encodes ADH2, the major anaerobically inducible Adh gene of Petunia. The availability of both Adh1 and Adh2 from Petunia has permitted us to compare their structures and patterns of expression to those of the well-studied Adh genes of maize, of which one is highly expressed developmentally, while both are induced in response to hypoxia. Despite their evolutionary distance, evidenced by deduced amino acid sequence as well as taxonomic classification, the pairs of genes are regulated in strikingly similar ways in maize and Petunia. Our findings suggest a significant biological basis for the regulatory strategy employed by these distant species for differential expression of multiple Adh genes.

scholarly journals Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengwen Liu ◽  
Xingfen Wang ◽  
Zhengwen Sun ◽  
Yan Zhang ◽  
Chengsheng Meng ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Rapid Evolution ◽  
Gene Clusters ◽  
Vital Role ◽  
Fiber Development ◽  
Rna Seq ◽  
Evolutionarily Conserved ◽  
Cell Wall Development ◽  
Tandem Duplications

Abstract Background Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton. Results In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls. Conclusions These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.

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