scholarly journals Repeated Evolution of Testis-Specific New Genes: The Case of Telomere-Capping Genes in Drosophila

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Raphaëlle Dubruille ◽  
Gabriel A. B. Marais ◽  
Benjamin Loppin
Keyword(s):  
Gene Family ◽  
Specific Expression ◽  
Functional Studies ◽  
Evolutionary Forces ◽  
New Genes ◽  
Male Gametes ◽  
Duplication Events ◽  
New Gene ◽  
Telomere Capping ◽  
Specific Expression Pattern

Comparative genome analysis has allowed the identification of various mechanisms involved in gene birth. However, understanding the evolutionary forces driving new gene origination still represents a major challenge. In particular, an intriguing and not yet fully understood trend has emerged from the study of new genes: many of them show a testis-specific expression pattern, which has remained poorly understood. Here we review the case of such a new gene, which involves a telomere-capping gene family in Drosophila. hiphop and its testis-specific paralog K81 are critical for the protection of chromosome ends in somatic cells and male gametes, respectively. Two independent functional studies recently proposed that these genes evolved under a reproductive-subfunctionalization regime. The 2011 release of new Drosophila genome sequences from the melanogaster group of species allowed us to deepen our phylogenetic analysis of the hiphop/K81 family. This work reveals an unsuspected dynamic of gene birth and death within the group, with recurrent duplication events through retroposition mechanisms. Finally, we discuss the plausibility of different evolutionary scenarios that could explain the diversification of this gene family.

The members of Arabidopsis thaliana PAO gene family exhibit distinct tissue- and organ-specific expression pattern during seedling growth and flower development

Amino Acids ◽  
2011 ◽  
Vol 42 (2-3) ◽  
pp. 831-841 ◽  
Author(s):  
Paola Fincato ◽  
Panagiotis N. Moschou ◽  
Abdellah Ahou ◽  
Riccardo Angelini ◽  
Kalliopi A. Roubelakis-Angelakis ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Expression Pattern ◽  
Seedling Growth ◽  
Flower Development ◽  
Specific Expression ◽  
Organ Specific ◽  
Organ Specific Expression ◽  
Specific Expression Pattern

scholarly journals Genome-Wide Analysis of Oligopeptide Transporters Gene Family in Medicago truncatula

2016 ◽  
Author(s):  
Renze Liu ◽  
Hongyu Shan ◽  
Yongjun Shu ◽  
Changhong Guo ◽  
Donglin Guo
Keyword(s):  
Gene Family ◽  
Medicago Truncatula ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Peptide Transport ◽  
Limited Information ◽  
Specific Expression ◽  
Specific Expression Pattern ◽  
Yellow Stripe

Oligopeptide transporters (OPTs) are a group of membrane localized proteins that have a broad range of substrate transport capabilities and contribute to numerous biological processes. However, limited information has been reported on OPTs in higher plants. In this study, a comprehensive analysis of the OPT gene family in Medicago truncatula was performed. A total of 26 OPT genes (MtOPT01-MtOPT26) have been identified in the Medicago truncatula genome. Phylogenetic analyses indicated that MtOPTs consisted of two distinct subgroups, 12 MtOPTs belonged to the peptide transport subgroup (PT-OPT) based on their predicted amino acid sequences containing the two highly conserved motifs (NPG and KIPPR) and 14 MtOPTs belonged to yellow stripe subgroup (YS-OPT). The MtOPTs distributed on each of 8 chromosomes in Medicago truncatula. Sequence analysis verified that MtOPTs significant similar to those in other plants. The copy number of MtOPTs was low and the multiply of MtOPTs was simple relatively. Gene structure analysis showed that most of the MtOPTs have various numbers of introns. The multiple of MtOPTs might play different biological roles which were supported by the fact that MtOPTs have a distinct tissue-specific expression pattern. The data obtained in this study will help to better understand the complexity of the MtOPTs gene family and provide new evidence for the function and evolution of the OPT gene family in higher plants.

scholarly journals On the Origin and Evolution of Drosophila New Genes during Spermatogenesis

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1796
Author(s):  
Qianwei Su ◽  
Huangyi He ◽  
Qi Zhou
Keyword(s):  
X Chromosome ◽  
Sex Chromosome ◽  
Expression Patterns ◽  
Cell Level ◽  
Origin And Evolution ◽  
Functional Studies ◽  
New Genes ◽  
Meiotic Sex Chromosome Inactivation ◽  
New Gene ◽  
Cell Transcriptome

The origin of functional new genes is a basic biological process that has significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testes and avoid the X chromosome, presumably because of meiotic sex chromosome inactivation (MSCI). Here, we analyze the published single-cell transcriptome data of Drosophila adult testis and find an enrichment of male germline mitotic genes, but an underrepresentation of meiotic genes on the X chromosome. This can be attributed to an excess of autosomal meiotic genes that were derived from their X-linked mitotic progenitors, which provides direct cell-level evidence for MSCI in Drosophila. We reveal that new genes, particularly those produced by retrotransposition, tend to exhibit an expression shift toward late spermatogenesis compared with their parental copies, probably due to the more intensive sperm competition or sexual conflict. Our results dissect the complex factors including age, the origination mechanisms and the chromosomal locations that influence the new gene origination and evolution in testes, and identify new gene cases that show divergent cell-level expression patterns from their progenitors for future functional studies.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals Genome-Wide Identification and Characterization of the Cyclophilin Gene Family in the Nematophagous Fungus Purpureocillium lilacinum

