Unraveling ancient segmental duplication events in human genome by phylogenetic analysis of multigene families residing on HOX-cluster paralogons

2010 ◽  
Vol 57 (2) ◽  
pp. 836-848 ◽  
Author(s):  
Amir Ali Abbasi
Keyword(s):  
Phylogenetic Analysis ◽  
Human Genome ◽  
Segmental Duplication ◽  
Multigene Families ◽  
Hox Cluster ◽  
Duplication Events

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
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.

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

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.

scholarly journals Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ruibin Wang ◽  
Jingfei Ma ◽  
Qian Zhang ◽  
Chunlai Wu ◽  
Hongyan Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Glutathione Transferase ◽  
Purifying Selection ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Qrt Pcr ◽  
Duplication Events

Abstract Background Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one of the most important crops, but the functions of GST genes in wheat were less studied. Results A total of 330 TaGST genes were identified from the wheat genome and named according to the nomenclature of rice and Arabidopsis GST genes. They were classified into eight classes based on the phylogenetic relationship among wheat, rice, and Arabidopsis, and their gene structure and conserved motif were similar in the same phylogenetic class. The 43 and 171 gene pairs were identified as tandem and segmental duplication genes respectively, and the Ka/Ks ratios of tandem and segmental duplication TaGST genes were less than 1 except segmental duplication gene pair TaGSTU24/TaGSTU154. The 59 TaGST genes were identified to have syntenic relationships with 28 OsGST genes. The expression profiling involved in 15 tissues and biotic and abiotic stresses suggested the different expression and response patterns of the TaGST genes. Furthermore, the qRT-PCR data showed that GST could response to abiotic stresses and hormones extensively in wheat. Conclusions In this study, a large GST family with 330 members was identified from the wheat genome. Duplication events containing tandem and segmental duplication contributed to the expansion of TaGST family, and duplication genes might undergo extensive purifying selection. The expression profiling and cis-elements in promoter region of 330 TaGST genes implied their roles in growth and development as well as adaption to stressful environments. The qRT-PCR data of 14 TaGST genes revealed that they could respond to different abiotic stresses and hormones, especially salt stress and abscisic acid. In conclusion, this study contributed to the further functional analysis of GST genes family in wheat.

The G-Protein-Coupled Receptors in the Human Genome Form Five Main Families. Phylogenetic Analysis, Paralogon Groups, and Fingerprints

2003 ◽  
Vol 63 (6) ◽  
pp. 1256-1272 ◽  
Author(s):  
Robert Fredriksson ◽  
Malin C. Lagerström ◽  
Lars-Gustav Lundin ◽  
Helgi B. Schiöth
Keyword(s):  
Phylogenetic Analysis ◽  
Human Genome ◽  
G Protein ◽  
G Protein Coupled Receptors ◽  
G Protein Coupled

Phylogenetic analysis and biogeography of Aegean taxa of the genus Dendarus (Coleoptera: Tenebrionidae)

2003 ◽  
Vol 34 (3) ◽  
pp. 295-312 ◽  
Author(s):  
◽  
◽  
◽  
Keyword(s):  
Phylogenetic Analysis ◽  
Strong Support ◽  
Component Analysis ◽  
Aegean Islands ◽  
Duplication Events ◽  
History Of ◽  
Tree Length ◽  
Species Groups ◽  
The Mediterranean Basin ◽  
Coleoptera Tenebrionidae

AbstractThe genus Dendarus Latr. is distributed throughout the Mediterranean basin with numerous species in the Aegean islands. This paper presents a phylogenetic analysis and the biogeography of most taxa present in the area. Phylogenetic analysis of two outgroup and 25 ingroup taxa based on adult morphology, including 50 characters and 119 character states, produced two equally parsimonious trees (tree length = 148, C.I. = 0.42, R.I. = 0.70, R.C. = 0.294). These trees provide strong support for the monophyly of Dendarus and also define four species groups: the foraminosus group, present mainly on the island of Crete; the rhodius group, present in Dodecanese islands, the sinuatus group present in the central Aegean islands, and another group consisting of taxa from mainland Greece (D. messenius, D. caelatus, D. tenellus, and D. plicatulus paganettii). All area cladograms produced by Compatibility Component Analysis, Brooks Parsimony Analysis, and especially by Component Analysis, correspond quite closely to the hypothesized palaeogeographic history of the studied area and therefore partly support the idea of a vicariant evolution of Dendarus taxa in this region. We distinguished certain monophyletic groups distributed (with some exceptions) within well-defined geographical and palaeogeographical regions of the Aegean. However, we found certain inconsistencies (with Reconciled Tree Analysis) that are probably the result of dispersal, extinction, or duplication events that are independent of the sequence of vicariance events.

scholarly journals Divergent Patterns of Recent Retroviral Integrations in the Human and Chimpanzee Genomes:Probable Transmissions between Other Primates and Chimpanzees

2006 ◽  
Vol 80 (3) ◽  
pp. 1367-1375 ◽  
Author(s):  
Patric Jern ◽  
Göran O. Sperber ◽  
Jonas Blomberg
Keyword(s):  
Phylogenetic Analysis ◽  
Human Genome ◽  
Pan Troglodytes ◽  
Horizontal Transfer ◽  
Genomic Sequence ◽  
Germ Line ◽  
Homo Sapiens ◽  
Endogenous Retrovirus ◽  
Chimpanzee Genome ◽  
Evolutionary Study

ABSTRACT The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. The sequencing of the human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes has facilitated the evolutionary study of ERVs and related sequences. We screened both the human genome (version hg16) and the chimpanzee genome (version PanTro1) for ERVs and conducted a phylogenetic analysis of recent integrations. We found a number of recent integrations within both genomes. They segregated into four groups. Two larger gammaretrovirus-like groups (PtG1 and PtG2) occurred in chimpanzees but not in humans. The PtG sequences were most similar to two baboon ERVs and a macaque sequence but neither to other chimpanzee ERVs nor to any human gammaretrovirus-like ERVs. The pattern was consistent with cross-species transfer via predation. This appears to be an example of horizontal transfer of retroviruses with occasional fixation in the germ line.

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