An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes

F-box genes play an important role in the growth and development of plants, but there are few studies on its role in a plant’s response to abiotic stresses. In order to further study the functions of F-box genes in tomato (Solanum lycopersicum, Sl), a total of 139 F-box genes were identified in the whole genome of tomato using bioinformatics methods, and the basic information, transcript structure, conserved motif, cis-elements, chromosomal location, gene evolution, phylogenetic relationship, expression patterns and the expression under cold stress, drought stress, jasmonic acid (JA) treatment and salicylic acid (SA) treatment were analyzed. The results showed that SlFBX genes were distributed on 12 chromosomes of tomato and were prone to TD (tandem duplication) at the ends of chromosomes. WGD (whole genome duplication), TD, PD (proximal duplication) and TRD (transposed duplication) modes seem play an important role in the expansion and evolution of tomato SlFBX genes. The most recent divergence occurred 1.3042 million years ago, between SlFBX89 and SlFBX103. The cis-elements in SlFBX genes’ promoter regions were mainly responded to phytohormone and abiotic stress. Expression analysis based on transcriptome data and qRT-PCR (Real-time quantitative PCR) analysis of SlFBX genes showed that most SlFBX genes were differentially expressed under abiotic stress. SlFBX24 was significantly up-regulated at 12 h under cold stress. This study reported the SlFBX gene family of tomato for the first time, providing a theoretical basis for the detailed study of SlFBX genes in the future, especially the function of SlFBX genes under abiotic stress.

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Genome-Wide Identification and Evolutionary Analysis of AOMT Gene Family in Pomegranate (Punica granatum)

Agronomy ◽

10.3390/agronomy11020318 ◽

2021 ◽

Vol 11 (2) ◽

pp. 318

Author(s):

Xinhui Zhang ◽

Weicheng Yuan ◽

Yujie Zhao ◽

Yuan Ren ◽

Xueqing Zhao ◽

...

Keyword(s):

Gene Family ◽

Gene Evolution ◽

Punica Granatum ◽

Gene Family Evolution ◽

Raw Material ◽

Whole Genome ◽

Evolutionary Analysis ◽

New Genes ◽

Genome Wide ◽

Duplication Events

Gene duplication is the major resource with which to generate new genes, which provide raw material for novel functions evolution. Thus, to elucidate the gene family evolution after duplication events is of vital importance. Anthocyanin O-methyltransferases (AOMTs) have been recognized as being capable of anthocyanin methylation, which increases anthocyanin diversity and stability and improves the protection of plants from environmental stress. Meanwhile, no detailed identification or genome-wide analysis of the AOMT gene family members in pomegranate (Punicagranatum) have been reported. Three published pomegranate genome sequences offer substantial resources with which to explore gene evolution based on the whole genome. Altogether, 58 identified OMTs from pomegranate and five other species were divided into the AOMT group and the OMT group, according to their phylogenetic tree and AOMTs derived from OMTs. AOMTs in the same subclade have a similar gene structure and protein conserved motifs. The PgAOMT family evolved and expanded primarily via whole-genome duplication (WGD) and tandem duplication. PgAOMTs expression pattern in peel and aril development by qRT-PCR verification indicated that PgAOMTs had tissue-specific patterns. The main fates of AOMTs were neo- or non-functionalization after duplication events. High expression genes of PgOMT04 and PgOMT09 were speculated to contribute to “Taishanhong” pomegranate’s bright red peel color. Finally, we integrated the above analysis in order to infer the evolutionary scenario of AOMT family.

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

10.21203/rs.2.16577/v1 ◽

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.

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

Frontiers in Genetics ◽

10.3389/fgene.2021.792250 ◽

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.

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Killer meiotic drive and dynamic evolution of the wtf gene family

10.1101/461004 ◽

2018 ◽

Author(s):

Michael T. Eickbush ◽

Janet M. Young ◽

Sarah E. Zanders

Keyword(s):

Gene Family ◽

Copy Number ◽

Gene Evolution ◽

Rapid Evolution ◽

Meiotic Drive ◽

Recombination Mechanism ◽

Evolutionary Force ◽

Drive Systems ◽

Dna Sequence Repeats ◽

Diploid Organism

AbstractNatural selection works best when the two alleles in a diploid organism are transmitted to offspring at equal frequencies. Despite this, selfish loci known as meiotic drivers that bias their own transmission into gametes are found throughout eukaryotes. Drive is thought to be a powerful evolutionary force, but empirical evolutionary analyses of drive systems are limited by low numbers of identified meiotic drive genes. Here, we analyze the evolution of the wtf gene family of Schizosaccharomyces pombe that contains both killer meiotic drive genes and suppressors of drive. We completed assemblies of all wtf genes for two S. pombe strains, as well as a subset of wtf genes from over 50 strains. We find that wtf copy number can vary greatly between strains, and that amino acid substitutions, expansions and contractions of DNA sequence repeats, and nonallelic gene conversion between family members all contribute to dynamic wtf gene evolution. This work demonstrates the power of meiotic drive to foster rapid evolution and identifies a recombination mechanism through which transposons can indirectly mobilize meiotic drivers.

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Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1417803112 ◽

2014 ◽

Vol 112 (5) ◽

pp. 1493-1498 ◽

Cited By ~ 83

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.

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