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Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones.

Yang Y, Yang S, Li J, Deng Y, Zhang Z, Xu S, Guo W, Zhong C, Zhou R, Shi S - BMC Genomics (2015)

Bottom Line: The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments.A total of 99 genes in A. ilicifolius were identified with signals of positive selection.These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China. yangyuchensysu@gmail.com.

ABSTRACT

Background: Acanthus is a unique genus consisting of both true mangrove and terrestrial species; thus, it represents an ideal system for studying the origin and adaptive evolution of mangrove plants to intertidal environments. However, little is known regarding the two respects of mangrove species in Acanthus. In this study, we sequenced the transcriptomes of the pooled roots and leaves tissues for a mangrove species, Acanthus ilicifolius, and its terrestrial congener, A. leucostachyus, to illustrate the origin of the mangrove species in this genus and their adaptive evolution to harsh habitats.

Results: We obtained 73,039 and 69,580 contigs with N50 values of 741 and 1557 bp for A. ilicifolius and A. leucostachyus, respectively. Phylogenetic analyses based on four nuclear segments and three chloroplast fragments revealed that mangroves and terrestrial species in Acanthus fell into different clades, indicating a single origin of the mangrove species in Acanthus. Based on 6634 orthologs, A. ilicifolius and A. leucostachyus were found to be highly divergent, with a peak of synonymous substitution rate (Ks) distribution of 0.145 and an estimated divergence time of approximately 16.8 million years ago (MYA). The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments. Gene ontology (GO) classifications of the full transcriptomes did not show any apparent differences between A. ilicifolius and A. leucostachyus, suggesting the absence of gene components specific to the mangrove transcriptomes. A total of 99 genes in A. ilicifolius were identified with signals of positive selection. Twenty-three of the 99 positively selected genes (PSGs) were found to be involved in salt, heat and ultraviolet stress tolerance, seed germination and embryo development under periodic inundation. These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus.

Conclusions: We characterized the transcriptomes of one mangrove species of Acanthus, A. ilicifolius, and its terrestrial relative, A. leucostachyus, and provided insights into the origin of the mangrove Acanthus species and their adaptive evolution to abiotic stresses in intertidal environments.

No MeSH data available.


Related in: MedlinePlus

Gene Ontology (GO) distributions for Acanthus ilicifolius (red) and A. leucostachyus (blue). Annotation results were mapped to categories in the second level of GO terms, respectively. GO terms that contain less than 1 % of total genes were excluded from this graph. *, p-value <0.05. **, p-value < 0.01
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Fig3: Gene Ontology (GO) distributions for Acanthus ilicifolius (red) and A. leucostachyus (blue). Annotation results were mapped to categories in the second level of GO terms, respectively. GO terms that contain less than 1 % of total genes were excluded from this graph. *, p-value <0.05. **, p-value < 0.01

Mentions: To access the GO classification for each gene, the full transcriptome sequences of A. ilicifolius and A. leucostachyus were annotated with the Swiss-Prot database in AgBase [17] with a cutoff e-value of 1e-6. A total of 29,244 (40.04 %) and 25,864 (37.2 %) genes, respectively, were successfully annotated with known GO terms. The GO distributions for the two species are shown in Fig. 3. In general, the GO classifications did not show significant differences between the transcriptome profiles of A. ilicifolius and A. leucostachyus. In the cellular component category, cell and organelle component-related functions were predominant. A total of 26,335 (90.1 %) and 23,206 (89.7 %) genes were assigned to cell and 26,335 (90.1 %) and 23,206 (89.7 %) to cell part for the two species, respectively. There were 21,979 and 11,797 genes in A. ilicifolius and 19,394 and 10,450 genes in A. leucostachyus annotated with organelle and organelle part. In molecular function category, binding and catalytic activity were the most enriched, comprising 16,896 (57.8 %) and 13,629 (46.6 %) genes in A. ilicifolius and 15,054 (58.2 %) and 11,904 (46.0 %) genes in A. leucostachyus, respectively. In the last category, biological process, 26,064 (89.1 %), 23,574 (80.6 %) and 17,676 (60.4 %) genes were annotated to three major GO terms in A. ilicifolius, including cellular and metabolic process and biological regulation, while 22,999 (88.9 %), 20,745 (80.2 %) and 15,475 (59.8 %) genes were assigned to these three terms in A. leucostachyus. It should be noted that 17,694 (60.5 %) and 15,461 (59.8 %) genes were assigned to the GO term response to stimulus, which also comprised a large proportion of the biological process category for both species. These results indicate that functions with enriched annotation may be quite fundamental and essential for plants.Fig. 3


Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones.

