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De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification.

Long Y, Zhang J, Tian X, Wu S, Zhang Q, Zhang J, Dang Z, Pei XW - BMC Genomics (2014)

Bottom Line: We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response.Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members.These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing 100081, China. 13669338239@163.com.

ABSTRACT

Background: Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants.

Results: Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length = 728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10-5. In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members.

Conclusions: Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.

No MeSH data available.


Pathway assignment based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. (A) Classification based on cellular process categories, (B) classification based on environmental information processing categories, (C) classification based on genetic information processing categories, (D) classification based on metabolism categories, and (E) classification based on organismal systems categories.
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Fig2: Pathway assignment based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. (A) Classification based on cellular process categories, (B) classification based on environmental information processing categories, (C) classification based on genetic information processing categories, (D) classification based on metabolism categories, and (E) classification based on organismal systems categories.

Mentions: The Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway database is a knowledge base for the systematic analysis of gene functions in terms of networks of genes and molecules in cells and their variants specific to particular organisms. To further analyse the transcriptome of H. ammodendron, all the unigenes were analysed with respect to the KEGG pathway database. Out of the 79,918 identified unigenes, 11,155 (13.96%) with significant matches in the database were assigned to 5 main categories that included 265 KEGG pathways (Figure 2, Additional file 3). Among the 5 main categories that were identified, metabolism was the category with the greatest number of unigenes (5,326, 47.75%), followed by genetic information (2,044, 18.39%), organismal systems (1,781, 16.02%), cellular processes (1022, 9.19%) and environmental information processing (982, 8.83%). These results indicate that active metabolic processes were occurring in the drought treatment condition. As shown in Additional file 3, the KEGG metabolism category contained 12 sub-categories, including carbohydrate metabolism, nucleotide metabolism, biosynthesis involved in secondary metabolism, amino acid metabolism, lipid metabolism, and energy metabolism, among others.Figure 2


De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification.

Long Y, Zhang J, Tian X, Wu S, Zhang Q, Zhang J, Dang Z, Pei XW - BMC Genomics (2014)

Pathway assignment based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. (A) Classification based on cellular process categories, (B) classification based on environmental information processing categories, (C) classification based on genetic information processing categories, (D) classification based on metabolism categories, and (E) classification based on organismal systems categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4377846&req=5

Fig2: Pathway assignment based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. (A) Classification based on cellular process categories, (B) classification based on environmental information processing categories, (C) classification based on genetic information processing categories, (D) classification based on metabolism categories, and (E) classification based on organismal systems categories.
Mentions: The Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway database is a knowledge base for the systematic analysis of gene functions in terms of networks of genes and molecules in cells and their variants specific to particular organisms. To further analyse the transcriptome of H. ammodendron, all the unigenes were analysed with respect to the KEGG pathway database. Out of the 79,918 identified unigenes, 11,155 (13.96%) with significant matches in the database were assigned to 5 main categories that included 265 KEGG pathways (Figure 2, Additional file 3). Among the 5 main categories that were identified, metabolism was the category with the greatest number of unigenes (5,326, 47.75%), followed by genetic information (2,044, 18.39%), organismal systems (1,781, 16.02%), cellular processes (1022, 9.19%) and environmental information processing (982, 8.83%). These results indicate that active metabolic processes were occurring in the drought treatment condition. As shown in Additional file 3, the KEGG metabolism category contained 12 sub-categories, including carbohydrate metabolism, nucleotide metabolism, biosynthesis involved in secondary metabolism, amino acid metabolism, lipid metabolism, and energy metabolism, among others.Figure 2

Bottom Line: We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response.Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members.These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing 100081, China. 13669338239@163.com.

ABSTRACT

Background: Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants.

Results: Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length = 728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10-5. In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members.

Conclusions: Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.

No MeSH data available.