Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus

Zhong, Hua; Kong, Weilong; Gong, Ziyun; Fang, Xuefeng; Deng, Xiaoxiao; Liu, Chang; Li, Yangsheng

doi:10.3389/fpls.2019.00565

Cited by 39 publications

(29 citation statements)

References 77 publications

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“…Gene duplication and syntenic analysis confirmed that no positive selection occurred in TaSPLs, additionally, TaSPL genes underwent strong purifying selection. Our results are consistent with the study of SPL genes in buckwheat [29] and rice [31], indicating that the evolution of TaSPL genes is comparable with that of other plants.…”

Section: Evolution Of Spl Family Genes In Wheatsupporting

confidence: 92%

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Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Zhu

Liu

et al. 2020

BMC Plant Biol

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Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

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Section: Evolution Of Spl Family Genes In Wheatsupporting

confidence: 92%

“…The ancestor SPL originally formed into two different lineages in land plants, named clade I and clade II. The clade I has conserved structure characteristics that possess more exons and longer protein sequences [31]. Our results showed that all SPL genes from wheat contained 1-11 exons.…”

Section: Evolution Of Spl Family Genes In Wheatmentioning

confidence: 68%

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Zhu

Liu

et al. 2020

BMC Plant Biol

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“…These results indicated similar gene numbers across a broad diversity of economically important grasses. In rice, a multitude of gene family members with high sequence similarity has been observed to cluster on the chromosomes as paralogous pairs [40,41]. However, we identified 12 OsDUF668s and found there were no collinearity relationships among them.…”

Section: Discussionmentioning

confidence: 70%

Characterization and Functional Divergence of a Novel DUF668 Gene Family in Rice Based on Comprehensive Expression Patterns

Zhong

Zhang

Guo

et al. 2019

Genes

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The domain of unknown function (DUF) superfamily encodes proteins of unknown functions in plants. Among them, DUF668 family members in plants possess a 29 amino-acid conserved domain, and this family has not been described previously. Here, we report this plant-specific novel DUF668 gene family containing 12 OsDUF668 genes in rice (Oryza sativa) and 91 DUF668s for the other seven plant species. In our study, DUF668 genes were present in both dicot and monocot plants, indicating that DUF668 is a conserved gene family that originated by predating the dicot–monocot divergence. Based on the gene structure and motif composition, the DUF668 family consists of two distinct clades, I and II in the phylogenetic tree. Remarkably, OsDUF668 genes clustered on the chromosomes merely show close phylogenetic relationships, suggesting that gene duplications or collinearity seldom happened. Cis-elements prediction display that over 80% of DUF668s contain phytohormone and light responsiveness factors. Further comprehensive experimental analyses of the OsDUF668 family are implemented in 22 different tissues, five hormone treatments, seven environmental factor stresses, and two pathogen-defense related stresses. The OsDUF668 genes express ubiquitously in analyzed rice tissues, and seven genes show tissue-specific high expression profiles. All OsDUF668s respond to drought, and some of Avr9/Cf-9 rapidly elicited genes resist to salt, wound, and rice blast with rapidly altered expression patterns. These findings imply that OsDUF668 is essential for drought-enduring and plant defense. Together, our results bring the important role of the DUF668 gene family in rice development and fitness to the fore.

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“…These results indicated that the domain organization has been constructed in the five Rosaceae species. These SBP domain locations, Zn1 and Zn2 binding sites, and NLS site were considered to be significant for specific recognition and binding to cis -elements in the promoter of nuclear genes [ 1 , 2 ]. Moreover, 11 SPLs belonging to the G10 group contain an ANK-2 domain ( Figure 4 ), which is associated with protein–protein interaction in plant cells [ 28 ].…”

Section: Resultsmentioning

confidence: 99%

“…SPL protein contains the very conservative DNA-binding domain, namely the squamosa promoter binding protein (SBP) domain, consisting of ∼76 amino acid (aa) residues to carry out sequence-specific DNA binding and nuclear localization [ 1 ]. The SBP domain was composed of two zinc-binding sites (Cys–Cys–Cys–His and Cys–Cys–His–Cys) and a nuclear localization signal (NLS) partially overlapping with Cys–Cys–His–Cys [ 2 ]. Since 1996, SPL genes have been reported in many plants, such as Arabidopsis thaliana [ 3 ], rice [ 4 ], maize [ 5 ], Petunia [ 6 ], Dichanthelium oligosanthes [ 1 ], tea [ 7 ], Jatropha curcas [ 8 ], apple [ 9 ], pear [ 10 ], peach, and strawberry [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the SPL gene family in five Rosaceae species: Fragaria vesca, Malus domestica, Prunus persica, Rubus occidentalis, and Pyrus pyrifolia

et al. 2021

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SQUAMOSA promoter-binding protein-like (SPL) transcription factors are very important for the plant growth and development. Here 15 RoSPLs were identified in Rubus occidentalis. The conserved domains and motifs, phylogenetic relationships, posttranscriptional regulation, and physiological function of the 92 SPL family genes in Fragaria vesca, Malus domestica, Prunus persica, R. occidentalis, and Pyrus pyrifolia were analyzed. Sequence alignment and phylogenetic analysis showed the SPL proteins had sequence conservation, some FvSPLs could be lost or developed, and there was a closer relationship between M. domestica and P. pyrifolia, F. vesca and R. occidentalis, respectively. Genes with similar motifs clustering together in the same group had their functional redundancy. Based on the function of SPLs in Arabidopsis thaliana, these SPLs could be involved in vegetative transition from juvenile to adult, morphological change in the reproductive phase, anthocyanin biosynthesis, and defense stress. Forty-eight SPLs had complementary sequences of miR156, of which nine PrpSPLs in P. persica and eight RoSPLs in R. occidentalis as the potential targets of miR156 were reported for the first time, suggesting the conservative regulatory effects of miR156 and indicating the roles of miR156-SPL modules in plant growth, development, and defense response. It provides a basic understanding of SPLs in Rosaceae plants.

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Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus

Cited by 39 publications

References 77 publications

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Characterization and Functional Divergence of a Novel DUF668 Gene Family in Rice Based on Comprehensive Expression Patterns

Comparative analysis of the SPL gene family in five Rosaceae species: Fragaria vesca, Malus domestica, Prunus persica, Rubus occidentalis, and Pyrus pyrifolia

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