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

Abstract

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 reversetranscription 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.

Genome-Wide Analysis of the Cyclin Gene Family and Their Expression Profile in Medicago truncatula

“…D-, CycJ18-, T-, SDS-, and U-type cyclins are not specific to Arabidopsis but are also present in other plants [ 15 ]. For conserved domains, our study indicated that most of the A-, B-, and D-types contained both cyclin_N and cyclin_C domains; however, each of the U- and T-types in all putative cyclins had only cyclin_N without cyclin_C domains, as also reported in Arabidopsis , maize, rice and poplar [ 15 , 18 , 19 , 20 ]. Additionally, together with the structures and motifs of these cyclins, the same types of cyclins in Arabidopsis and legume plants were located in the same clades and shared high sequence similarity.…”

“…Phylogenetic analysis indicated that all putative legume cyclins were classified into ten types (A-, B-,C-, D-, H-, L-, T-, U-, SDS-, and J18-types), sharing the same types with Arabidopsis , whereas the D-type was the largest clade in the legume species, and the CycB-like types, including CycBL;1-8, were specific to Medicago, lacking any clear homologues in Arabidopsis , common bean and soybean. Likewise, F-type cyclins, lacking clear homologues in Arabidopsis , were unique to rice, and Q- and Z-types were defined as new putative types of poplar cyclin genes [ 19 , 20 ]. D-, CycJ18-, T-, SDS-, and U-type cyclins are not specific to Arabidopsis but are also present in other plants [ 15 ].…”

“…Forty-nine cyclins forming nine families have been detected in the rice ( Oryza sativa) genome, and F-type cyclins are specific to monocots [ 18 ]. Previous studies have identified 59 cyclins in the maize ( Zea mays ) genome and 52 in tomato, and have predicted 45 in poplar ( Populus trichocarpa ) [ 19 , 20 ]. Distinguished by the classes of organisms, cyclins have also been classified into M-cyclins and G1-cyclins according to the phase in which they function in the cell cycle.…”

Effect of exogenous IAA on tension wood formation by facilitating polar auxin transport and cellulose biosynthesis in hybrid poplar (Populus deltoids × Populus nigra) wood

“…About 1 g sample was placed into a 50 ml steel jar together with a steel bead and frozen by liquid nitrogen for more than 10 min firstly, and then the jar was set in a high throughput ball mill (DHS, Beijing, China) for powdering the samples for 2 min. Total RNA was isolated by the improved cetyl trimethylammonium bromide (CTAB) method (Dong et al 2011). A 2 μg of total RNA was reverse transcribed by means of the PrimeScript RT reagent Kit (TaKaRa, Dalian, China) to generate cDNA.…”

Evolution of the cyclin gene family in plants

“…& A. Gray ex Hook., hereafter called poplar; Dong et al, ), but the evidence presented was not strong enough because an extensive phylogenetic analysis was lacking. In addition, because representatives of non‐seed plants have not been included, it remains unclear how plant cyclins have evolved and whether the previously defined groups and subgroups are reasonable.…”