2019 ◽  
Vol 20 (12) ◽  
pp. 2978 ◽  
Author(s):  
Chenmi Mo ◽  
Chong Xie ◽  
Gaofeng Wang ◽  
Juan Liu ◽  
Qiuyan Hao ◽  
...  
Keyword(s):  
High Temperature ◽  
Gene Family ◽  
Gene Structure ◽  
Molecular Mechanisms ◽  
Nematophagous Fungus ◽  
Parasitic Nematodes ◽  
Whole Genome Analysis ◽  
Specific Expression ◽  
Purpureocillium Lilacinum ◽  
Specific Expression Pattern

Purpureocillium lilacinum has been widely used as a commercial biocontrol agent for the control of plant parasitic nematodes. Whole genome analysis promotes the identification of functional genes and the exploration of their molecular mechanisms. The Cyclophilin (CYP) gene family belongs to the immunophillin superfamily, and has a conserved cyclophilin-like domain (CLD). CYPs are widely identified in prokaryotes and eukaryotes, and can be divided into single- and multi-domain proteins. In the present study, 10 CYP genes possessing the CLD, named PlCYP1–P10, were identified from the genome of P. lilacinum strain 36-1. Those 10 PlCYPs were predicted to have different cellular localizations in P. lilacinum. Phylogenetic and gene structure analysis revealed the evolutionary differentiation of CYPs between Ascomycotina and Saccharomycotina fungi, but conservation within the Ascomycotina fungi. Motif and gene structure distributions further support the result of phylogenetic analysis. Each PlCYP gene had a specific expression pattern in different development stages of P. lilacinum and its parasitism stage on eggs of Meloidogyne incognita. In addition, the 10 PlCYP genes exhibited different expression abundances in response to abiotic stresses, among which PlCYP4 was highly expressed at a high temperature (35 °C), while PlCYP6 was up-regulated under 5 mM of H2O2 stress. Furthermore, the heterologous expression of PlCYP4 and PlCYP6 in Escherichia coli enhanced the cellular tolerance against a high temperature and H2O2. In summary, our study indicates the potential functions of PlCYPs in virulence and the stress response, and also provides a frame for further analysis of the CYP gene family in Ascomycotina fungi.

scholarly journals Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus

2022 ◽  
Vol 12 ◽  
Author(s):  
Rehman Sarwar ◽  
Rui Geng ◽  
Lei Li ◽  
Yue Shan ◽  
Ke-Ming Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Future Research ◽  
Plant Tolerance ◽  
Specific Expression ◽  
Biotic Stresses ◽  
Organ Specific ◽  
Duplication Events

BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.

scholarly journals Apolipoprotein L gene family: tissue-specific expression, splicing, promoter regions; discovery of a new gene

2001 ◽  
Vol 42 (4) ◽  
pp. 620-630
Author(s):  
Philippe N. Duchateau ◽  
Clive R. Pullinger ◽  
Min H. Cho ◽  
Celeste Eng ◽  
John P. Kane
Keyword(s):  
Gene Family ◽  
Promoter Regions ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
New Gene

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

Agronomy ◽  
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.

scholarly journals Genome-Wide Analysis of the PIN Auxin Efflux Carrier Gene Family in Coffee

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1061
Author(s):  
Xing Huang ◽  
Xuehui Bai ◽  
Tieying Guo ◽  
Zhouli Xie ◽  
Margit Laimer ◽  
...  
Keyword(s):  
Gene Family ◽  
Rust Fungus ◽  
Functional Characterization ◽  
Specific Expression ◽  
Fractionation Process ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Pin Genes ◽  
Specific Expression Pattern

Coffee is one of the most popular beverages around the world, which is mainly produced from the allopolyploid Coffea arabica. The genomes of C. arabica and its two ancestors C. canephora and C. eugenioides have been released due to the development of next generation sequencing. However, few studies on C. arabica are related to the PIN-FORMED (PIN) auxin efflux transporter despite its importance in auxin-mediated plant growth and development. In the present study, we conducted a genome-wide analysis of the PIN gene family in the three coffee species. Totals of 17, 9 and 10 of the PIN members were characterized in C. Arabica, C. canephora and C. eugenioides, respectively. Phylogenetic analysis revealed gene loss of PIN1 and PIN2 homologs in C. arabica, as well as gene duplication of PIN5 homologs during the fractionation process after tetraploidy. Furthermore, we conducted expression analysis of PIN genes in C. arabica by in silico and qRT-PCR. The results revealed the existence of gene expression dominance in allopolyploid coffee and illustrated several PIN candidates in regulating auxin transport and homeostasis under leaf rust fungus inoculation and the tissue-specific expression pattern of C. arabica. Together, this study provides the basis and guideline for future functional characterization of the PIN gene family.

scholarly journals On the origin and evolution of Drosophila new genes during spermatogenesis

2021 ◽  
Author(s):  
Qianwei Su ◽  
Huangyi He ◽  
Qi Zhou
Keyword(s):  
X Chromosome ◽  
Sex Chromosome ◽  
Origin And Evolution ◽  
Functional Studies ◽  
New Genes ◽  
Male Germline ◽  
New Gene ◽  
Direct Cell ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Origin of functional new genes is a basic biological process that has a significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testis, and avoid the X chromosome presumably because meitoic sex chromosome inactivation (MSCI). Here we analyse the published single-cell transcriptome data of Drosophila adult testis and find an enrichment of male germline mitotic genes, but an underrepresentation of meiotic genes on the X chromosome. This can be attributed to an excess of autosomal meiotic genes that were derived from their X-linked mitotic progenitors, which provides direct cell-level evidence for MSCI in Drosophila. We reveal that new genes, particularly those produced by retrotransposition, tend to exhibit an expression shift toward late spermatogenesis compared to their parental copies, probably due to more intensive sperm competition or sexual conflict. Our results dissect the complex factors including the age, the origination mechanisms and the chromosomal locations that influence the new gene origination and evolution in testis, and identify new gene cases that show divergent expression pattern from their progenitors for future functional studies.

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