Molecular Evolutionary Analysis of the HCRTR Gene Family in Vertebrates

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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Comparative genomic analysis of a mammalian β-defensin gene cluster

Physiological Genomics ◽

10.1152/physiolgenomics.00263.2006 ◽

2007 ◽

Vol 30 (3) ◽

pp. 213-222 ◽

Cited By ~ 12

Author(s):

Yashwanth Radhakrishnan ◽

Mario A. Fares ◽

Frank S. French ◽

Susan H. Hall

Keyword(s):

Positive Selection ◽

Gene Cluster ◽

Genomic Analysis ◽

Urogenital Tract ◽

Comparative Genomic ◽

Evolutionary Analysis ◽

Defensin Gene ◽

Duplication Events ◽

Molecular Evolutionary Analysis

Comparative genomic analyses have yielded valuable insights into conserved and divergent aspects of gene function, regulation, and evolution. Herein, we describe the characterization of a mouse β-defensin gene cluster locus on chromosome 2F6. In addition, we present the evolutionary analysis of this cluster and its human, rhesus, and rat orthologs. Expression analysis in mouse revealed the occurrence of defensin cluster transcripts in multiple tissues, with the highest abundance in the urogenital tract. Molecular evolutionary analysis suggests that this cluster originated by a series of duplication events, and by positive selection occurring even after the rodent-primate split. In addition, the constraints analysis showed higher positive selection in rodents than in primates, especially distal to the six-cysteine array. Positive selection in the evolution of these defensins may relate not only to the evolving enhancement of ancestral host defense but also to functional innovations in reproduction. The multiplicity of defensins and their preferential overexpression in the urogenital tract indicate that defensins function in the protection and maintenance of fertility.

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Importance of Gene Duplication in the Evolution of Genomic Imprinting Revealed by Molecular Evolutionary Analysis of the Type I MADS-Box Gene Family in Arabidopsis Species

PLoS ONE ◽

10.1371/journal.pone.0073588 ◽

2013 ◽

Vol 8 (9) ◽

pp. e73588 ◽

Cited By ~ 15

Author(s):

Takanori Yoshida ◽

Akira Kawabe

Keyword(s):

Gene Duplication ◽

Gene Family ◽

Genomic Imprinting ◽

Type I ◽

Evolutionary Analysis ◽

Mads Box ◽

Mads Box Gene ◽

Molecular Evolutionary Analysis ◽

Arabidopsis Species

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Molecular evolutionary analysis of the psbP gene family of the photosystem II oxygen-evolving complex in Nicotiana

Genome ◽

10.1139/g93-066 ◽

1993 ◽

Vol 36 (3) ◽

pp. 483-488 ◽

Cited By ~ 8

Author(s):

Shao-Bing Hua ◽

Shyam K. Dube ◽

Shain-dow Kung

Keyword(s):

Molecular Evolution ◽

Photosystem Ii ◽

Gene Family ◽

Oxygen Evolution ◽

Oxygen Evolving Complex ◽

Photosynthetic Oxygen Evolution ◽

Evolutionary Analysis ◽

Protein Patterns ◽

Oxygen Evolving ◽

Molecular Evolutionary Analysis

Photosystem II psbP protein of the oxygen-evolving complex is involved in the photosynthetic oxygen evolution in plants. Four psbP polypeptides were detected in Nicotiana tabacum on a two-dimensional gel by immunostaining the proteins with antiserum against the pea psbP Comparison of the protein patterns of psbP from N. tabacum and its ancestral parents, N. sylvestris and N. tomentosiformis, indicated that each of the ancestral parents has contributed a pair of psbP proteins. This was supported by Southern hybridization results, which suggested that psbP in Nicotiana is encoded by a gene family consisting of four members in N. tabacum and two members each in N. glauca, N. langsdorffii, N. sylvestris, and N. tomentosiformis. A scheme of molecular evolution of the psbP genes in Nicotiana is also proposed.Key words: molecular evolution, Nicotiana, oxygen evolution, photosystem II.

