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Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)
- Source :
- BMC Evolutionary Biology, BMC Evolutionary Biology, Vol 11, Iss 1, p 255 (2011)
- Publication Year :
- 2011
- Publisher :
- BioMed Central, 2011.
-
Abstract
- Background The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of LEAFY and the alcohol dehydrogenase gene (Adh) were selected to investigate their molecular evolution and phylogenetic utility. Results DNA sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some Adh homologs are putatively nonfunctional. A partial region of Adh1 was sequenced for 18 Pyrus species and three subparalogs representing Adh1-1 were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of LEAFY, multiple inparalogs were discovered for both LFY1int2 and LFY2int2. LFY1int2 is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of Pyrus using LFY2int2-N. Conclusions Our study represents the first phylogenetic analyses based on LCNGs in Pyrus. Ancient and recent duplications lead to a complex structure of Adh outparalogs and inparalogs in Pyrus and Malus, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs, LFY2int2-N is the best nuclear marker for phylogenetic reconstruction of Pyrus due to suitable sequence divergence and the absence of lineage sorting.
- Subjects :
- Genetic Markers
Nuclear gene
Evolution
Lineage (evolution)
Molecular Sequence Data
Genes, Plant
Evolution, Molecular
Pyrus
Molecular evolution
Phylogenetics
QH359-425
Cluster Analysis
Ecology, Evolution, Behavior and Systematics
Phylogeny
DNA Primers
Genetics
Maloideae
biology
Phylogenetic tree
Base Sequence
Models, Genetic
Alcohol Dehydrogenase
Genetic Variation
Bayes Theorem
Sequence Analysis, DNA
biology.organism_classification
Introns
Subfunctionalization
Neofunctionalization
Research Article
Transcription Factors
Subjects
Details
- Language :
- English
- ISSN :
- 14712148
- Volume :
- 11
- Database :
- OpenAIRE
- Journal :
- BMC Evolutionary Biology
- Accession number :
- edsair.doi.dedup.....5ff3f354497246bfcd4a62f92e1f835d