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Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement.

Blazier JC, Ruhlman TA, Weng ML, Rehman SK, Sabir JS, Jansen RK - Sci Rep (2016)

Bottom Line: Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order.The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat.We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.

ABSTRACT
Genes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP α subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled and analyzed from each of the three angiosperm families. Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order. The ratio of non-synonymous to synonymous substitutions indicated that these genes are under purifying selection, and bioinformatic prediction of conserved domains indicated that functional domains are preserved. One of the lineages (Pelargonium, Geraniaceae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene conversion. The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat. We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

No MeSH data available.


Related in: MedlinePlus

Histogram of dN/dS ratios for seven genes for Geraniaceae.In addition to MAFFT results presented here, three other alignment algorithms were used (See Table S2). For each gene, dN/dS values are given for all branches of interest, the branch leading to the family (Geraniaceae), to Pelargonium, to the branch to clades A/B, to clade A, to clade B, and to clade C1.
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f5: Histogram of dN/dS ratios for seven genes for Geraniaceae.In addition to MAFFT results presented here, three other alignment algorithms were used (See Table S2). For each gene, dN/dS values are given for all branches of interest, the branch leading to the family (Geraniaceae), to Pelargonium, to the branch to clades A/B, to clade A, to clade B, and to clade C1.

Mentions: The branches of interest for the Pelargonium rates analyses were different from those in the previous two data sets: the terminal branches were excluded as intra-clade divergence among species was extremely low due to dense taxon sampling in this dataset. Low sequence divergence between closely related taxa caused error values to be returned in the calculation of dN/dS where either or both of the parameters were calculated to be zero or close to zero (not shown). Therefore the branches of interest were chosen as those where the greatest divergence in rpoA has occurred and are highlighted in Fig. 5.


Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement.

Blazier JC, Ruhlman TA, Weng ML, Rehman SK, Sabir JS, Jansen RK - Sci Rep (2016)

Histogram of dN/dS ratios for seven genes for Geraniaceae.In addition to MAFFT results presented here, three other alignment algorithms were used (See Table S2). For each gene, dN/dS values are given for all branches of interest, the branch leading to the family (Geraniaceae), to Pelargonium, to the branch to clades A/B, to clade A, to clade B, and to clade C1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834550&req=5

f5: Histogram of dN/dS ratios for seven genes for Geraniaceae.In addition to MAFFT results presented here, three other alignment algorithms were used (See Table S2). For each gene, dN/dS values are given for all branches of interest, the branch leading to the family (Geraniaceae), to Pelargonium, to the branch to clades A/B, to clade A, to clade B, and to clade C1.
Mentions: The branches of interest for the Pelargonium rates analyses were different from those in the previous two data sets: the terminal branches were excluded as intra-clade divergence among species was extremely low due to dense taxon sampling in this dataset. Low sequence divergence between closely related taxa caused error values to be returned in the calculation of dN/dS where either or both of the parameters were calculated to be zero or close to zero (not shown). Therefore the branches of interest were chosen as those where the greatest divergence in rpoA has occurred and are highlighted in Fig. 5.

Bottom Line: Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order.The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat.We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.

ABSTRACT
Genes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP α subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled and analyzed from each of the three angiosperm families. Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order. The ratio of non-synonymous to synonymous substitutions indicated that these genes are under purifying selection, and bioinformatic prediction of conserved domains indicated that functional domains are preserved. One of the lineages (Pelargonium, Geraniaceae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene conversion. The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat. We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

No MeSH data available.


Related in: MedlinePlus