Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

BACKGROUND: Red maple (Acer rubrum L.) is one of the most common and widespread trees with colorful leaves. We found a mutant with red, yellow, and green leaf phenotypes in different branches, which provided ideal materials with the same genetic relationship, and little interference from the environment, for the study of complex metabolic networks that underly variations in the coloration of leaves. We applied a combination of NGS and SMRT sequencing to various red maple tissues. RESULTS: A total of 125,448 unigenes were obtained, of which 46 and 69 were thought to be related to the synthesis of anthocyanins and carotenoids, respectively. In addition, 88 unigenes were presumed to be involved in the chlorophyll metabolic pathway. Based on a comprehensive analysis of the pigment gene expression network, the mechanisms of leaf color were investigated. The massive accumulation of Cy led to its higher content and proportion than other pigments, which caused the redness of leaves. Yellow coloration was the result of the complete decomposition of chlorophyll pigments, the unmasking of carotenoid pigments, and a slight accumulation of Cy. CONCLUSIONS: This study provides a systematic analysis of color variations in the red maple. Moreover, mass sequence data obtained by deep sequencing will provide references for the controlled breeding of red maple. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1850-7) contains supplementary material, which is available to authorized users.