Molecular evolution of the plant R regulatory gene family.

Abstract Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-terminal and C-terminal domains; mean replacement rates for these conserved regions are 1.02 x 10(-9) nonsynonymous nucleotide substitutions per site per year. More than one-half of the protein, however, is diverging rapidly, with nonsynonymous substitution rates of 4.08 x 10(-9) substitutions per site per year. Detailed analysis of R homologs within the grasses (Poaceae) confirm that these variable regions are indeed evolving faster than the flanking conserved domains. Both nucleotide substitutions and small insertion/deletions contribute to the diversification of the variable regions within these regulatory genes. These results demonstrate that large tracts of sequence in these regulatory loci are evolving at a fairly rapid rate.

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Isolation and Characterization Of Rice R Genes: Evidence for Distinct Evolutionary Paths in Rice and Maize

Genetics ◽

10.1093/genetics/142.3.1021 ◽

1996 ◽

Vol 142 (3) ◽

pp. 1021-1031 ◽

Cited By ~ 3

Author(s):

Jianping Hu ◽

Beth Anderson ◽

Susan R Wessler

Keyword(s):

Gene Family ◽

Gene Families ◽

Chromosome 1 ◽

R Gene ◽

R Genes ◽

Helix Loop Helix ◽

Isolation And Characterization ◽

Undetermined Function ◽

Evolutionary Paths

Abstract R and B genes and their homologues encode basic helix-loop-helix (bHLH) transcriptional activators that regulate the anthocyanin biosynthetic pathway in flowering plants. In maize, R/B genes comprise a very small gene family whose organization reflects the unique evolutionary history and genome architecture of maize. To know whether the organization of the R gene family could provide information about the origins of the distantly related grass rice, we characterized members of the R gene family from rice Oryza sativa. Despite being a true diploid, O. sativa has at least two R genes. An active homologue (Ra) with extensive homology with other R genes is located at a position on chromosome 4 previously shown to be in synteny with regions of maize chromosomes 2 and 10 that contain the B and R loci, respectively. A second rice R gene (Rb) of undetermined function was identified on chromosome 1 and found to be present only in rice species with AA genomes. All non-AA species have but one R gene that is Ra-like. These data suggest that the common ancestor shared by maize and rice had a single R gene and that the small R gene families of grasses have arisen recently and independently.

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Ancient Diversification of the Pto Kinase Family Preceded Speciation in Solanum

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2001.14.8.996 ◽

2001 ◽

Vol 14 (8) ◽

pp. 996-1005 ◽

Cited By ~ 17

Author(s):

Vivianne G. A. A. Vleeshouwers ◽

Adrie Martens ◽

Willem van Dooijeweert ◽

Leontine T. Colon ◽

Francine Govers ◽

...

Keyword(s):

Gene Family ◽

Plant Disease Resistance ◽

Phylogenetic Analyses ◽

Leaf Tissue ◽

Solanum Species ◽

R Genes ◽

Variable Regions ◽

Kinase Activation ◽

Nucleotide Binding Sites ◽

Duplication Events

Recent phylogenetic analyses of the nucleotide binding sites (NBS)-leucine-rich repeats (LRR) class of plant disease resistance (R) genes suggest that these genes are ancient and coexist next to susceptibility alleles at resistance loci. Another class of R genes encodes serine-threonine protein kinases related to Pto that were originally identified from wild relatives of tomato. In this study, we exploit the highly diverse genus Solanum to identify Pto-like sequences and test various evolutionary scenarios for Pto-like genes. Polymerase chain reaction amplifications with the use of primers that were developed on the basis of conserved and variable regions of Pto revealed an extensive Pto gene family and yielded 32 intact Pto-like sequences from six Solanum species. Furthermore, Pto-like transcripts were detected in the leaf tissue of all tested plants. The kinase consensus and autophosphorylation sites were highly conserved, in contrast to the kinase activation domain, which is involved in ligand recognition in Pto. Phylogenetic analyses distinguished nine classes of Pto-like genes and revealed that orthologs were more similar than paralogs, suggesting that the Pto gene family evolved through a series of ancient gene duplication events prior to speciation in Solanum. Thus, like the NBS-LRR class, the kinase class of R genes is highly diverse and ancient.

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The 18S rRNA from Odontophrynus americanus 2n and 4n (Amphibia, Anura) reveals unusual extra sequences in the variable region V2

Genome ◽

10.1139/g03-145 ◽

2004 ◽

Vol 47 (3) ◽

pp. 421-428 ◽

Cited By ~ 1

Author(s):

Lúcia E Alvares ◽

Jan Wuyts ◽

Yves Van de Peer ◽

Eduardo P Silva ◽

Luiz L Coutinho ◽

...

