cis-Regulatory Elements in Plant Development, Adaptation, and Evolution

AP Marand, AL Eveland, K Kaufmann… - Annual review of …, 2023 - annualreviews.org
cis-Regulatory elements encode the genomic blueprints that ensure the proper
spatiotemporal patterning of gene expression necessary for appropriate development and …

Cis-regulatory sequences in plants: their importance, discovery, and future challenges

RJ Schmitz, E Grotewold, M Stam - The plant cell, 2022 - academic.oup.com
The identification and characterization of cis-regulatory DNA sequences and how they
function to coordinate responses to developmental and environmental cues is of paramount …

PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

M Van Bel, F Silvestri, EM Weitz, L Kreft… - Nucleic Acids …, 2022 - academic.oup.com
PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a
broad set of genomes, data types and analysis tools available to researchers through a user …

Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

J You, Z Liu, Z Qi, Y Ma, M Sun, L Su, H Niu, Y Peng… - Nature …, 2023 - nature.com
Polyploidy complicates transcriptional regulation and increases phenotypic diversity in
organisms. The dynamics of genetic regulation of gene expression between coresident …

A pan-Zea genome map for enhancing maize improvement

S Gui, W Wei, C Jiang, J Luo, L Chen, S Wu, W Li… - Genome biology, 2022 - Springer
Abstract Background Maize (Zea mays L.) is at the vanguard facing the upcoming breeding
challenges. However, both a super pan-genome for the Zea genus and a comprehensive …

Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit

X Wang, L Aguirre, D Rodríguez-Leal, A Hendelman… - Nature Plants, 2021 - nature.com
Cis-regulatory mutations underlie important crop domestication and improvement traits,.
However, limited allelic diversity has hindered functional dissection of the large number of …

Charting plant gene functions in the multi-omics and single-cell era

T Depuydt, B De Rybel, K Vandepoele - Trends in Plant Science, 2023 - cell.com
Despite the increased access to high-quality plant genome sequences, the set of genes with
a known function remains far from complete. With the advent of novel bulk and single-cell …

New whole-genome alignment tools are needed for tapping into plant diversity

B Song, ES Buckler, MC Stitzer - Trends in Plant Science, 2024 - cell.com
Genome alignment is one of the most foundational methods for genome sequence studies.
With rapid advances in sequencing and assembly technologies, these newly assembled …

PlantPAN 4.0: Updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters

CN Chow, CW Yang, NY Wu, HT Wang… - Nucleic acids …, 2024 - academic.oup.com
Abstract PlantPAN 4.0 (http://PlantPAN. itps. ncku. edu. tw/) is an integrative resource for
constructing transcriptional regulatory networks for diverse plant species. In this release, the …

Machine learning: its challenges and opportunities in plant system biology

M Hesami, M Alizadeh, AMP Jones… - Applied Microbiology and …, 2022 - Springer
Sequencing technologies are evolving at a rapid pace, enabling the generation of massive
amounts of data in multiple dimensions (eg, genomics, epigenomics, transcriptomic …