scholarly journals Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples

2018 ◽  
Vol 19 (9) ◽  
pp. 2807 ◽  
Author(s):  
Baiquan Ma ◽  
Yangyang Yuan ◽  
Meng Gao ◽  
Tonghui Qi ◽  
Mingjun Li ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Gene Family ◽  
Functional Divergence ◽  
Aluminum Tolerance ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Gene Families ◽  
Biochemical Properties ◽  
Evolutionary Pattern

Aluminum-activated malate transporters (ALMTs) play an important role in aluminum tolerance, stomatal opening, and fruit acidity in plants. However, the evolutionary pattern of the ALMT gene family in apples remains relatively unknown. In this study, a total of 25 MdALMT genes were identified from the apple reference genome of the “Golden Delicious” doubled-haploid tree (GDDH13). The physiological and biochemical properties, gene structure, and conserved motifs of MdALMT genes were examined. Chromosome location and gene-duplication analysis indicated that whole-genome duplication/segmental duplication played an important role in the expansion of the MdALMT gene family. The Ka/Ks ratio of duplicated MdALMT genes showed that members of this family have undergone strong purifying selection. Through exploration of the phylogenetic relationships, seven subgroups were classified, and higher old gene duplication frequency and significantly different evolutionary rates of the ALMT gene families were detected. In addition, the functional divergence of ALMT genes occurred during the evolutionary process of Rosaceae species. Furthermore, the functional divergence of MdALMT genes was confirmed by expression discrepancy and different subcellular localizations. This study provides the foundation to better understand the molecular evolution of MdALMT genes and further facilitate functional analysis to unravel their exact role in apples.

scholarly journals Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence

2019 ◽  
Vol 20 (7) ◽  
pp. 1750 ◽  
Author(s):  
Ghulam Qanmber ◽  
Ji Liu ◽  
Daoqian Yu ◽  
Zhao Liu ◽  
Lili Lu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Plant Species ◽  
Functional Divergence ◽  
Rapid Evolution ◽  
Purifying Selection ◽  
Gene Families ◽  
Promoter Regions ◽  
Large Gene ◽  
Receptor Kinases

Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor kinases in plants. Receptor kinases comprise large gene families in many plant species, including the 15 PERK genes in Arabidopsis. At present, there is no comprehensive published study of PERK genes in G. hirsutum. Our study identified 33 PERK genes in G. hirsutum. Phylogenetic analysis of conserved PERK protein sequences from 15 plant species grouped them into four well defined clades. The GhPERK gene family is an evolutionarily advanced gene family that lost its introns over time. Several cis-elements were identified in the promoter regions of the GhPERK genes that are important in regulating growth, development, light responses and the response to several stresses. In addition, we found evidence for gene loss or addition through segmental or whole genome duplication in cotton. Gene duplication and synteny analysis identified 149 orthologous/paralogous gene pairs. Ka/Ks values show that most GhPERK genes experienced strong purifying selection during the rapid evolution of the gene family. GhPERK genes showed high expression levels in leaves and during ovule development. Furthermore, the expression of GhPERK genes can be regulated by abiotic stresses and phytohormone treatments. Additionally, PERK genes could be involved in several molecular, biological and physiological processes that might be the result of functional divergence.

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

2019 ◽  
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis Enrique Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Common Ancestry ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

scholarly journals Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes

2017 ◽  
Author(s):  
Daniel S. Carvalho ◽  
James C. Schnable ◽  
Ana Maria R. Almeida
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Gene Tree ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Phylogenetic Methods ◽  
Combined Use ◽  
Approaches To Study ◽  
Additional Support ◽  
Network Approaches

AbstractThe study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations of branches with low support in a conventional gene tree. The network approach used here may also better reflect known and suspected patterns of functional divergence relative to phylogenetic methods. Overall, we believe that the combined use of phylogenetic and network tools provide more robust assessments of gene family evolution.

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9861
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Marine Bacteria ◽  
Evolutionary History ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene ◽  
Enzymatic Adaptation

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

scholarly journals RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Nosheen Kabir ◽  
Xin Zhang ◽  
Le Liu ◽  
Ghulam Qanmber ◽  
Lian Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Selection Pressure ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Amino Acid Residues ◽  
Specific Expression ◽  
Protein Motifs ◽  
Response Data ◽  
Myb Gene ◽  
Family Analysis

Abstract Background RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. Results Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. Conclusions Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.

scholarly journals Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Tianyu Zhou ◽  
Xiping Yan ◽  
Guosong Wang ◽  
Hehe Liu ◽  
Xiang Gan ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Hormone Receptors ◽  
Expression Patterns ◽  
Family Members ◽  
Duplication Event ◽  
Promoter Regions ◽  
Evolutionary Pattern ◽  
Duplication Events ◽  
Differential Transcription

Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3′ UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3′ UTR are essential for PPARs evolution and diversity functions acquired.

Molecular evolution and functional divergence of HAK potassium transporter gene family in rice (Oryza sativa L.)

2009 ◽  
Vol 36 (3) ◽  
pp. 161-172 ◽  
Author(s):  
Zefeng Yang ◽  
Qingsong Gao ◽  
Changsen Sun ◽  
Wenjuan Li ◽  
Shiliang Gu ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Molecular Evolution ◽  
Gene Family ◽  
Oryza Sativa L ◽  
Functional Divergence ◽  
Transporter Gene ◽  
Potassium Transporter
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