Phylotranscriptomic analyses of mycoheterotrophic monocots show a continuum of convergent evolutionary changes in expressed nuclear genes from three …

PR Timilsena, CF Barrett… - Genome biology and …, 2023 - academic.oup.com
Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and
other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have …

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

JA Hadish, HL Hargarten, H Zhang, JP Mattheis… - Plos one, 2024 - journals.plos.org
Gene expression is highly impacted by the environment and can be reflective of past events
that affected developmental processes. It is therefore expected that gene expression can …

A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora

NP Winters, EK Wafula, BJ Knollenberg, T Hämälä… - BMC biology, 2024 - Springer
Background Plants have complex and dynamic immune systems that have evolved to resist
pathogens. Humans have worked to enhance these defenses in crops through breeding …

[PDF][PDF] Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit

JM Waite, EA Kelly, H Zhang… - G3: Genes …, 2023 - academic.oup.com
Apples grown in high heat, high light, and low humidity environments are at risk for sun
injury disorders like sunburn and associated crop losses. Understanding the physiological …

[HTML][HTML] Peach LAZY1 and DRO1 protein-protein interactions and co-expression with PRAF/RLD family support conserved gravity-related protein interactions across …

JM Waite, CA Hollender, JR Eilers… - Micropublication …, 2024 - ncbi.nlm.nih.gov
IGT/LAZY proteins play a central role in determining gravitropic set point angle and
orientation of lateral organs across plant species. Recent work in model systems has …

kakapo: easy extraction and annotation of genes from raw RNA-seq reads

K Ramanauskas, B Igić - PeerJ, 2023 - peerj.com
Abstract kakapo (kākāpō) is a Python-based pipeline that allows users to extract and
assemble one or more specified genes or gene families. It flexibly uses original RNA-seq …

Bioinformatics for gene identification and crop improvement in wheat

PK Gupta, J Chaudhary… - Bioinformatics for Plant …, 2024 - Wiley Online Library
In recent years, the availability of high‐throughput genome/transcriptome sequencing data
and sophisticated bioinformatics tools facilitated in silico identification of novel genes for …

A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'

H Zhang, I Ko, A Eaker, S Haney, N Khuu, K Ryan… - bioRxiv, 2024 - biorxiv.org
Genome sequencing for agriculturally important Rosaceous crops has made rapid progress
both in completeness and annotation quality. Whole genome sequence and annotation …

[PDF][PDF] A Phased, Chromosome-scale Genome for Malus domestica 'WA 38'

H Zhang, A Eaker, I Ko, S Haney, N Khuu, K Ryan… - 2024 - scholar.archive.org
Genome sequencing for agriculturally important Rosaceous crops has made rapid progress
both in completeness and annotation quality. Whole genome sequence and annotation …