Comparative and Evolutionary Analysis of the HES/HEY Gene Family Reveal Exon/Intron Loss and Teleost Specific Duplication Events

Hypocretin system is composed of hypocretins (hcrts) and their receptors (hcrtrs), which has multiple vital functions. Hypocretins work via hypocretin receptors and it is reported that functional differentiation occurred in hcrtrs. It is necessary to figure out the evolution process of hypocretin receptors. In our study, we adopt a comprehensive approach and various bioinformatics tools to analyse the evolution process of HCRTR gene family. It turns out that the second round of whole genome duplication in early vertebrate ancestry and the independent round in fish ancestry may contribute to the diversity of HCRTR gene family. HCRTR1 of fishes and mammals are not the same receptor, which means that there are three members in the family. HCRTR2 is proved to be the most ancient one in HCRTR gene family. After duplication events, the structure of HCRTR1 diverged from HCRTR2 owing to relaxed selective pressure. Negative selection is the predominant evolutionary force acting on the HCRTR gene family but HCRTR1 of mammals is found to be subjected to positive selection. Our study gains insight into the molecular evolution process of HCRTR gene family, which contributes to the further study of the system.

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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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Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Plants ◽

10.3390/plants8020030 ◽

2019 ◽

Vol 8 (2) ◽

pp. 30 ◽

Cited By ~ 14

Author(s):

Weilong Kong ◽

Hua Zhong ◽

Xiaoxiao Deng ◽

Mayank Gautam ◽

Ziyun Gong ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Salinity Stress ◽

Common Ancestor ◽

Oryza Rufipogon ◽

Oryza Species ◽

Evolutionary Analysis ◽

Wild Rice Species ◽

Oryza Punctata ◽

Duplication Events

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

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Genome-Wide Characterization of the Nuclear Receptor Gene Family in Macrostomum lignano Imply Its Evolutionary Diversification

Frontiers in Marine Science ◽

10.3389/fmars.2021.653447 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yunying Cheng ◽

Jinlin Chen ◽

Irum Mukhtar ◽

Jianming Chen

Keyword(s):

Gene Family ◽

Adaptive Evolution ◽

Phylogenetic Analyses ◽

Receptor Gene ◽

Clonorchis Sinensis ◽

Purifying Selection ◽

Intron Loss ◽

Evolutionary Diversification ◽

Macrostomum Lignano ◽

Duplication Events

Nuclear receptors (NRs), a series of key transcription factors that are mostly activated by endogenous ligands or environmental xenobiotics, are reportedly good phylogenetic markers of animal genome evolution. As the early diverging class of bilaterians, however, a comprehensive view of the NR family in a marine free-living flatworm Macrostomum lignano and comparative information in flatworms are still lacking, which is of significance to address the evolutionary diversification of the NR family and imply the adaptive evolution in the early diverging Bilateria. Herein, a total of 51, 26, and 23 putative NR genes were identified in M. lignano, Sparganum proliferum, and Clonorchis sinensis, respectively, which were classified into eight subfamilies, implying an extensive expansion of the NR family in M. lignano. It is presumed that the extensive expansion was mainly attributed to the M. lignano-specific hidden polyploidy, segmental, and tandem duplication events. The duplicated NR pairs in M. lignano and the NR orthologs in flatworms all experienced the purifying selection. Phylogenetic analyses indicated the presence of NR3-like genes in M. lignano, which is first reported in flatworms. Intron loss and reduced intron size were mainly contributed to the structural divergence of NR genes in flatworms. The combined data provide indispensable information for a better understanding of the complexity and the adaptive evolution of the NR gene family in metazoans.

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Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽

10.3390/genes12081190 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1190

Author(s):

Yuqi Huang ◽

Minghao Sun ◽

Lenan Zhuang ◽

Jin He

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Functional Characterization ◽

Vertebrate Evolution ◽

Molecular Phylogenetic Analysis ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Molecular Phylogenetic ◽

Duplication Events ◽

Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

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Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

Journal of Cotton Research ◽

10.1186/s42397-021-00079-3 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Lingling DOU ◽

Limin LV ◽

Yangyang KANG ◽

Ruijie TIAN ◽

Deqing HUANG ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Gene Family ◽

Segmental Duplication ◽

Gene Expression Pattern ◽

Cell Development ◽

Fiber Cell ◽

Fiber Cells ◽

Genome Wide ◽

Duplication Events ◽

Signaling Receptors

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

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Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

Horticultural Plant Journal ◽

10.1016/j.hpj.2020.07.007 ◽

2021 ◽

Author(s):

Yongxian Tian ◽

Qigang Wang ◽

Hao Zhang ◽

Ningning Zhou ◽

Huijun Yan ◽

...

Keyword(s):

Gene Family ◽

Evolutionary Analysis ◽

Genome Wide ◽

Mlo Gene Family

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Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

International Journal of Molecular Sciences ◽

10.3390/ijms20225796 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5796

Author(s):

Qianqian Zhou ◽

Qingchang Li ◽

Peng Li ◽

Songtao Zhang ◽

Che Liu ◽

...

Keyword(s):

Gene Family ◽

Physiological Stress ◽

Expression Patterns ◽

Functional Characterization ◽

Hormone Treatment ◽

Nicotiana Sylvestris ◽

Regulatory Elements ◽

Evolutionary Analysis ◽

Comprehensive Overview ◽

Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

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Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

International Journal of Molecular Sciences ◽

10.3390/ijms23020614 ◽

2022 ◽

Vol 23 (2) ◽

pp. 614

Author(s):

Weiqi Sun ◽

Mengdi Li ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Gene Structure ◽

Stress Responses ◽

Stress Protein ◽

Purifying Selection ◽

Cis Acting ◽

Genome Wide ◽

Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.707708 ◽

2021 ◽

Vol 9 ◽

Author(s):

Abdullah ◽

Sahar Faraji ◽

Parviz Heidari ◽

Péter Poczai

Keyword(s):

Gene Family ◽

Theobroma Cacao ◽

Critical Role ◽

Divergence Time ◽

Purifying Selection ◽

Plant Metabolites ◽

Corchorus Capsularis ◽

Cell Stability ◽

Duplication Events ◽

And Function

The benzyl alcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase, and deacetylvindoline 4-O-acetyltransferase (BAHD) enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, members of the BAHD gene family were recognized in the genome of Theobroma cacao and characterized using various bioinformatics tools. We found 27 non-redundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. When analyzed with BAHDs of Gossypium raimondii and Corchorus capsularis clustered into four main groups. According to phylogenetic analysis, BAHD genes probably evolved drastically after their divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 to 15.50 MYA. Pocket analysis revealed that serine amino acid is more common in the binding site than other residuals, reflecting its key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to the responsiveness of stress and hormone, particularly ABA and MeJA, were frequently observed in the promoter region of tcBAHD genes. RNA-seq analysis further illustrated that tcBAHD13 and tcBAHD26 are involved in response to Phytophthora megakarya fungi. In conclusion, it is likely that evolutionary processes, such as duplication events, have caused high diversity in the structure and function of tcBAHD genes.

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