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Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize.

ABSTRACT: SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Systematic analysis of the SPL family has been performed in numerous plants, such as Arabidopsis, rice, and Populus. However, no comparative analysis has been performed across different species to examine evolutionary features. In this study, we present a comparative analysis of SPLs in different species. The results showed that 84 SPLs of the four species can be divided into six groups according to phylogeny. We found that most of the SPL-containing regions in maize showed extensive conservation with duplicated regions of rice and sorghum. A gene duplication analysis in maize indicated that ZmSPLs showed a significant excess of segmental duplication. The Ka/Ks analysis indicated that 9 out of 18 duplicated pairs in maize experienced positive selection, while SPL gene pairs of rice and sorghum mainly evolved under purifying selection, suggesting novel evolutionary features for ZmSPLs. The 31 ZmSPLs were further analyzed by describing their gene structure, phylogenetic relationships, chromosomal location, and expression, Among the ZmSPLs, 13 were predicated to be targeted by miR156s and involved in drought stress response. These results provide the foundation for future functional analyses of ZmSPLs.

SUBMITTER: Peng X

PROVIDER: S-EPMC6726161 | biostudies-literature | 2019 Apr-Jun

REPOSITORIES: biostudies-literature

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Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize.

Peng Xiaojian X Wang Qianqian Q Zhao Yang Y Li Xiaoyu X Ma Qing Q Ma Qing Q

Genetics and molecular biology 20190401 2

SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Systematic analysis of the SPL family has been performed in numerous plants, such as Arabidopsis, rice, and Populus. However, no comparative analysis has been performed across different species to examine evolutionary features. In this study, we present a comparative analysis of SPLs in different species. The results showed that 84 SPLs of the four species can be divided into six g ...[more]

PMID: 31271590

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Project description:BACKGROUND: PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. RESULTS: The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. CONCLUSION: PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out to dissect the PHB gene function. The conserved gene evolution indicated that the study in the model species can be translated to human and mammalian studies.

Project description:BackgroundsPomegranate is an excellent tree species with nutritional, medicinal, ornamental and ecological values. Studies have confirmed that SPL factors play an important role in floral transition and flower development.ResultsUsed bioinformatics methods, 15 SPL (SQUAMOSA promoter-binding protein-like) genes were identified and analyzed from the 'Taishanhong' pomegranate (P. granatum L.) genome. Phylogenetic analysis showed that PgSPLs were divided into six subfamilies (G1 ~ G6). PgSPL promoter sequences contained multiple cis-acting elements associated with abiotic stress or hormonal response. Based on the transcriptome data, expression profiles of different tissues and different developmental stages showed that PgSPL genes had distinct temporal and spatial expression characteristics. The expression analysis of miR156 in small RNA sequencing results showed that miR156 negatively regulated the expression of target genes. qRT-PCR analysis showed that the expression levels of PgSPL2, PgSPL3, PgSPL6, PgSPL11 and PgSPL14 in leaves were significantly higher than those in buds and stems (p < 0.05). The expression levels of PgSPL5, PgSPL12 and PgSPL13 in flower buds were significantly higher than that in leaves and stems (p < 0.05). The full-length of coding sequence of PgSPL5 and PgSPL13 were obtained by homologous cloning technology. The full length of PgSPL5 is 1020 bp, and PgSPL13 is 489 bp, which encodes 339 and 162 amino acids, respectively. Further investigation revealed that PgSPL5 and PgSPL13 proteins were located in the nucleus. Exogenous plant growth regulator induction experiments showed that PgSPL5 was up-regulated in leaves and stems. PgSPL13 was up-regulated in leaves and down-regulated in stems. When sprayed with 6-BA, IBA and PP333 respectively, PgSPL5 and PgSPL13 were up-regulated most significantly at P2 (bud vertical diameter was 5.1 ~ 12.0 mm) stage of bisexual and functional male flowers.ConclusionsOur findings suggested that PgSPL2, PgSPL3, PgSPL6, PgSPL11 and PgSPL14 played roles in leaves development of pomegranate. PgSPL5, PgSPL12 and PgSPL13 played roles in pomegranate flower development. PgSPL5 and PgSPL13 were involved in the response process of different plant hormone signal transduction in pomegranate development. This study provided a robust basis for further functional analyses of SPL genes in pomegranate.

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Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize.

Publications

Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize.

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