Research Article: Metacaspase gene family in Rosaceae genomes: Comparative genomic analysis and their expression during pear pollen tube and fruit development

Date Published: February 22, 2019

Publisher: Public Library of Science

Author(s): Yunpeng Cao, Dandan Meng, Tianzhe Chen, Yu Chen, Wei Zeng, Lei Zhang, Qi Wang, Wei Hen, Muhammad Abdullah, Qing Jin, Yi Lin, Yongping Cai, Muthamilarasan Mehanathan.

http://doi.org/10.1371/journal.pone.0211635

Abstract

Metacaspase (MC), which is discovered gene family with distant caspase homologs in plants, fungi, and protozoa, may be involved in programmed cell death (PCD) processes during plant development and respond abiotic and biotic stresses. To reveal the evolutionary relationship of MC gene family in Rosaceae genomes, we identified 8, 7, 8, 12, 12, and 23 MC genes in the genomes of Fragaria vesca, Prunus mume, Prunus persica, Pyrus communis, Pyrus bretschneideri and Malus domestica, respectively. Phylogenetic analysis suggested that the MC genes could be grouped into three clades: Type I*, Type I and Type II, which was supported by gene structure and conserved motif analysis. Microsynteny analysis revealed that MC genes present in the corresponding syntenic blocks of P. communis, P. bretschneideri and M. domestica, and further suggested that large-scale duplication events play an important role in the expansion of MC gene family members in these three genomes than other Rosaceae plants (F. vesca, P. mume and P. persica). RNA-seq data showed the specific expression patterns of PbMC genes in response to drought stress. The expression analysis of MC genes demonstrated that PbMC01 and PbMC03 were able to be detected in all four pear pollen tubes and seven fruit development stages. The current study highlighted the evolutionary relationship and duplication of the MC gene family in these six Rosaceae genomes and provided appropriate candidate genes for further studies in P. bretschneideri.

Partial Text

Programmed cell death (PCD) is a developmental and genetically controlled cell death process, which is divided into two broad categories: environmentally induced PCD and developmentally regulated PCD in plants [1–4]. Environmentally induced PCD is primarily caused by external abiotic or biotic signals, such as drought, hormone, heat shock and pathogens stresses [5–8]. In contrast, developmentally regulated PCD covers most of the organs and tissues of plants, such as fruit, root, stem, leave and xylem, which caused by internal factors and occurs at predictable locations and times [9–11].

In recent studies, the vast majority of published articles suggested that the MC genes exist as multi-gene families in the genome [2, 18, 19]. Although the number of MC gene family have been investigated in several species [18–23], such as Arabidopsis thaliana, Vitis vinifera, Hevea brasiliensis and Oryza sativa. However, the MC genes from Rosaceae genomes have not been characterized in detail to our knowledge. In the present study, 70 MC genes were identified in six Rosaceae genomes; 12 of these sequences were from P. bretschneideri, and 8, 7, 8, 12, and 23 MC genes in F. vesca, P. mume, P. persica, P. communis and M. domestica, respectively. By using the MEROPS online tool (https://www.ebi.ac.uk/merops/) [2], we predicted the distribution of Type-I* (8), Type-I (42) and Type-II (20) MC genes in these genomes, which consistent with the predictions of phylogenetic analysis of these MC gene family numbers. Using a comparative genomic approach, Fagundes et al. (2015) identified MC genes in Viridiplantae, and then the distribution of Type-I and -II MC genes was predicted in 42 plant species [1]. They found that the total number of Type-I MC genes was more than twice the number of Type-II MC genes [1], which is basically consistent with our results. The diversity of gene structure not only provides additional evidence for supporting phylogenetic groupings, but it also plays an important role in the evolution of gene families [58]. Exon-intron structure analysis suggested that the most of Type I MC genes contained four or five exons and Type II MC genes had two or three exons. We also noted that the lengths of the exons were more conserved than the introns in Type I MC genes (Fig 2). Our data was consistent with the previous published articles that Type I MC genes contained more exon numbers than Type II MC genes [1, 22]. Additionally, the identification and phylogenetic classification of MC genes were further supported by the exon-intron structure analysis in Rosaceae genomes.

In the present study, 70 MC genes were identified in Rosaceae genomes, which including 8, 7, 8, 12, 12, and 23 MC genes in the genomes of F. vesca, P. mume, P. persica, P. communis, P. bretschneideri and M. domestica, respectively. Subsequently, we carried out comparative genomic and systematic analysis, such as phylogenetic relationships, exon-intron structures, microsynteny, conserved motifs, and expression patterns. Our results suggested the vast majority of MC gene of P. communis, P. bretschneideri and M. domestica was expanded by large-scale gene duplication. Expression profiling revealed that PbMC01 and PbMC03 were able to be detected in all four pear pollen tube and seven fruit development stages. This understanding of MC expression provides a new avenue for functional analyses of pear during pollen tube and fruit development.

 

Source:

http://doi.org/10.1371/journal.pone.0211635

 

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