Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package [PDF]
Methods in Ecology and Evolution, 2023 Comparative genomics has become an indispensable part of modern biology due to the advancements in high‐throughput sequencing technologies and the accumulation of genomic data in public databases.
Fabricio Almeida‐Silva +1 more
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Sequence-based comparative secretome analysis reveals conserved core effectors and host lineage-specific divergence between monocot- and dicot-associated powdery mildew lineages [PDF]
Frontiers in Plant SciencePowdery mildew fungi are obligate biotrophs that parasitize living plant tissues and deploy secreted proteins to support host colonization. We compared predicted secretomes from 26 powdery mildew isolates representing five genera (Blumeria, Erysiphe ...
Noman Ali, Nan Wu, Mahinur S. Akkaya
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Finding Species-Specific Extracellular Surface-Facing Proteomes in Toxic Dinoflagellates
Toxins, 2021 As a sequel to our previous report of the existence of species-specific protein/peptide expression profiles (PEPs) acquired by mass spectrometry in some dinoflagellates, we established, with the help of a plasma-membrane-impermeable labeling agent, a ...
Pui Kam Sirius Tse +2 more
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Comparative Genomic Analysis Uncovers the Evolutionary Basis of Siliceous Cell Wall Formation Across Diverse Lineages [PDF]
BiologyIn this study, we constructed a comparative genomic framework encompassing 57 genome sequences from four key taxonomic groups—Bacillariophyta, Parmales, choanoflagellates, and Bacillus—all of which possess either siliceous cell walls or silicon ...
Limin Jia +7 more
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REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories. [PDF]
PLoS Computational BiologyREvolutionH-tl is a fast, scalable, and integrated software platform for inferring orthology relationships, gene trees, species trees, and reconciled evolutionary scenarios directly from sequence data. Built upon the formal framework of best match graphs
José Antonio Ramírez-Rafael +8 more
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Lineage-specific selection signals in the Growth arrest-specific protein 8 (GAS8) domain protein of Trypanosoma melophagium [PDF]
Scientific ReportsThe Growth arrest-specific protein 8 (GAS8) domain-containing gene family (Orthogroup 6127at5690) is a highly conserved, single-copy orthologous group in the Trypanosoma taxa retained for codon-based evolutionary analysis (10 validated species).
Anumita Das +6 more
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Tracing the Evolutionary Dynamics and the Transcriptional Partitioning of Terpene Synthase Gene Family in and Its Diploid Progenitors [PDF]
Bioinformatics and Biology InsightsTerpenes represent a diverse class of plant secondary metabolites that play important roles in development, ecological interactions, and aroma, and are synthesized by the terpene synthase (TPS) gene family.
Makarim Elfadil M. Osman +7 more
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Comparative genomics of microalgae: molecular mechanisms underlying efficient CO₂ assimilation [PDF]
BMC GenomicsRising atmospheric CO₂ levels necessitate the development of effective carbon capture strategies. Some species of microalgae, with their high growth rates and exceptional CO₂ fixation efficiency—up to 10–50 times greater than terrestrial plants—represent
Jessica Di Martino +11 more
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Evolutionary and pan-genomic analysis of the bZIP gene family in 21 Camellia sinensis [PDF]
Frontiers in Plant ScienceBasic leucine zipper (bZIP) transcription factors are important regulators of plant development and stress responses, yet their evolutionary dynamics in tea plant have largely been inferred from a single reference genome.
Quanlong Liu +3 more
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Life, 2022 Late embryogenesis abundant (LEA) proteins comprise a diverse superfamily involved in plant development and stress responses. This study presents a first genome-wide analysis of LEA genes in papaya (Carica papaya L., Caricaceae), an economically ...
Zhi Zou +4 more
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