Molecular evolution of the chalcone synthase multigene family in the morning glory genome (original) (raw)
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Journal of Molecular Evolution, 2004
Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A-E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio (x = d N /d S ) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.
Plant Science, 2005
Chalcone synthase (CHS), the first committed enzyme in the flavonoid biosynthetic pathway, is commonly encoded by multi-gene families with select members of these families accounting for the majority of expression. We have examined the CHS gene family in Viola cornuta, a plant whose flowers undergo ontogenetic color change. Using both RNA and RNA/DNA samples isolated from floral tissues at different pigment stages, we obtained 14 unique sequences from 60 total clones of a 288 bp fragment from the catalytic region of CHS. The V. cornuta sequences were monophyletic when compared to CHS orthologs from other taxa. Substitution models generally indicated unequal rates of transition and transversion as well as significant rate variation among sites. With a Tamura-Nei correction, nucleotide divergence ranged from 0.3 to 10.6% with the vast majority as synonymous changes. The nucleotide divergence pattern suggests designation of three V. cornuta CHS clades; based on divergence of CHS orthologs, these clades are consistent with three CHS orthologs in V. cornuta. Sequences from only a single clade were found to be expressed in all three floral pigment stages.
Comparative genomics of chalcone synthase and Myb genes in the grass family
Genes & Genetic Systems, 2000
Most plant genes occur as members of multigene families where new copies arise through duplication. Duplicate genes that do not confer an adaptive advantage to the plant are expected to rapidly erode into pseudogenes owing to the accumulation of transpositions, insertion/deletion mutations and nucleotide changes. Nonfunctional copies will drift to fixation within a few million years and ultimately erode beyond recognition. Duplicate genes that are retained over longer periods of evolutionary time must be positively selected based on some adaptive advantage conferred on the plant species. We explore the dynamics of the recruitment of new duplicate genes for chalcone synthase, the enzyme that catalyzes the first committed step of flavonoid biosynthesis, and for the myb family of transcriptional activators. Our analyses show that new chs genes are recruited into the genome of grasses at a rate of one new copy every 15 to 25 million years. In contrast, the myb gene family is much older and many duplicate copies appear to predate the separation of the angiosperm lineage from other seed plants. The general pattern suggests a rapid adaptive proliferation of new chs genes but a more ancient elaboration of regulatory gene functions. Our analyses also reveal accelerated rates of protein evolution following gene duplication and evidence is presented for interlocus exchange among duplicate gene loci.
Cellular & molecular biology letters, 2004
Two full copy cDNA sequences encoding chalcone synthase (CHS) were selected from a yellow lupin (Lupinus luteus L.) root and nodule cDNA library, and sequenced. Analysis of their open reading frames gave evidence that both encode the functional enzyme. Sequence alignment and phylogenetic studies on the DNA and protein level of these clones compared to the sequences of chalcone synthases from 54 other plant species reveal the possibility that lupin chalcone synthase is encoded by a multigene family consisting of at least two distinct genes that probably diverged by gene duplication. The duplication event is estimated to have taken place about 16 million years ago.
Scientific Reports
Begonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in o...
New Phytologist, 2014
Chalcone synthase (CHS) is the key enzyme in the first committed step of the flavonoid biosynthetic pathway and catalyzes the stepwise condensation of 4-coumaroyl-CoA and malonyl-CoA to naringenin chalcone. In plants, CHS is often encoded by a small family of genes that are temporally and spatially regulated. Our earlier studies have shown that GCHS4 is highly activated by ectopic expression of an MYB-type regulator GMYB10 in gerbera (Gerbera hybrida).
Plant Molecular Biology, 1995
Recent studies on chalcone synthase (CHS) and the related stilbene synthase (STS) suggest that the structure of chs-like genes in plants has evolved into different forms, whose members have both different regulation and capacity to code for different but related enzymatic activities. We have studied the diversity of chs-like genes by analysing the structure, expression patterns and catalytic properties of the corresponding enzymes of three genes that are active during corolla development in Gerbera hybrida. The expression patterns demonstrate that chs-like genes are representatives of three distinct genetic programmes that are active during organ differentiation in gerbera. Gchsl and gchs3 code for typical CHS enzymes, and their gene expression pattern temporally correlates with flavonol (gchsl, gchs3) and anthocyanin (gchsl) synthesis during corolla development. Gchs2 is different. The expression pattern does not correlate with the pigmentation pattern, the amino acid sequence deviates considerably from the consensus of typical CHSs, and the catalytic properties are different. The data indicate that it represents a new member in the large superfamily of chs and chs-related genes.
Evolution of the chalcone synthase gene family in the genus Ipomoea
Proceedings of the National Academy of Sciences, 1995
The evolution of the chalcone synthase [CHS; malonyl-CoA:4-coumaroyl-CoA malonyltransferase (cyclizing), EC 2.3.1.74] multigene family in the genus Ipomoea is explored. Thirteen CHS genes from seven Ipomoea species (family Convolvulaceae) were sequenced-three from genomic clones and the remainder from PCR amplification with primers designed from the 5' flanking region and the end of the 3' coding region of Ipomoea purpurea Roth. Analysis of the data indicates a duplication of CHS that predates the divergence of the Ipomoea species in this study. The Ipomoea CHS genes are among the most rapidly evolving of the CHS genes sequenced to date. The CHS genes in this study are most closely related to the Petunia CHS-B gene, which is also rapidly evolving and highly divergent from the rest of the Petunia CHS sequences.