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Open Access Research article

Identification of genes specifically or preferentially expressed in maize silk reveals similarity and diversity in transcript abundance of different dry stigmas

Xiao Hui Xu1, Hao Chen1, Ya Lin Sang12, Fang Wang1, Jun Ping Ma1, Xin-Qi Gao1 and Xian Sheng Zhang1*

Author Affiliations

1 State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China

2 College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China

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BMC Genomics 2012, 13:294  doi:10.1186/1471-2164-13-294

Published: 2 July 2012

Additional files

Additional file 1:

Assessment of the raw sequencing results of MS, MP, MO and SL libraries. A, Sequencing quality evaluation. Raw reads were classified into four different kinds of reads as adaptor only, N-containing, low quality and clean reads. The first three kinds of reads were removed, and only clean reads were used for further analysis; B, Sequencing saturation analysis. In the beginning of the sequencing, with the number of reads increasing, the number of detected genes is increasing. However, when the number of reads reaches certain value, the growth rate of detected genes flattens, indicating that the number of detected genes tends to saturation; C, Distribution of reads on reference genes. Since reference genes have various lengths, the reads per location on a gene is standardized to a relative position, and the number of reads in each position is counted. If the reads in every position is evenly distributed, the randomness is good.

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Additional file 2:

Distribution of the experimental tags sequenced in reference maize genome and gene database from the four libraries. 1a, summary of tag-to-genome mapping data; 1b, summary of tag-to-gene mapping data.

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Additional file 3:

Distribution of reads on maize inbred line B73 genome. The distribution of genes and mapped reads on each chromosome were shown in three pictures (green, red and blue). In Gene Number picture (blue), every window (total 500 windows) contains the number of genes on the corresponding nucleotide region (the number in the round bracket). “Coverage” means the ratio of length reads covered in the length of every window. “Log2Reads Number” means the binary logarithm of the average sequencing depth of every window.

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Additional file 4:

Genes expressed in MS, MP, MO and SL. Locus, Locus identifier in AGPv2 5b filtered gene set transcripts database (Maize Genome Sequence Project, 2011); Uniq_reads_num, the number of reads that uniquely mapped to genes; Coverage, the percentage of a gene covered by reads; RPKM, gene expression; Annotation, the annotations were derived from AGPv2 annotation database directly.

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Additional file 5:

Pearson Correlation Coefficient (PCC) analysis of four studied tissues.

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Additional file 6:

Cross-comparison analysis of genes expressed in MS, MP, MO and SL results by PAGE. All genes expressed in at least one of the four tissues were analyzed by PAGE, and the comparison result is displayed in HTML table mode. Accompanied by the color in the block changed from gray to red, gene expression level increased. The FDR value of each term determines the degree of color saturation of the corresponding box.

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Additional file 7:

A list of real-time PCR primers used in this study.

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Additional file 8:

Stigma specifically/preferentially expressed genes in maize, rice and Arabidopsis. Rice and Arabidopsis stigma specifically/preferentially expressed genes were derived directly from the previous studies [12,13]. Gene category of maize, rice and Arabidopsis stigma-specific/preferential genes were based on MapMan annotation.

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Additional file 9:

Subcellular localization prediction of MS-specific/preferential genes and the longest transcripts of all filtered genes in maize AGPv2 5b.

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Additional file 10:

Distribution of cysteine-rich proteins in maize, rice and Arabidopsis stigma-specific/preferential datasets.

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Additional file 11:

Sequence comparison among maize, rice and Arabidopsis stigma-specific/preferential datasets. A, 471 maize silk specifically/preferentially expressed genes hit 213 rice stigma specific/preferential genes; B, 140 maize silk specifically/preferentially expressed genes hit 37 Arabidopsis stigma-specific/preferential genes; C, 221 rice stigma specifically/preferentially expressed genes hit 179 maize silk-specific/preferential genes; D, 53 Arabidopsis stigma specifically/preferentially expressed genes hit 48 maize silk-specific/preferential expressed genes.

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Additional file 12:

Distribution of the homologs of maize silk specifically/preferentially expressed genes. A, Common genes in the three species; B, Maize silk-specific/preferential genes that can only hit rice stigma-specific/preferential dataset; C, Distinct stigma-specific/preferential genes that only expressed in maize silk.

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Additional file 13:

Comparative analysis of maize transcriptomic data between inbred lines Zheng58 and B73.

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Additional file 14:

Mature pollen grains germinate well in liquid medium.

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