Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene.

Elena N Pushkova,Anna V Kudryavtseva,Artemy D Beniaminov,Roman O Novakovskiy,Nataliya V Melnikova,Liubov V Povkhova,George S Krasnov,Alexey A Dmitriev,Valentina A Lakunina,Anastasiya V Snezhkina,Maria S Fedorova,Ekaterina M Dvorianinova

doi:10.3389/fgene.2021.676935

Abstract

Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.

Highlights

In contrast to animals, hermaphroditism is common in angiosperm plants—about 90% of these species produce bisexual flowers, about 5% are monoecious and have both male and female flowers on the same individual, and only about 5% are dioecious and have male and female flowers on separate individuals (Yampolsky and Yampolsky, 1922; Renner, 2014)
We performed targeted sequencing of T-complex protein subunit gamma (TCP), CLC, and methyltransferase 1 (MET1) gene regions for DNA and cDNA (RNA extracted from leaves, catkin axes, and flowers) samples of 10 male and 10 female plants of P. × sibirica
Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of P. × sibirica and genome sequencing of the same plants were performed for the first time

Summary

Introduction

Hermaphroditism is common in angiosperm plants—about 90% of these species produce bisexual flowers, about 5% are monoecious and have both male and female flowers on the same individual, and only about 5% are dioecious and have male and female flowers on separate individuals (Yampolsky and Yampolsky, 1922; Renner, 2014). There are gynodioecious plant species (with female and hermaphroditic individuals) and androdioecious species (with male and hermaphroditic individuals) that are less common (Bawa, 1980). It is known that dioecy can emerge from hermaphroditism directly or form via gynodioecy, androdioecy, monoecy, and, in some cases, heterostyly (Bawa, 1980). Poplars are wind-pollinated trees, and different species are crossed, resulting in the emergence of natural interspecific hybrids and a high level of genetic diversity (Rae et al, 2007; Roe et al, 2014; Jiang et al, 2016)

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Conclusion