Identification of new marker genes from plant single-cell RNA-seq data using interpretable machine learning methods.

An essential step in the analysis of single-cell RNA sequencing data is to classify cells into specific cell types using marker genes. In this study, we have developed a machine learning pipeline called single-cell predictive marker (SPmarker) to identify novel cell-type marker genes in the Arabidopsis root. Unlike traditional approaches, our method uses interpretable machine learning models to select marker genes.

DeepTE: a computational method for de novo classification of transposons with convolutional neural network.

Motivation: Transposable elements (TEs) classification is an essential step to decode their roles in genome evolution. With a large number of genomes from non-model species becoming available, accurate and efficient TE classification has emerged as a new challenge in genomic sequence analysis.

Results: We developed a novel tool, DeepTE, which classifies unknown TEs using convolutional neural networks (CNNs).

Whole-Genome Resequencing of Seven Eggplant () and One Wild Relative () Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement.

Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant () and one wild relative () accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population.

Genetic insights into the modification of the pre-fertilization mechanisms during plant domestication.

Plant domestication is the process of adapting plants to human use by selecting specific traits. The selection process often involves the modification of some components of the plant reproductive mechanisms. Allelic variants of genes associated with flowering time, vernalization, and the circadian clock are responsible for the adaptation of crops, such as rice, maize, barley, wheat, and tomato, to non-native latitudes.