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Open Access Research article

Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)

Xiaoyan Zheng1, Chunyun Hu1, David Spooner2, Jing Liu1, Jiashu Cao1 and Yuanwen Teng1*

Author Affiliations

1 Department of Horticulture, the State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, Zhejiang 310058, China

2 USDA, Agricultural Research Service, Department of Horticulture, University of Wisconsin, Madison, WI 53706-1590, USA

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BMC Evolutionary Biology 2011, 11:255  doi:10.1186/1471-2148-11-255

Published: 14 September 2011

Additional files

Additional file 1:

50% majority-rule consensus tree based on amino acid sequences of Adh loci from diverse plant taxa. ADH sequences in Rosaceae are highlighted in blue. Numbers above the branches or near the branch nodes indicate bootstrap values (1000 replicates). Accession number was given for sequences from GenBank. Multiple intraindividual sequences for Adh1 (Adh1-1 and Adh1-2) and Adh2 (Adh2-1 and Adh2-2) are differentiated by the number in the brackets following the taxa name*: Though Adh2-1 was not obtained by G-PCR in Malus, its transcription was detected by RT-PCR in 'Fuji' (M. domestica), which was described in the text.

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Additional file 2:

Transcription of Adh1 homologs revealed by neighbor joining (NJ) analyses. Sequences obtained from genomic PCR are marked by G followed by the corresponding Adh1-1 subparalogs name in the square brackets. Sequences obtained from RT-PCR are marked by RT followed by the plant tissues used in parenthesis. Sequences obtained from specific genomic PCR are marked by SG. Multiple intraindividual sequences obtained from different PCR or plant tissues are differentiated by the fraction in the brackets following the taxa name. Putative pseudogenes obtained by G-PCR are marked by 'ψ'.

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Open Data

Additional file 3:

Transcription of Adh2 homologs revealed by neighbor joining (NJ) analyses. Sequences obtained from genomic PCR are marked by G followed by the paralogs name in the square brackets. Sequences obtained from RT-PCR are marked by RT followed by the plant tissues used in parenthesis. Sequences obtained from specific genomic PCR are marked by SG. Multiple intraindividual sequences obtained from different PCR or plant tissues are differentiated by the fraction in the brackets following the taxa name. Putative pseudogenes obtained by G-PCR are marked by 'ψ.

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Additional file 4:

Alignment of ADH amino acid sequences from different plant taxa.

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Additional file 5:

Alignment of the reduced Adh1 nucleotide sequences from Malus and Pyrus.

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Additional file 6:

Alignment of LFY1int2 nucleotide sequences from Malus and Pyrus.

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Open Data

Additional file 7:

Alignment of LFY2int2 sequences from different plant taxa.

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Open Data