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Transcriptome analysis and gene expression profiling of abortive and developing ovules during fruit development in hazelnut.

Cheng Y, Liu J, Zhang H, Wang J, Zhao Y, Geng W - PLoS ONE (2015)

Bottom Line: The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage.These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO.A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Jilin Normal University, Siping, Jilin Province 136000, China.

ABSTRACT

Background: A high ratio of blank fruit in hazelnut (Corylus heterophylla Fisch) is a very common phenomenon that causes serious yield losses in northeast China. The development of blank fruit in the Corylus genus is known to be associated with embryo abortion. However, little is known about the molecular mechanisms responsible for embryo abortion during the nut development stage. Genomic information for C. heterophylla Fisch is not available; therefore, data related to transcriptome and gene expression profiling of developing and abortive ovules are needed.

Methodology/principal findings: In this study, de novo transcriptome sequencing and RNA-seq analysis were conducted using short-read sequencing technology (Illumina HiSeq 2000). The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage. Two digital gene expression libraries were constructed, one for a full (normally developing) ovule and one for an empty (abortive) ovule. Transcriptome sequencing and assembly results revealed 55,353 unigenes, including 18,751 clusters and 36,602 singletons. These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO. Using digital gene expression profiling, gene expression differences in developing and abortive ovules were identified. A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules. Quantitative real-time polymerase chain reaction analysis was used in order to verify the differential expression of some genes.

Conclusions/significance: The transcriptome and digital gene expression profiling data of normally developing and abortive ovules in hazelnut provide exhaustive information that will improve our understanding of the molecular mechanisms of abortive ovule formation in hazelnut.

No MeSH data available.


Unigene size distribution.All of the unigene sizes were calculated.
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pone.0122072.g001: Unigene size distribution.All of the unigene sizes were calculated.

Mentions: A total of 54,000,000 raw reads were generated after Illumina sequencing analysis. Reads with adaptors, unknown nucleotides larger than 5%, and low-quality reads with more than 20% low-quality bases (base quality ≤ 10) were removed. A total of 48,585,250 clean reads with 4,372,672,500 nucleotides (nt) was obtained with a Q20 percentage of 98.17%. The final sequence assembly results using Trinity [9] was 55,353 unigenes, including 18,751 clusters and 36,602 singletons, with a mean length of 844 nt. The unigene size distribution is shown in Fig 1, which indicates that unigenes shorter than 2000 nt accounted for 91.45% of the total unigenes.


Transcriptome analysis and gene expression profiling of abortive and developing ovules during fruit development in hazelnut.

Cheng Y, Liu J, Zhang H, Wang J, Zhao Y, Geng W - PLoS ONE (2015)

Unigene size distribution.All of the unigene sizes were calculated.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383543&req=5

pone.0122072.g001: Unigene size distribution.All of the unigene sizes were calculated.
Mentions: A total of 54,000,000 raw reads were generated after Illumina sequencing analysis. Reads with adaptors, unknown nucleotides larger than 5%, and low-quality reads with more than 20% low-quality bases (base quality ≤ 10) were removed. A total of 48,585,250 clean reads with 4,372,672,500 nucleotides (nt) was obtained with a Q20 percentage of 98.17%. The final sequence assembly results using Trinity [9] was 55,353 unigenes, including 18,751 clusters and 36,602 singletons, with a mean length of 844 nt. The unigene size distribution is shown in Fig 1, which indicates that unigenes shorter than 2000 nt accounted for 91.45% of the total unigenes.

Bottom Line: The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage.These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO.A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Jilin Normal University, Siping, Jilin Province 136000, China.

ABSTRACT

Background: A high ratio of blank fruit in hazelnut (Corylus heterophylla Fisch) is a very common phenomenon that causes serious yield losses in northeast China. The development of blank fruit in the Corylus genus is known to be associated with embryo abortion. However, little is known about the molecular mechanisms responsible for embryo abortion during the nut development stage. Genomic information for C. heterophylla Fisch is not available; therefore, data related to transcriptome and gene expression profiling of developing and abortive ovules are needed.

Methodology/principal findings: In this study, de novo transcriptome sequencing and RNA-seq analysis were conducted using short-read sequencing technology (Illumina HiSeq 2000). The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage. Two digital gene expression libraries were constructed, one for a full (normally developing) ovule and one for an empty (abortive) ovule. Transcriptome sequencing and assembly results revealed 55,353 unigenes, including 18,751 clusters and 36,602 singletons. These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO. Using digital gene expression profiling, gene expression differences in developing and abortive ovules were identified. A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules. Quantitative real-time polymerase chain reaction analysis was used in order to verify the differential expression of some genes.

Conclusions/significance: The transcriptome and digital gene expression profiling data of normally developing and abortive ovules in hazelnut provide exhaustive information that will improve our understanding of the molecular mechanisms of abortive ovule formation in hazelnut.

No MeSH data available.