Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families.

Dof proteins are a family of plant-specific transcription factors that contain a particular class of zinc-finger DNA-binding domain. Members of this family have been found to play diverse roles in gene regulation of processes restricted to the plants. The completed genome sequences of rice and Arabidopsis constitute a valuable resource for comparative genomic analyses, since they are representatives of the two major evolutionary lineages within the angiosperms. In this framework, the identification of phylogenetic relationships among Dof proteins in these species is a fundamental step to unravel functionality of new and yet uncharacterised genes belonging to this group. We identified 30 different Dof genes in the rice Oryza sativa genome and performed a phylogenetic analysis of a complete collection of the 36-reported Arabidopsis thaliana and the rice Dof transcription factors identified herein. This analysis led to a classification into four major clusters of orthologous genes and showed gene loss and duplication events in Arabidopsis and rice, that occurred before and after the last common ancestor of the two species. According to our analysis, the Dof gene family in angiosperms is organized in four major clusters of orthologous genes or subfamilies. The proposed clusters of orthology and their further analysis suggest the existence of monocot specific genes and invite to explore their functionality in relation to the distinct physiological characteristics of these evolutionary groups.

Lijavetzky D ，Carbonero P ，Vicente-Carbajosa J 《BMC EVOLUTIONARY BIOLOGY》

Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis.

The heat shock transcription factors (HSFs) are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins (HSPs), which are critical in the protection against stress damage and many other important biological processes. Study of the HSF gene family is important for understanding the mechanism by which plants respond to stress. The completed genome sequences of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) constitute a valuable resource for comparative genomic analysis, as they are representatives of the two major evolutionary lineages within the angiosperms: the monocotyledons and the dicotyledons. The identification of phylogenetic relationships among HSF proteins in these species is a fundamental step to unravel the functionality of new and yet uncharacterized genes belonging to this family. In this study, the full complement of HSF genes in rice and Arabidopsis has probably been identified through the genome-wide scan. Phylogenetic analyses resulted in the identification of three major clusters of orthologous genes that contain members belonging to both species, which must have been represented in their common ancestor before the taxonomic splitting of the angiosperms. Further analysis of the phylogenetic tree reveals a possible dicot specific gene group. We also identified nine pairs of paralogs, as evidence for studies on the evolution history of rice HSF family and rice genome evolution. Expression data analysis indicates that HSF proteins are widely expressed in plants. These results provide a solid base for future functional genomic studies of the HSF gene family in rice and Arabidopsis.

Guo J ，Wu J ，Ji Q ，Wang C ，Luo L ，Yuan Y ，Wang Y ，Wang J ... -  《Journal of Genetics and Genomics》

Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa).

Auxin response factors (ARFs) are transcription factors that bind with specificity to TGTCTC-containing auxin response elements (AuxREs) found in promoters of primary/early auxin response genes and mediate responses to the plant hormone auxin. The ARF genes are represented by a large multigene family in plants. A comprehensive genome-wide analysis was carried out in this study to find all ARFs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa subsp. japonica), 23 and 25 ARF genes, named as AtARFs and OsARFs, were identified, respectively. Chromosomal locations of all OsARFs were presented and it was found that the duplication of OsARFs was associated with only the chromosomal block duplications but not local tandem duplications. A phylogenetic tree was generated from alignments of the full-length protein sequences of 25 OsARFs and 23 AtARFs to examine the phylogenetic relationships of rice and Arabidopsis ARF proteins. All 48 members of ARF gene families fell into three major classes, a total of 13 sister pairs, including 9 OsARF-OsARF, 2 AtARF-AtARF and 2 AtARF-OsARF sister pairs were formed, showing different orthologous relationships between AtARFs and OsARFs. EST analysis and RT-PCR assays demonstrated that 24 of all 25 OsARF genes were active and the transcript abundance of some OsARF genes was affected by auxin treatment or light- and dark-grown conditions. The outcome of the present study provides basic genomic information for the rice ARF gene family and will pave the way for elucidating the precise role of OsARFs in plant growth and development in the future.

Wang D ，Pei K ，Fu Y ，Sun Z ，Li S ，Liu H ，Tang K ，Han B ，Tao Y ... -  《GENE》

[Comparative phylogenetic analysis of the rice and Arabidopsis PHD-finger proteins].

PHD-finger (plant homeodomain finger), a unique Cys4-His-Cys3 pattern zinc-containing domain, is widely found in many transcriptional regulation proteins from plants or animals. This protein has many different family members distributing in plant or animal proteome,and plays key roles in the development. Here, we identified 44 different putative PHD-finger proteins in the rice (Oryza sativa) genome and performed a phylogenetic analysis with 45 Arabidopsis thaliana proteins. The analysis led to a classification of the 89 proteins into two major groups based on the number of PHD-fingers. Phylogentic analysis of these proteins indicated that there are common ancestors in both plant and human genomes, from which two or three PHD-finger containing proteins might duplicate.

Feng Y ，Liu QP ，Xue QZ 《-》

Comparative study of SBP-box gene family in Arabidopsis and rice.

SBP-box proteins are plant-specific putative transcription factors, which contain highly conserved SBP domain and could bind specifically to promoters of the floral meristem identity gene SQUAMOSA and its orthologous genes to regulate their expressions. In this study, 17 non-redundant SBP-box genes in Arabidopsis genome and 19 in rice genome were identified by using the known SBP domain sequences as queries. The phylogenetic analysis suggested that the main characteristics of this family might have been in existence before the split of Arabidopsis and rice, and most SBP-box genes expanded in a species-specific manner after the split of monocotyledon and dicotyledon. All the SBP-box proteins were classified into 9 subgroups based on the phylogenetic tree, where each group shared similar motifs and the orders of the motifs in the same group were found almost identical. Analysis of nonsynonymous and synonymous substitution rates revealed that the SBP domain had gone through purifying selection, whereas some regions outside SBP domain had gone through positive or relaxed purifying selection. The expression patterns of the SBP-box genes were further investigated by searching against the EST database. Results showed that the Arabidopsis SBP-box genes are expressed chiefly in flowers, leaves, roots and seeds, while those in rice mainly in flowers and callus.

Yang Z ，Wang X ，Gu S ，Hu Z ，Xu H ，Xu C ... -  《GENE》