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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.


Genes’ coverage distribution of empty and full ovules in hazelnut.The numbers preceding the parentheses indicate the percentage of unique reads in each category, and the data in parentheses indicate the number of unique reads.
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pone.0122072.g004: Genes’ coverage distribution of empty and full ovules in hazelnut.The numbers preceding the parentheses indicate the percentage of unique reads in each category, and the data in parentheses indicate the number of unique reads.

Mentions: In total, 45,641 unigenes in the empty library and 44,863 unigenes in the full library were mapped to our transcriptome reference database. The average length of mapped unigenes was about 800 bp, and their average coverage was about 55% (Table 2). The gene expression level was calculated using the RPKM method [16]. The RPKM method eliminates the influence of different gene lengths and sequencing discrepancies on the calculation of gene expression level. The calculated values of the gene expression level may be directly used to compare the differences in gene expression among samples. The reads per kb per million reads of mapped unigenes was about 19 (Table 2). Detailed information about unigenes in the empty and full libraries that could be mapped to our transcriptome reference database is listed in S5 and S6 Tables, respectively. Coverage represents the percentage of a gene covered by reads, and the genes’ distribution coverage of the empty and full libraries is shown in Fig 4.


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)

Genes’ coverage distribution of empty and full ovules in hazelnut.The numbers preceding the parentheses indicate the percentage of unique reads in each category, and the data in parentheses indicate the number of unique reads.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0122072.g004: Genes’ coverage distribution of empty and full ovules in hazelnut.The numbers preceding the parentheses indicate the percentage of unique reads in each category, and the data in parentheses indicate the number of unique reads.
Mentions: In total, 45,641 unigenes in the empty library and 44,863 unigenes in the full library were mapped to our transcriptome reference database. The average length of mapped unigenes was about 800 bp, and their average coverage was about 55% (Table 2). The gene expression level was calculated using the RPKM method [16]. The RPKM method eliminates the influence of different gene lengths and sequencing discrepancies on the calculation of gene expression level. The calculated values of the gene expression level may be directly used to compare the differences in gene expression among samples. The reads per kb per million reads of mapped unigenes was about 19 (Table 2). Detailed information about unigenes in the empty and full libraries that could be mapped to our transcriptome reference database is listed in S5 and S6 Tables, respectively. Coverage represents the percentage of a gene covered by reads, and the genes’ distribution coverage of the empty and full libraries is shown in Fig 4.

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.