Functional genomics of Brassica napus: Progress, challenges, and perspectives

Z Tan, X Han, C Dai, S Lu, H He, X Yao… - Journal of Integrative …, 2024 - Wiley Online Library
Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing
over 13% to the stable supply of edible vegetable oil worldwide. Identification and …

Arabidopsis as a model for translational research

AE Yaschenko, JM Alonso, AN Stepanova - The Plant Cell, 2024 - academic.oup.com
Arabidopsis thaliana is currently the most-studied plant species on earth, with an
unprecedented number of genetic, genomic, and molecular resources having been …

Sea-ATI unravels novel vocabularies of plant active cistrome

C Wen, Z Yuan, X Zhang, H Chen, L Luo… - Nucleic Acids …, 2023 - academic.oup.com
The cistrome consists of all cis-acting regulatory elements recognized by transcription
factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific …

Deep learning the cis-regulatory code for gene expression in selected model plants

FF Peleke, SM Zumkeller, M Gültas, A Schmitt… - Nature …, 2024 - nature.com
Elucidating the relationship between non-coding regulatory element sequences and gene
expression is crucial for understanding gene regulation and genetic variation. We explored …

The PATROL1 function in roots contributes to the increase in shoot biomass

M Notaguchi, M Ichita, T Kawasoe, K Monda… - Planta, 2024 - Springer
Main conclusion PATOL1 contributes to increasing biomass not only by effective stomatal
movement but also by root meristematic activity. Abstract PATROL1 (PROTON ATPase …

Machine learning assists prediction of genes responsible for plant specialized metabolite biosynthesis by integrating multi-omics data

W Bai, C Li, W Li, H Wang, X Han, P Wang, L Wang - BMC genomics, 2024 - Springer
Background Plant specialized (or secondary) metabolites (PSM), also known as
phytochemicals, natural products, or plant constituents, play essential roles in interactions …

Identification of lineage‐specific cistrans regulatory networks related to kiwifruit ripening initiation

E Kuwada, K Takeshita, T Kawakatsu… - The Plant …, 2024 - Wiley Online Library
Previous research on the ripening process of many fruit crop varieties typically involved
analyses of the conserved genetic factors among species. However, even for seemingly …

Gene regulatory network inference in soybean upon infection by Phytophthora sojae

B Hale, S Ratnayake, A Flory, R Wijeratne, C Schmidt… - Plos one, 2023 - journals.plos.org
Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and
stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are …

Identification, characterization, and design of plant genome sequences using deep learning

Z Wang, H Yuan, J Yan, J Liu - The Plant Journal, 2024 - Wiley Online Library
Due to its excellent performance in processing large amounts of data and capturing complex
non‐linear relationships, deep learning has been widely applied in many fields of plant …

Collaboration with AI in horticultural science

E Kuwada, T Akagi - The Horticulture Journal, 2024 - jstage.jst.go.jp
Artificial Intelligence, or AI, is becoming increasingly prevalent in a wide variety of scientific
fields. The recent progress in deep neural networks, or simply “deep learning”, in particular …