Differential evolutionary patterns and expression levels between sex-specific and somatic tissue-specific genes in peanut

Hui Song,Qingping Zhang,Zhibiao Nan,Pei Tian

doi:10.1038/s41598-017-09905-8

Abstract

The patterns of evolution and expression of tissue-specific genes are poorly understood beyond sex-specific genes. Accordingly, we identified 3,191 tissue-specific genes and 38,745 common genes using 22 RNA-seq datasets from cultivated peanut. The expression levels of tissue-specific genes were significantly lower than those of common genes. Further, the expression levels of sex-specific genes were significantly higher than those of somatic tissue-specific genes. Among sex-specific genes, the expression levels of gynoecium-specific genes were significantly higher than those of androecium-specific genes. Function-specific genes were lacking among tissue-specific genes, and tissue-specific gene annotations overlapped among different tissues. Duplicate gene pairs were classified as homogeneous pairs expressed within the same tissue or heterogeneous pairs expressed in different tissues. Heterogeneous gene pairs evolved more rapidly than homogeneous gene pairs. In addition, somatic tissue-specific genes evolved faster than sex-specific genes. Molecular signatures of selection indicated that somatic tissue-specific genes have mainly experienced relaxed selection, while sex-specific genes have been under stronger selective constraint. Somatic tissue-specific genes had higher codon usage bias than sex-specific genes. These contrasting patterns between somatic tissue-specific and sex-specific genes provide new insights into the basic biology and evolution of peanut, an important crop.

Highlights

Since the publication of the Arabidopsis thaliana genome, many genomic sequences and RNA-seq datasets of other plants have been released
We found that different evolutionary patterns and gene expression levels are observed between sex-specific and somatic tissue-specific genes based on these RNA-seq datasets
The largest number of tissue-specific genes were expressed in gynoecium tissue, while the fewest tissue-specific genes were expressed in seedling leaf tissue (Fig. 1)

Summary

Introduction

Since the publication of the Arabidopsis thaliana genome, many genomic sequences and RNA-seq datasets of other plants have been released. Female-biased genes tend to be highly expressed in specific tissues, while male-biased genes tend to be expressed at low levels in the same tissues[6, 7]. RNA-seq datasets based on cultivated peanut have examined 22 different tissues, including both sexual and somatic tissues[10]. These datasets are a powerful resource for research into the evolutionary patterns and gene expression levels exhibited in sex-specific and somatic tissue-specific genes. We found that different evolutionary patterns and gene expression levels are observed between sex-specific and somatic tissue-specific genes based on these RNA-seq datasets. Somatic tissue-specific genes experienced relaxed selection, while sex-specific genes have been subject to stronger selective constraint

Methods

Results

Conclusion