Genome-wide identification and characterization of the cyclin gene family in Populus trichocarpa

The cell cycle is controlled by the interplay of many different molecules. Foremost in this process are the cyclin family of proteins that serve to regulate the cell cycle by interacting with cyclin-dependent kinases (CDKs). To date, the cell cycle and functions of the cyclin gene family have been extensively analyzed in Arabidopsis, rice, and humans. However, the cyclin gene family in poplar has rarely been researched. In the present study, cyclin genes were predicted in the poplar draft genome sequence by comparison with Arabidopsis cyclin genes, and analyzed by phylogenetic relationships, chromosomal distributions, protein motifs, and expression patterns. A conserved cyclin_N domain distinguished poplar, and 45 predicted cyclin genes were classified into seven types, including A-, B-, C-, D-, Q-, T-, and Z-types. Phylogenetic analyses indicated that five of the seven cyclin types were consistent with Arabidopsis types, the poplar cyclin D gene subfamily exhibited more classes than observed in Arabidopsis and rice, and Q- and Z-types each possessed only one cyclin gene, which we defined as new putative types of poplar cyclin genes. We selected the special cyclin genes (Q- and Z-types and D3 subgroups) to study the expression patterns in different tissues by semiquantitative reverse-transcription polymerase chain reaction (RT-PCR). The outcomes indicated that almost all of the D3 subgroup genes were expressed in various tissues, the Q cyclin gene was detected in roots and stems, and the Z cyclin gene was only identified in roots. Analysis of the poplar cyclin gene family provides insights into cell cycle mechanisms and cyclin gene functions.