New structure-based methods for the phylogeneticanalysis of ribosomal RNA sequences using the

parsimony optimality criterion

Joseph J. GillespieMatthew J. Yoder*

Anthony I. Cognato

1

2

3

1. RAA/RSC/REC coding

2. RNA basepair coding

RNA molecules havecharacteristic higherorder structure that isconserved across all life

Using structure to guidethe assignment of positionalnucleotide homology, weoffer two new approaches toanalyzing rRNA sequences:

CCUGAGA

AAC

CC

GAAA G G

UCG

AAA

GAGGAAAUUCAUUC

GCGUUUCGACUGUCGA

UUG

GAUGU

U

ACGGAUAGCGUU

UCGGCGUCGUCCG

UUAUAUUCUUCGU

GUCGAU

GUC

GAACGCGU

GCACUUUUCCUCUAGU

AG

GACGUCGC

G

AUCCGUUGGGUG

UCUGUCUAAGAC

UCGAGGUGGAGC

CCGCGUAAUUUUU

AAUUAUGCGG

AC

CCUUGGUGUU

C

C

GACAGACUCACUCGACGGUAU

ACUAA

UGGCG

CGGGG C C

GCUA

CUUUA

GU

UAGCG

UUCGG

C

CCGUAGCA

AGCA

CGUUCUG UG

UUUG

ACGGCG

AUCGG

AC

CUG

GUGCCGAU

UCUGUC

C

CAGAACGAC UGUU

GGUUACGGU

GUU C

UCGAACAGACCUCG

UAUGA A A C G C C G

AUC AG C

GA C

GCU C

U A G A UU

GG

G

UAC U

UUCAGG

2

2f

2e

2d

2c

2b

2a

3g

3a

3e

3d

3c

3b

3f

3h

3i

3o

3n

3m

3l

3k

3j

3p

3

1b

1a

AG

5’

U

GC

AUUUGC

UU

3’

RAA/RSC/REC coding*

Methods for characterizing regions of RNA sequencealignments wherein positional nucleotide homologycannot be assigned with confidence

Based on the premise of using information fromsecondary structure (i.e., compensatory base changeevidence) to delimit unalignable positions

*Gillespie (2004) Mol. Phylogenet. Evol. 33: 936-943

RAA/RSC/REC coding

RAA/RSC/REC coding*

Region of ambiguous alignment

Two or more adjacent, non-pairing positions withina sequence wherein positional homology cannot beconfidently assigned due to the high occurrence ofindels in other sequences

RAA

*Gillespie (2004) Mol. Phylogenet. Evol. 33: 936-943

RAA/RSC/REC coding*

Region of slipped-strand compensation

Region involved in base-pairing wherein positionalhomology cannot be defended across a multiplesequence alignment; inconsistency in pairing likelydue to slipped-strand mispairing

RSC

*Gillespie (2004) Mol. Phylogenet. Evol. 33: 936-943

RAA/RSC/REC coding*

Region of expansion and contraction

Variable helical region flanked by conserved basepairsat the 3’ and 5’ ends, and an unpaired terminal bulgeof at least three nucleotides; characteristic of RNAhairpin-stem loops

REC

*Gillespie (2004) Mol. Phylogenet. Evol. 33: 936-943

RAA/RSC/REC coding*

Subdividing large ambiguously aligned regions intosmaller components provides:

why?

1. a means for comparing structurally similar nucleotides in fragment level alignment methods (INAASE, POY)

2. fewer character state transformations between taxa, with less potential to exceed the number of allotted states in a given phylogenetic software

4. improvements to existing global structural models for the various rRNA molecules on public databases

*Gillespie (2004) Mol. Phylogenet. Evol. 33: 936-943

3. the ability to objectively assign different substitution weights to pairing (RSC, REC) and non-pairing (RAA) regions

5. a more explicit set of homologies

RNA basepair coding

A = A AA = C CA = H GA = M UA = T C = R AC = Q CC = I GC = F UC = W G = N AG = E CG = L GG = P UG = Y U = D AU = G CU = K GU = S UU = V

*adopted from Smith et al. (2004) Mol. Biol. Evol. 21: 419-427

non-pairing pairing

code (20 states)*RNA basepair coding

substitution matrix

non-pairing

canonical

non-canonical

(-)

(-)

RNA basepair coding

weighting, i.e.RNA basepair coding

RNA basepair coding scripts

available via the Jrna script package

http://hymenoptera.tamu.edu/rna

This project was funded by NSF-PEET DEB grants 0328922 toRobert Wharton and 0358920 to Anthony Cognato.