Keyword(s):

Molecular Evolution ◽

Secondary Structure ◽

Nucleotide Sequence ◽

Xenopus Laevis ◽

Ribosomal Dna ◽

18S Rrna ◽

Variable Region ◽

Tetraploid Species ◽

Nucleotide Substitutions ◽

Variable Regions

The nucleotide sequence of the rDNA 18S region isolated from diploid and tetraploid species of the amphibian Odontophrynus americanus was determined and used to predict the secondary structure of the corresponding 18S rRNA molecules. Comparison of the primary and secondary structures for the 2n and 4n species confirmed that these species are very closely related. Only three nucleotide substitutions were observed, accounting for 99% identity between the 18S sequences, whereas several changes were detected by comparison with the Xenopus laevis 18S sequence (96% identity). Most changes were located in highly variable regions of the molecule. A noticeable feature of the Odontophrynus 18S rRNA was the presence of unusual extra sequences in the V2 region, between helices 9 and 11. These extra sequences do not fit the model for secondary structure predicted for vertebrate 18S rRNA.Key words: Odontophrynus americanus, Amphibia, polyploidy, 18S ribosomal DNA, molecular evolution.

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Molecular evolution of GDP-L-galactose phosphorylase (GGP), a key regulatory gene in plant ascorbate biosynthesis

10.21203/rs.2.16500/v1 ◽

2019 ◽

Author(s):

Junjie Tao ◽

Zhuan Hao ◽

Chunhui Huang

Keyword(s):

Molecular Evolution ◽

Plant Species ◽

Regulatory Gene ◽

Purifying Selection ◽

Plant Evolution ◽

Rapid Expansion ◽

Evolutionary Patterns ◽

Site Model ◽

Early Stages ◽

Evolutionary Innovation

Abstract Background Ascorbic acid (AsA) is a multi-functional molecule and plays essential roles in maintaining the normal life activities of living organisms. Although widely present in plants, the concentration of AsA varies greatly in different plant species. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood in previous works. However, the molecular evolutionary patterns of the gene remain unclear.Results In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, including angiosperms, gymnosperms, lycophytes, bryophytes and chlorophytes, and their phylogenetic relationships, gene duplication and molecular evolution analyses were investigated. Phylogenetic analysis showed that GGP exists widely in various plants, and five major duplication events and several taxon-specific duplications were found, which led to the rapid expansion of GGP genes in seed plants, especially in angiosperms. The structure of GGP genes were more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins have a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that plant GGP genes was predominated by strong purifying selection, indicating the functional importance and conservativeness of plant GGP genes during evolution. Most of the branches under positive selection identified by branch-site model were mainly in the chlorophytes lineage, indicating the evolutionary innovation of GGP genes also mainly occurred in the early stages of plant evolution and episodic diversifying selection contributed to the evolution of plant GGP genes.Conclusions The molecular evolutionary patterns of GGP were first systematically explored in this study. The conservative function of GGP and its rapid expansion in angiosperms may be one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.

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Genome-wide identification, molecular evolution, and expression divergence of the hexokinase gene family in apple

Journal of Integrative Agriculture ◽

10.1016/s2095-3119(20)63562-6 ◽

2021 ◽

Vol 20 (8) ◽

pp. 2112-2125

Author(s):

Ling-cheng ZHU ◽

Jing SU ◽

Yu-ru JIN ◽

Hai-yan ZHAO ◽

Xiao-cheng TIAN ◽

...

Keyword(s):

Molecular Evolution ◽

Gene Family ◽

Expression Divergence ◽

Genome Wide

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Molecular Evolution of the CPP-like Gene Family in Plants: Insights from Comparative Genomics of Arabidopsis and Rice

Journal of Molecular Evolution ◽

10.1007/s00239-008-9143-z ◽

2008 ◽

Vol 67 (3) ◽

pp. 266-277 ◽

Cited By ~ 52

Author(s):

Zefeng Yang ◽

Shiliang Gu ◽

Xuefeng Wang ◽

Wenjuan Li ◽

Zaixiang Tang ◽

...

Keyword(s):

Molecular Evolution ◽

Comparative Genomics ◽

Gene Family

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Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus

Genome ◽

10.1139/g04-026 ◽

2004 ◽

Vol 47 (4) ◽

pp. 732-741 ◽

Cited By ~ 2

Author(s):

Wolfgang Staiber

Keyword(s):

Molecular Evolution ◽

Dna Sequences ◽

Sequence Data ◽

Structural Evolution ◽

5S Rdna ◽

Oligonucleotide Primer ◽

Homologous Gene ◽

Gene Sequences ◽

Nucleotide Substitutions ◽

Degenerate Oligonucleotide

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.

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