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RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album.

Zhang X, Berkowitz O, Teixeira da Silva JA, Zhang M, Ma G, Whelan J, Duan J - Front Plant Sci (2015)

Bottom Line: Our results suggest that genes encoding nodulin-like proteins may be important for haustorial morphogenesis in S. album.The obtained sequence data will become a rich resource for future research in this interesting species.This information improves our understanding of haustorium development in root hemiparasitic species and will allow further exploration of the detailed molecular mechanisms underlying plant parasitism.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China.

ABSTRACT
Santalum album (sandalwood) is one of the economically important plant species in the Santalaceae for its production of highly valued perfume oils. Sandalwood is also a hemiparasitic tree that obtains some of its water and simple nutrients by tapping into other plants through haustoria which are highly specialized organs in parasitic angiosperms. However, an understanding of the molecular mechanisms involved in haustorium development is limited. In this study, RNA sequencing (RNA-seq) analyses were performed to identify changes in gene expression and metabolic pathways associated with the development of the S. album haustorium. A total of 56,011 non-redundant contigs with a mean contig size of 618 bp were obtained by de novo assembly of the transcriptome of haustoria and non-haustorial seedling roots. A substantial number of the identified differentially expressed genes were involved in cell wall metabolism and protein metabolism, as well as mitochondrial electron transport functions. Phytohormone-mediated regulation might play an important role during haustorial development. Especially, auxin signaling is likely to be essential for haustorial initiation, and genes related to cytokinin and gibberellin biosynthesis and metabolism are involved in haustorial development. Our results suggest that genes encoding nodulin-like proteins may be important for haustorial morphogenesis in S. album. The obtained sequence data will become a rich resource for future research in this interesting species. This information improves our understanding of haustorium development in root hemiparasitic species and will allow further exploration of the detailed molecular mechanisms underlying plant parasitism.

No MeSH data available.


Gene ontology analyses of all contigs. SaGI01 contigs were assigned to GO slim terms for biological processes (A), molecular functions (B), and cellular components (C). Numbers indicate percentages of each GO slim term within main ontologies.
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Figure 1: Gene ontology analyses of all contigs. SaGI01 contigs were assigned to GO slim terms for biological processes (A), molecular functions (B), and cellular components (C). Numbers indicate percentages of each GO slim term within main ontologies.

Mentions: For functional annotation of the contigs, a BlastX search was performed against the NCBI non-redundant protein (Nr) database with a cut-off E < 10−15. Of the 56,011 contigs, 26,626 sequences were annotated as homologs of known proteins. Furthermore, the S. album contigs were compared with the genomes of Vitis vinifera, Populus trichocarpa, and Arabidopsis thaliana. About 54, 53, and 49% of the S. album contigs showed a homology hit with genes in these three species, respectively (data not shown). Based on this annotation, the S. album contigs were classified into 98 GO slim terms (Figures 1A–C). Classification into cellular component proteins and cell proteins dominated the cellular component category, accounting for about 17 and 14% of the contigs, respectively. The molecular function category was classified into two main groups: binding proteins and enzyme activity proteins. Of these, binding (17.1%), protein binding (10.1%), nucleotide binding (9.2%), transferase activity (11.4%), catalytic activity (10.9%), and hydrolase activity (10.0%) were the most prominent. In the biological process category, 48.9% of contigs were classified into three categories: biological, cellular, and metabolic processes.


RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album.

Zhang X, Berkowitz O, Teixeira da Silva JA, Zhang M, Ma G, Whelan J, Duan J - Front Plant Sci (2015)

Gene ontology analyses of all contigs. SaGI01 contigs were assigned to GO slim terms for biological processes (A), molecular functions (B), and cellular components (C). Numbers indicate percentages of each GO slim term within main ontologies.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555033&req=5

Figure 1: Gene ontology analyses of all contigs. SaGI01 contigs were assigned to GO slim terms for biological processes (A), molecular functions (B), and cellular components (C). Numbers indicate percentages of each GO slim term within main ontologies.
Mentions: For functional annotation of the contigs, a BlastX search was performed against the NCBI non-redundant protein (Nr) database with a cut-off E < 10−15. Of the 56,011 contigs, 26,626 sequences were annotated as homologs of known proteins. Furthermore, the S. album contigs were compared with the genomes of Vitis vinifera, Populus trichocarpa, and Arabidopsis thaliana. About 54, 53, and 49% of the S. album contigs showed a homology hit with genes in these three species, respectively (data not shown). Based on this annotation, the S. album contigs were classified into 98 GO slim terms (Figures 1A–C). Classification into cellular component proteins and cell proteins dominated the cellular component category, accounting for about 17 and 14% of the contigs, respectively. The molecular function category was classified into two main groups: binding proteins and enzyme activity proteins. Of these, binding (17.1%), protein binding (10.1%), nucleotide binding (9.2%), transferase activity (11.4%), catalytic activity (10.9%), and hydrolase activity (10.0%) were the most prominent. In the biological process category, 48.9% of contigs were classified into three categories: biological, cellular, and metabolic processes.

Bottom Line: Our results suggest that genes encoding nodulin-like proteins may be important for haustorial morphogenesis in S. album.The obtained sequence data will become a rich resource for future research in this interesting species.This information improves our understanding of haustorium development in root hemiparasitic species and will allow further exploration of the detailed molecular mechanisms underlying plant parasitism.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China.

ABSTRACT
Santalum album (sandalwood) is one of the economically important plant species in the Santalaceae for its production of highly valued perfume oils. Sandalwood is also a hemiparasitic tree that obtains some of its water and simple nutrients by tapping into other plants through haustoria which are highly specialized organs in parasitic angiosperms. However, an understanding of the molecular mechanisms involved in haustorium development is limited. In this study, RNA sequencing (RNA-seq) analyses were performed to identify changes in gene expression and metabolic pathways associated with the development of the S. album haustorium. A total of 56,011 non-redundant contigs with a mean contig size of 618 bp were obtained by de novo assembly of the transcriptome of haustoria and non-haustorial seedling roots. A substantial number of the identified differentially expressed genes were involved in cell wall metabolism and protein metabolism, as well as mitochondrial electron transport functions. Phytohormone-mediated regulation might play an important role during haustorial development. Especially, auxin signaling is likely to be essential for haustorial initiation, and genes related to cytokinin and gibberellin biosynthesis and metabolism are involved in haustorial development. Our results suggest that genes encoding nodulin-like proteins may be important for haustorial morphogenesis in S. album. The obtained sequence data will become a rich resource for future research in this interesting species. This information improves our understanding of haustorium development in root hemiparasitic species and will allow further exploration of the detailed molecular mechanisms underlying plant parasitism.

No MeSH data available.