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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

Representative maximum likelihood trees and dN/dS values for the nine taxa of Annonaceae.(A) Likelihood scores for the matK and rpoA trees were −5638.2661 lnL and −5506.0125 lnL, respectively. Branches in bold are members of Annonaceae. Bootstrap values greater than 50 are shown at the nodes. Scale bar indicates non-synonymous substitutions per codon. (B) Histogram of dN/dS values for seven genes for the Annonaceae. For each gene, dN/dS values (y axis) are given for all branches of interest: the branch leading to the family, the internal branch to Annona/Asimina, and the terminal branches to Annona, Asimina, and Cananga. Only one ratio was marginally >1, the terminal branch to Asimina for matK (dN/dS = 1.0069).
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f2: Representative maximum likelihood trees and dN/dS values for the nine taxa of Annonaceae.(A) Likelihood scores for the matK and rpoA trees were −5638.2661 lnL and −5506.0125 lnL, respectively. Branches in bold are members of Annonaceae. Bootstrap values greater than 50 are shown at the nodes. Scale bar indicates non-synonymous substitutions per codon. (B) Histogram of dN/dS values for seven genes for the Annonaceae. For each gene, dN/dS values (y axis) are given for all branches of interest: the branch leading to the family, the internal branch to Annona/Asimina, and the terminal branches to Annona, Asimina, and Cananga. Only one ratio was marginally >1, the terminal branch to Asimina for matK (dN/dS = 1.0069).

Mentions: The dN/dS ratio was calculated for the three different lineages of angiosperms. Seven plastid genes (rpoA, rpoB, rpoC1, rpoC2, ndhF, matK and rbcL) were analyzed in PAML for three datasets to compare the dN/dS ratio of rpoA to the other rpo genes as well as to other non-rpo plastid genes. These same seven genes were used to generate constraint trees for each dataset. Constraint tree topologies were identical to the matK trees for Annonaceae (Fig. 2A) and Passifloraceae (Fig. 3A). The seven gene constraint tree for Geraniaceae is shown as an inset in Fig. 4.


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)

Representative maximum likelihood trees and dN/dS values for the nine taxa of Annonaceae.(A) Likelihood scores for the matK and rpoA trees were −5638.2661 lnL and −5506.0125 lnL, respectively. Branches in bold are members of Annonaceae. Bootstrap values greater than 50 are shown at the nodes. Scale bar indicates non-synonymous substitutions per codon. (B) Histogram of dN/dS values for seven genes for the Annonaceae. For each gene, dN/dS values (y axis) are given for all branches of interest: the branch leading to the family, the internal branch to Annona/Asimina, and the terminal branches to Annona, Asimina, and Cananga. Only one ratio was marginally >1, the terminal branch to Asimina for matK (dN/dS = 1.0069).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Representative maximum likelihood trees and dN/dS values for the nine taxa of Annonaceae.(A) Likelihood scores for the matK and rpoA trees were −5638.2661 lnL and −5506.0125 lnL, respectively. Branches in bold are members of Annonaceae. Bootstrap values greater than 50 are shown at the nodes. Scale bar indicates non-synonymous substitutions per codon. (B) Histogram of dN/dS values for seven genes for the Annonaceae. For each gene, dN/dS values (y axis) are given for all branches of interest: the branch leading to the family, the internal branch to Annona/Asimina, and the terminal branches to Annona, Asimina, and Cananga. Only one ratio was marginally >1, the terminal branch to Asimina for matK (dN/dS = 1.0069).
Mentions: The dN/dS ratio was calculated for the three different lineages of angiosperms. Seven plastid genes (rpoA, rpoB, rpoC1, rpoC2, ndhF, matK and rbcL) were analyzed in PAML for three datasets to compare the dN/dS ratio of rpoA to the other rpo genes as well as to other non-rpo plastid genes. These same seven genes were used to generate constraint trees for each dataset. Constraint tree topologies were identical to the matK trees for Annonaceae (Fig. 2A) and Passifloraceae (Fig. 3A). The seven gene constraint tree for Geraniaceae is shown as an inset in Fig. 4.

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