Genome-Wide Identification and Characterization of the ALOG Domain Genes in Rice

Abstract

The ALOG domain genes, named after the Arabidopsis LSH1 and Oryza G1 (ALOG) proteins, have frequently been reported as key developmental regulators in rice and Arabidopsis. However, the investigation of the ALOG gene family is limited. Here, we conducted a genome-wide investigation of the ALOG gene family in rice and six other species. In total, eighty-four ALOG domain genes were identified from the seven species, of which fourteen ALOG domain genes (OsG1/G1Ls) were identified in the rice genome. The fourteen OsG1/G1Ls were unevenly distributed on eight chromosomes, and we found that eight segmental duplications contributed to the expansion of OsG1/G1Ls in the rice genome. The eighty-four ALOG family genes from seven species were classified into six clusters, and the ALOG domain-defined motifs 1, 2, and 3 were highly conserved across species according to the phylogenetic and structural analysis. However, the newly identified motifs 4 and 5 were only present in monocots, indicating a specified function in monocots. Moreover, OsG1/G1Ls exhibited tissue-specific expression patterns. Coexpression analysis suggested that OsG1 integrates OsMADS50 and the downstream MADS-box genes, such as OsMADS1, to regulate the development of rice inflorescence; OsG1L7 potentially associates with OsMADS22 and OsMADS55 to regulate stem elongation. In addition, comparative expression analysis revealed the conserved biological functions of ALOG family genes among rice, maize, and Arabidopsis. These results have shed light on the functional study of ALOG family genes in rice and other plants.

Genome-wide identification and characterization of the ALOG gene family in Petunia

“…The results demonstrate that all PhLSH proteins contain a conserved ALOG domain in the middle region, which consists of four helixes with a zinc ribbon insert and a nuclear location signal (NLS) sequence (Fig. 4), however, the similarity of the N- and C-terminal sequences is very low (Additional file 7), which is consistent with previous reports in other species [29, 31, 32]. Motif analysis shows that a total of 20 motifs are present in PhLSH proteins and the number of motifs in each protein varies from 5 to 8 (Fig.…”

Transcriptome Analysis Reveals Key Pathways and Candidate Genes Controlling Seed Development and Size in Ricebean (Vigna umbellata)

“…Similarly, a small genotype across the time point (S5_S10) contributed to 14,544 DEGs (Figure3A; Table 2). In contrast to B5_B10 expression results, S5_S10 had a high number of downregulated genes (7,862) in comparison with the upregulated genes (6,682), indicating that these downregulated genes might be repressing any transcriptional activity or downstream pathways resulting in the small size of ricebean seeds (Li et al, 2019b). To gain a better understanding of molecular processes/regulatory networks associated with the seed size in ricebeans, the pattern of differentially expressed genes was analyzed between genotypes in each time point and across the time point using a Venn diagram (Figure 3B).…”

“…Comparative transcriptome analysis was performed between two genotypes with contrasting seed size at two time points, namely, 5 and 10 DPA. A similar type of study using two genotypes with a contrasting seed size has also been done in the peanut (Li et al, 2019b). The expression profile was checked for the individual genotypes across the time points (B5_B10, S5_S10) as well as between the genotypes at each time point (B5_S5, B10_S10) (Supplementary Table S1).…”

Genetic Conservation of CBS Domain Containing Protein Family in Oryza Species and Their Association with Abiotic Stress Responses

“…Thus, preserving the functional properties of CDCPs in all the 10 Oryza genomes evaluated even after duplication, as a further adaptive advantage by a mutation on a non-synonymous site might be an unlikely event. Several other gene families in Oryza sp., such as WRKY [52], ALOG domain [53], DUF-221 domain containing gene family [54], F-box, and NB-ARC gene families [55], have also been found to be shaped majorly by negative selection. The gene duplication has contributed to the expansion of the gene family through segmental or whole-genome duplication in rice species [56].…”