Dataset Information

Characterization and expression of the ABC family (G group) in 'Dangshansuli' pear (Pyrus bretschneideri Rehd.) and its russet mutant.

ABSTRACT: The plant genes encoding ABCGs that have been identified to date play a role in suberin formation in response to abiotic and biotic stress. In the present study, 80 ABCG genes were identified in 'Dangshansuli' Chinese white pear and designated as PbABCGs. Based on the structural characteristics and phylogenetic analysis, the PbABCG family genes could be classified into seven main groups: classes A-G. Segmental and dispersed duplications were the primary forces underlying the PbABCG gene family expansion in 'Dangshansuli' pear. Most of the PbABCG duplicated gene pairs date to the recent whole-genome duplication that occurred 30~45 million years ago. Purifying selection has also played a critical role in the evolution of the ABCG genes. Ten PbABCG genes screened in the transcriptome of 'Dangshansuli' pear and its russet mutant 'Xiusu' were validated, and the expression levels of the PbABCG genes exhibited significant differences at different stages. The results presented here will undoubtedly be useful for better understanding of the complexity of the PbABCG gene family and will facilitate the functional characterization of suberin formation in the russet mutant.

SUBMITTER: Hou Z

PROVIDER: S-EPMC5901498 | biostudies-literature | 2018 Jan-Mar

REPOSITORIES: biostudies-literature

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Characterization and expression of the ABC family (G group) in 'Dangshansuli' pear (Pyrus bretschneideri Rehd.) and its russet mutant.

Hou Zhaoqi Z Jia Bing B Li Fei F Liu Pu P Liu Li L Ye Zhenfeng Z Zhu Liwu L Wang Qi Q Heng Wei W

Genetics and molecular biology 20180101 1

The plant genes encoding ABCGs that have been identified to date play a role in suberin formation in response to abiotic and biotic stress. In the present study, 80 ABCG genes were identified in 'Dangshansuli' Chinese white pear and designated as PbABCGs. Based on the structural characteristics and phylogenetic analysis, the PbABCG family genes could be classified into seven main groups: classes A-G. Segmental and dispersed duplications were the primary forces underlying the PbABCG gene family e ...[more]

PMID: 29658971

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Project description:BackgroundPear (Pyrus spp) is an important fruit species worldwide; however, its genetics and genomic information is limited. Combining the Solexa/Illumina RNA-seq high-throughput sequencing approach (RNA-seq) with Digital Gene Expression (DGE) analysis would be a powerful tool for transcriptomic study. This paper reports the transcriptome profiling analysis of Chinese white pear (P. bretschneideri) using RNA-seq and DGE to better understand the molecular mechanisms in fruit development and maturation of Chinese white pear.ResultsDe novo transcriptome assembly and gene expression analysis of Chinese white pear were performed in an unprecedented depth (5.47 gigabase pairs) using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system. Approximately, 60.77 million reads were sequenced, trimmed, and assembled into 90,227 unigenes. These unigenes comprised 17,619 contigs and 72,608 singletons with an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR, and COGs at NCBI, Pfam, InterPro, and KEGG) found that 61,636 unigenes can be annotated with gene descriptions, conserved protein domains, or gene ontology terms. By BLASTing all 61,636 unigenes in KEGG, a total of 31,215 unigenes were annotated into 121 known metabolic or signaling pathways in which a few primary, intermediate, and secondary metabolic pathways are directly related to pear fruit quality. DGE libraries were constructed for each of the five fruit developmental stages. Variations in gene expression among all developmental stages of pear fruit were significantly different in a large amount of unigenes.ConclusionExtensive transcriptome and DGE profiling data at five fruit developmental stages of Chinese white pear have been obtained from a deep sequencing, which provides comprehensive gene expression information at the transcriptional level. This could facilitate understanding of the molecular mechanisms in fruit development and maturation. Such a database can also be used as a public information platform for research on molecular biology and functional genomics in pear and other related species.

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Dataset Information

Characterization and expression of the ABC family (G group) in 'Dangshansuli' pear (Pyrus bretschneideri Rehd.) and its russet mutant.

Publications

Characterization and expression of the ABC family (G group) in 'Dangshansuli' pear (Pyrus bretschneideri Rehd.) and its russet mutant.

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