Identification and expression of the CEP gene family in apple (Malus×domestica)

Plant peptide hormones play important roles in plant growth and development. Among these hormones, the C-TERMINALLYENCODED PEPTIDE（CEP） belongs to a newly found peptide family that regulates root development in Arabidopsis as well as in other species. However, nothing is known about the CEP genes in apple（Malus×domestica, MdCEP）. In this study, a total of 27 apple CEP genes were identified through a genome-wide analysis and were phylogenetically divided into three classes（Ⅰ, Ⅱ and Ⅲ）. The predicted MdCEP genes were distributed across 10 of 17 chromosomes with different densities. Next, the gene structures and motif compositions of the MdCEP genes were analyzed. Subsequently, the expression analysis suggested that the MdCEP genes were highly activated in roots and that MdCEP23 may play an important role in regulating the growth and development of roots. Moreover, all of the MdCEP genes were responsive to multiple abiotic stresses, indicating that MdCEP genes may be involved with various aspects of physiological processes in apple. Nearly one-third of MdCEP genes had a significant response to low nitrogen treatment. Most of the MdCEP genes were up-regulated under stress, including mannitol, polyethylene glycol（PEG） and abscisic acid（ABA）, suggesting that MdCEP genes may be involved in the drought stress response. This study provides insight into the putative functions of the MdCEP genes using a genome-wide analysis of the CEP gene family.

Identification and Phylogenetic Analysis of the POLYGALACTURONASE Gene Family in Apple

In this study, a total of 85 apple polygalacturonase genes were characterized and clustered into seven groups based on the Malus × domestica whole-genome sequence. These genes coded for proteins containing 176–1 125 amino acids with isoelectric points ranging from 4.68 to 9.58.The predicted Md PG genes were distributed on all chromosomes except the 14 th. We then systematically analyzed conserved Md PG protein motifs and the structures of Md PG genes. We identified Md PG proteins containing four conserved motifs that are widely found in different PG proteins.Additionally, we found that Md PG75 was the largest gene, encompassing 18 exons. Finally, we systematically analyzed the functional connection network of Md PG proteins and predicted the functions of related Md PG genes before undertaking a preliminary validation. Overall, we have described the genome-wide identification and analysis of the apple PG gene family.

Molecular evolutionary analysis of gene families encoding DNA recombination and repair proteins and histone demethylases,and their functional implications

Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between