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Molecular evolutionary analysis of the duck MYOD gene family and its differential expression pattern in breast muscle development

British Poultry Science ◽

10.1080/00071668.2011.590795 ◽

2011 ◽

Vol 52 (4) ◽

pp. 423-431 ◽

Cited By ~ 2

Author(s):

He-he Liu ◽

Ji-wen Wang ◽

Liang Li ◽

Chun-chun Han ◽

Kai-liang Huang ◽

...

Keyword(s):

Gene Family ◽

Differential Expression ◽

Expression Pattern ◽

Muscle Development ◽

Breast Muscle ◽

Evolutionary Analysis ◽

Differential Expression Pattern ◽

Myod Gene ◽

Molecular Evolutionary Analysis

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Evolutionary analysis of the most polymorphic gene family in falciparum malaria

Wellcome Open Research ◽

10.12688/wellcomeopenres.15590.1 ◽

2019 ◽

Vol 4 ◽

pp. 193 ◽

Cited By ~ 12

Author(s):

Thomas D. Otto ◽

Sammy A. Assefa ◽

Ulrike Böhme ◽

Mandy J. Sanders ◽

Dominic Kwiatkowski ◽

...

Keyword(s):

Gene Family ◽

Immune Evasion ◽

Malaria Parasite ◽

Large Scale ◽

Evolutionary Analysis ◽

Selective Sweeps ◽

Human Malaria Parasite ◽

Worldwide Distribution ◽

The Family ◽

Polymorphic Gene

The var gene family of the human malaria parasite Plasmodium falciparum encode proteins that are crucial determinants of both pathogenesis and immune evasion and are highly polymorphic. Here we have assembled nearly complete var gene repertoires from 2398 field isolates and analysed a normalised set of 714 from across 12 countries. This therefore represents the first large scale attempt to catalogue the worldwide distribution of var gene sequences We confirm the extreme polymorphism of this gene family but also demonstrate an unexpected level of sequence sharing both within and between continents. We show that this is likely due to both the remnants of selective sweeps as well as a worrying degree of recent gene flow across continents with implications for the spread of drug resistance. We also address the evolution of the var repertoire with respect to the ancestral genes within the Laverania and show that diversity generated by recombination is concentrated in a number of hotspots. An analysis of the subdomain structure indicates that some existing definitions may need to be revised From the analysis of this data, we can now understand the way in which the family has evolved and how the diversity is continuously being generated. Finally, we demonstrate that because the genes are distributed across the genome, sequence sharing between genotypes acts as a useful population genetic marker.

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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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Septin genomics: a road less travelled

Biological Chemistry ◽

10.1515/bc.2011.079 ◽

2011 ◽

Vol 392 (8-9) ◽

pp. 763-767 ◽

Cited By ~ 26

Author(s):

S.E. Hilary Russell ◽

Peter A. Hall

Keyword(s):

Gene Family ◽

Common Ancestor ◽

Current Knowledge ◽

Detailed Understanding ◽

The Family ◽

Heterotypic Interactions ◽

Insight Into

Abstract The human septins are part of a gene family, that is a group of genes with similar sequences and usually but not invariably share similar functions that are descended from a common ancestor. Here we review our current knowledge of the human septin gene family and highlight areas of uncertainty. Currently 13 human septin genes are known (SEPT1 to SEPT12 and SEPT14). What was known as SEPT13 is now defined as one of many SEPT7 related pseudogenes. The family is characterized by complex genomics and extensive (but not universal) splicing, giving rise to a plethora of septin isoforms. For only a few members of the family do we have a comprehensive insight into these transcripts and isoforms. Given the formation of countless septin homotypic and heterotypic interactions our understanding of the biology and pathobiology of the septin family will require a detailed understanding of the genomics, transcriptomics and regulation of all members of this diverse and complex family.

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