Evolutionary Dynamics in the Aphid Genome: Search for Genes Under Positive Selection and Detection of Gene Family Expansions

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

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Adaptive evolution of interferon induced protein with tetratricopeptide repeats 5(IFIT5) in birds

10.21203/rs.3.rs-119100/v1 ◽

2020 ◽

Author(s):

Bei Zhang ◽

Chuansheng Zhang ◽

Jie Meng ◽

Yifan Ren ◽

Jing Gong ◽

...

Keyword(s):

Positive Selection ◽

Gene Family ◽

Purifying Selection ◽

Functional Domain ◽

Immune Mechanism ◽

Tetratricopeptide Repeats ◽

Host Interaction ◽

Domestic Bird ◽

Episodic Selection ◽

Joint Influence

Abstract Background : Previous studies have revealed that wild birds are reservoirs and mobile vectors of viruses, many of which cause illness and mortality in domestic bird and humans. In birds, the invasion of viruses will quickly trigger the innate immune mechanism induced by interferon (IFN). As IFN-stimulated genes (ISGs), the IFIT gene family plays an important role in innate immunity. However, only IFIT5 of the IFIT gene family exists in birds, and the direction and strength of selection acting on IFIT5 are largely unknown. Results : Here, we studied the selection on IFIT5 based on the coding sequence (CDS) data of 20 birds. We identified 12 persistent positive selection sites (PSS), other sites suffered purifying selection and neutral selection; probably due to functional constraints. We also found humans have only 3PSS (189,197and 295), likely due to having more IFIT gene family member that can cooperate to resist virus invasion. The 12 PSS located in the closed clamp structure of the IFIT5 protein, except for position 45. In particular, 3 PSS (335, 342 and 367) were located in the TPR domain, which implied their important roles in virus recognition. We only found 2 episodic PSS (30,332) in Passeriformes, indicating episodic selection pressure in Passeriformes lineage. The positive selection of IFIT5 might provide a theoretical basis for the pathogen-host interaction in birds. Conclusions : We found that the diversity of IFIT5 domains in birds, and that the PSS of IFIT5 is the joint influence of functional domain conservation and the pressure of virus evolution.We speculated that persistent PSS may affect the antiviral function of IFIT5, especially in the region of closed clamp structure. These results lay a theoretical foundation for the further study of the antiviral immune mechanism of IFIT5 in birds.

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Recent duplication and positive selection of the GAGE gene family

Genetica ◽

10.1007/s10709-007-9179-9 ◽

2007 ◽

Vol 133 (1) ◽

pp. 31-35 ◽

Cited By ~ 10

Author(s):

Yang Liu ◽

Qiyun Zhu ◽

Naishuo Zhu

Keyword(s):

Positive Selection ◽

Gene Family ◽

Recent Duplication ◽

Selection Of

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Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution

BMC Evolutionary Biology ◽

10.1186/1471-2148-11-149 ◽

2011 ◽

Vol 11 (1) ◽

Cited By ~ 41

Author(s):

Yinhua Huang ◽

Nicholas D Temperley ◽

Liming Ren ◽

Jacqueline Smith ◽

Ning Li ◽

...

Keyword(s):

Molecular Evolution ◽

Gene Duplication ◽

Positive Selection ◽

Gene Family ◽

Gene Conversion ◽

History Of

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Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

BMC Genomics ◽

10.1186/s12864-020-07226-1 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Manyi Sun ◽

Mingyue Zhang ◽

Jugpreet Singh ◽

Bobo Song ◽

Zikai Tang ◽

...

Keyword(s):

Genetic Variation ◽

Disease Resistance ◽

Positive Selection ◽

Gene Family ◽

Selection Pressure ◽

Black Spot ◽

Orthologous Gene ◽

European Pear ◽

Encoding Gene ◽

Encoding Genes

Abstract Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. Results In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. Conclusion Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

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Evolutionary Dynamics of the DM Domain Gene Family in Metazoans

Journal of Molecular Evolution ◽

10.1007/s00239-003-0033-0 ◽

2003 ◽

Vol 57 (0) ◽

pp. S241-S249 ◽

Cited By ~ 80

Author(s):

Jean-Nicolas Volff ◽

David Zarkower ◽

Vivian J. Bardwell ◽

Manfred Schartl

Keyword(s):

Gene Family ◽

Evolutionary Dynamics ◽

Dm Domain

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