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Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance

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ABSTRACT

Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca2+) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance.

No MeSH data available.


Unigenes Kyoto Encyclopedia of Genes and Genomes (KEGG) of divergent orthologous genes.
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Figure 4: Unigenes Kyoto Encyclopedia of Genes and Genomes (KEGG) of divergent orthologous genes.

Mentions: After using the branch-site model and likelihood ratio test, 18 divergent orthologous genes, 57 conserved orthologous genes and 331 none (neutral) orthologous genes were identified (Figure 3). The annotation results of divergent orthologous genes indicated that there were two 28S ribosomal RNA genes, two calmodulins, two histidine kinases, two nuclear transcription factor Y genes, and two WRKY transcription factors, and the other orthologous genes were apolipoprotein, calcipressin, cysteine proteinase inhibitor, F-actin capping protein, proteasome, receptor-like protein kinase, RNA polymerase C-terminal repeat and vacuolar-sorting receptor (Table 2). KEGG pathway enrichment indicated that only three genes were significantly enriched in the KEGG pathway, including plant-pathogen interaction, plant hormone signal transduction and mRNA surveillance pathway (Figure 4), implying that these pathways may evolve under heavy metal stress.


Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance
Unigenes Kyoto Encyclopedia of Genes and Genomes (KEGG) of divergent orthologous genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383727&req=5

Figure 4: Unigenes Kyoto Encyclopedia of Genes and Genomes (KEGG) of divergent orthologous genes.
Mentions: After using the branch-site model and likelihood ratio test, 18 divergent orthologous genes, 57 conserved orthologous genes and 331 none (neutral) orthologous genes were identified (Figure 3). The annotation results of divergent orthologous genes indicated that there were two 28S ribosomal RNA genes, two calmodulins, two histidine kinases, two nuclear transcription factor Y genes, and two WRKY transcription factors, and the other orthologous genes were apolipoprotein, calcipressin, cysteine proteinase inhibitor, F-actin capping protein, proteasome, receptor-like protein kinase, RNA polymerase C-terminal repeat and vacuolar-sorting receptor (Table 2). KEGG pathway enrichment indicated that only three genes were significantly enriched in the KEGG pathway, including plant-pathogen interaction, plant hormone signal transduction and mRNA surveillance pathway (Figure 4), implying that these pathways may evolve under heavy metal stress.

View Article: PubMed Central - PubMed

ABSTRACT

Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca2+) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance.

No MeSH data available.