Yang Y, Yang S, Li J, Deng Y, Zhang Z, Xu S, Guo W, Zhong C, Zhou R, Shi S - BMC Genomics (2015)

Gene Ontology (GO) distributions for Acanthus ilicifolius (red) and A. leucostachyus (blue). Annotation results were mapped to categories in the second level of GO terms, respectively. GO terms that contain less than 1 % of total genes were excluded from this graph. *, p-value <0.05. **, p-value < 0.01
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4536770&req=5

Fig3: Gene Ontology (GO) distributions for Acanthus ilicifolius (red) and A. leucostachyus (blue). Annotation results were mapped to categories in the second level of GO terms, respectively. GO terms that contain less than 1 % of total genes were excluded from this graph. *, p-value <0.05. **, p-value < 0.01
Mentions: To access the GO classification for each gene, the full transcriptome sequences of A. ilicifolius and A. leucostachyus were annotated with the Swiss-Prot database in AgBase [17] with a cutoff e-value of 1e-6. A total of 29,244 (40.04 %) and 25,864 (37.2 %) genes, respectively, were successfully annotated with known GO terms. The GO distributions for the two species are shown in Fig. 3. In general, the GO classifications did not show significant differences between the transcriptome profiles of A. ilicifolius and A. leucostachyus. In the cellular component category, cell and organelle component-related functions were predominant. A total of 26,335 (90.1 %) and 23,206 (89.7 %) genes were assigned to cell and 26,335 (90.1 %) and 23,206 (89.7 %) to cell part for the two species, respectively. There were 21,979 and 11,797 genes in A. ilicifolius and 19,394 and 10,450 genes in A. leucostachyus annotated with organelle and organelle part. In molecular function category, binding and catalytic activity were the most enriched, comprising 16,896 (57.8 %) and 13,629 (46.6 %) genes in A. ilicifolius and 15,054 (58.2 %) and 11,904 (46.0 %) genes in A. leucostachyus, respectively. In the last category, biological process, 26,064 (89.1 %), 23,574 (80.6 %) and 17,676 (60.4 %) genes were annotated to three major GO terms in A. ilicifolius, including cellular and metabolic process and biological regulation, while 22,999 (88.9 %), 20,745 (80.2 %) and 15,475 (59.8 %) genes were assigned to these three terms in A. leucostachyus. It should be noted that 17,694 (60.5 %) and 15,461 (59.8 %) genes were assigned to the GO term response to stimulus, which also comprised a large proportion of the biological process category for both species. These results indicate that functions with enriched annotation may be quite fundamental and essential for plants.Fig. 3

Bottom Line: The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments.A total of 99 genes in A. ilicifolius were identified with signals of positive selection.These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China. yangyuchensysu@gmail.com.

ABSTRACT

Background: Acanthus is a unique genus consisting of both true mangrove and terrestrial species; thus, it represents an ideal system for studying the origin and adaptive evolution of mangrove plants to intertidal environments. However, little is known regarding the two respects of mangrove species in Acanthus. In this study, we sequenced the transcriptomes of the pooled roots and leaves tissues for a mangrove species, Acanthus ilicifolius, and its terrestrial congener, A. leucostachyus, to illustrate the origin of the mangrove species in this genus and their adaptive evolution to harsh habitats.

Results: We obtained 73,039 and 69,580 contigs with N50 values of 741 and 1557 bp for A. ilicifolius and A. leucostachyus, respectively. Phylogenetic analyses based on four nuclear segments and three chloroplast fragments revealed that mangroves and terrestrial species in Acanthus fell into different clades, indicating a single origin of the mangrove species in Acanthus. Based on 6634 orthologs, A. ilicifolius and A. leucostachyus were found to be highly divergent, with a peak of synonymous substitution rate (Ks) distribution of 0.145 and an estimated divergence time of approximately 16.8 million years ago (MYA). The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments. Gene ontology (GO) classifications of the full transcriptomes did not show any apparent differences between A. ilicifolius and A. leucostachyus, suggesting the absence of gene components specific to the mangrove transcriptomes. A total of 99 genes in A. ilicifolius were identified with signals of positive selection. Twenty-three of the 99 positively selected genes (PSGs) were found to be involved in salt, heat and ultraviolet stress tolerance, seed germination and embryo development under periodic inundation. These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus.

Conclusions: We characterized the transcriptomes of one mangrove species of Acanthus, A. ilicifolius, and its terrestrial relative, A. leucostachyus, and provided insights into the origin of the mangrove Acanthus species and their adaptive evolution to abiotic stresses in intertidal environments.

No MeSH data available.


Related in: MedlinePlus