Results 41 to 50 of about 2,610 (179)

Assembly and annotation of the Gossypium barbadense L. ‘Pima-S6’ genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes

BMC Genomics, 2023
Background Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market.
Ricardo A. Chávez Montes, Mauricio Ulloa, Tammy Biniashvili, Arik Zackay, Nir Kfir, Damar Lopez-Arredondo, Luis Herrera-Estrella   +6 more
doaj   +1 more source

OrthoFinder: phylogenetic orthology inference for comparative genomics

Genome Biology, 2019
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative
David M. Emms, Steven Kelly
doaj   +1 more source

OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations

BMC Genomics, 2017
Background Complete and accurate annotation of sequenced genomes is of paramount importance to their utility and analysis. Differences in gene prediction pipelines mean that genome annotations for a species can differ considerably in the quality and ...
Michael P. Dunne, Steven Kelly
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Comparative genomic analysis reveals differential genomic characteristics and featured genes between rapid- and slow-growing non-tuberculous mycobacteria

Frontiers in Microbiology, 2023
IntroductionNon-tuberculous mycobacteria (NTM) is a major category of environmental bacteria in nature that can be divided into rapidly growing mycobacteria (RGM) and slowly growing mycobacteria (SGM) based on their distinct growth rates.
Menglu Zhang, Peihan Wang, Peihan Wang, Cuidan Li, Ofir Segev, Jie Wang, Jie Wang, Xiaotong Wang, Liya Yue, Xiaoyuan Jiang, Yongjie Sheng, Asaf Levy, Chunlai Jiang, Fei Chen, Fei Chen, Fei Chen, Fei Chen   +16 more
doaj   +1 more source

Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP)

BMC Bioinformatics, 2022
Background Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, in whole organisms, tissues, and ...
Yiru Sheng, R. Ayesha Ali, Andreas Heyland   +2 more
doaj   +1 more source

Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis

Frontiers in Microbiology, 2022
Ceriporia lacerata is an endophytic white-rot fungus that has lignocellulolytic and terpenoid-biosynthetic abilities. However, little is known about the genomic architecture of this fungus, even at the genus level.
Zhitao Mao, Zhitao Mao, Zhitao Mao, Ping Yang, Ping Yang, Ping Yang, Huanhuan Liu, Yufeng Mao, Yufeng Mao, Yufeng Mao, Yu Lei, Yu Lei, Dongwei Hou, Dongwei Hou, Hongwu Ma, Hongwu Ma, Hongwu Ma, Xiaoping Liao, Xiaoping Liao, Xiaoping Liao, Wenxia Jiang, Wenxia Jiang, Wenxia Jiang   +22 more
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Orthogroup and phylotranscriptomic analyses identify transcription factors involved in the plant cold response: A case study of Arabidopsis BBX29

Plant Communications, 2023
C-repeat binding factors (CBFs) are well-known transcription factors (TFs) that regulate plant cold acclimation. RNA sequencing (RNA-seq) data from diverse plant species provide opportunities to identify other TFs involved in the cold response. However, this task is challenging because gene gain and loss has led to an intertwined community of co ...
Shuo Wang, Yirong Shen, Deyin Deng, Liangyu Guo, Yixian Zhang, Yuqi Nie, Yunfei Du, Xijuan Zhao, Xiaoxue Ye, Jianqin Huang, Huahong Huang, Jian-Kang Zhu, Wenwu Wu   +12 more
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PlantTribes2: Tools for comparative gene family analysis in plant genomics

Frontiers in Plant Science, 2023
Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large.
Eric K. Wafula, Huiting Zhang, Huiting Zhang, Gregory Von Kuster, James H. Leebens-Mack, Loren A. Honaas, Claude W. dePamphilis, Claude W. dePamphilis   +7 more
doaj   +1 more source

Marine gregarine genomes reveal the breadth of apicomplexan diversity with a partially conserved glideosome machinery

BMC Genomics, 2022
Our current view of the evolutionary history, coding and adaptive capacities of Apicomplexa, protozoan parasites of a wide range of metazoan, is currently strongly biased toward species infecting humans, as data on early diverging apicomplexan lineages ...
Julie Boisard, Evelyne Duvernois-Berthet, Linda Duval, Joseph Schrével, Laure Guillou, Amandine Labat, Sophie Le Panse, Gérard Prensier, Loïc Ponger, Isabelle Florent   +9 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

Frontiers in Plant Science
Powdery 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
doaj   +1 more source