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

Abstract

BackgroundThe 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.ResultsDNA 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.ConclusionsOur 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.

Development of genic SSR markers from transcriptome sequencing of pear buds

“…In addition, the Oriental pear cluster contained two subgroups: A1, consisting of three P. betulifolia accessions, and A2, which clustered the other cultivars and species together. The position of P. betulifolia at the first independent branch in the Oriental pears might be related to its older origin (Zheng et al, 2011), which was confirmed by recent phylogenetic research from our research group (unpublished data). The species and cultivars in A2 displayed a complex relationship with a lower confidence coefficient, probably due to wide hybridization within Pyrus (Aldasoro et al, 1996).…”

“…In addition, P. ussuriensis and 'Yali' formed a branch in agreement with Yao (2010). 'Cili', another cultivar from the P. pyrifolia white pear group, clustered with P. pyrifolia from Japan, which supports the viewpoint that Chinese white pears are a variety or ecotype of P. pyrifolia (P. pyrifolia white pear group) (Teng and Tanabe, 2004;Bao et al, 2007;Zheng et al, 2011).…”

“…Some species of unknown or controversial origin were also included in this validation experiment, such as P. hopeiensis and P. phaeocarpa. P. hopeiensis was grouped together with P. pashia, and P. phaeocarpa clustered with P. serrulata, indicating their hybrid origins (Zheng et al, 2011). In addition, P. ussuriensis and 'Yali' formed a branch in agreement with Yao (2010).…”

“…It is a functionally diploid genus (2n=34) of allopolyploid origin and is believed to have arisen about 55-65 million years ago in the mountainous regions of western and southwestern China (Rubtsov, 1944). However, because pears are considered to be typically self-incompatible and interspecies compatible, phylogenetic relationships within the genus Pyrus are complicated and difficult to be established because of high heterozygosity from widespread crossing and low morphological diversity or poor differentiating characters (Teng et al, 2002;Bao et al, 2007;Yao et al, 2010;Zheng et al, 2011). Hence, more DNA-based genetic markers need to be exploited to resolve these problems.…”

Genetic diversity and population structure of wild pear (Pyrus pyraster (L.) Burgsd.) in Poland

“…genus is variously said to consist of from 20 to over 70 wild or domesticated species [22][23][24][25]. It is relatively difficult to give an accurate number of pear species, because they easily cross-pollinate and the obtained crosses have ambiguous taxonomic status.…”