Results 51 to 60 of about 3,202 (209)

PhyloMCL: Accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events

Methods in Ecology and Evolution, 2020
AbstractIdentification of homology relationships is essential for inferring gene functions, detecting phylogeny of gene families, discovering evolutionary history of life, and usually, is the first step of many genetic and genomic studies. However, the presence of gene duplicates, variation on evolutionary rates of homologs, fusion and fission of genes,
Shengyu Zhou, Yamao Chen, Chunce Guo, Ji Qi   +3 more
openaire   +1 more source

Evolutionary framework and tribal circumscription of Amaranthaceae sensu stricto based on a comprehensive phylogenomic analysis

Cladistics, EarlyView.
Abstract The evolutionary history of Amaranthaceae sensu stricto (s.s.) has been shaped by multiple whole‐genome duplications and rapid radiations, producing an ecologically diverse lineage whose internal relationships have long remained unresolved.
Tina Kiedaisch, Anže Žerdoner Čalasan, Ross A. McCauley, Gudrun Kadereit   +3 more
wiley   +1 more source

.fasta files corresponding to each orthogroup in the analysis

, 2019
.fasta files corresponding to each orthogroup in the ...
Price, Dana C, Lyska, Dagmar, Mark Seger (3078852), Seger, Mark, Debashish Bhattacharya (35009), Andreas P M Weber (7852070), Dagmar Lyska (289626), Alessandro W Rossoni (7852061), Lammers, Peter, Bhattacharya, Debashish, Peter Lammers (7852067), Weber, Andreas P M, Dana C Price (7852064), Rossoni, Alessandro W   +13 more
core   +1 more source

SupplementaryDataset3.tar.gz

, 2023
Supplementary Dataset 3: original multiple sequence alignment (fasta format, "[OrthoGroup ID].renamed.aln"), processed multiple sequence alignments (input for phylogenetic inference, fasta format, "[OrthoGroup ID].renamed.length_filtered"), unprocessed ...
Laura Eme (10586552), Jolien van Hooff (14515847)   +1 more
core   +1 more source

Genome assembly of Elcysma westwoodi provides insights into host‐plant cyanogenic glucoside detoxification and chemical defence gene evolution

Insect Molecular Biology, EarlyView.
A chromosome‐level genome of Elcysma westwoodi was assembled. The genome encodes 272 detoxification‐related genes. A single‐copy bCAS was retained for cyanide detoxification. CYP405A and CYP332A were recruited into cyanogenic defence evolution. UGT33A retained a conserved GT‐B fold and catalytic domains.
Minyoung Choi, Murtaza Khan, Juil Kim
wiley   +1 more source

Most common ESPs based on orthology analysis.

, 2021
ESPs were assigned to orthogroups in OrthoFinder. The number of species where at least one protein was assigned to a given orthogroup is indicated, along with the species where the orthogroup was found to be absent.
Timothy G. Geary (11502449), Robin Beech (209601), Lucienne Tritten (336564), Cristina Ballesteros (344378), Yovany Moreno (199549)   +4 more
core   +1 more source

Radicals of semigroup rings of orthogroups

Semigroup Forum, 1990
Let S be an orthogroup, that is a completely regular semigroup the idempotent set of which is a subsemigroup. By a result of \textit{M. Petrich} [Proc. Am. Math. Soc. 99, 617-622 (1987; Zbl 0622.20050)], S is a semilattice Y of semigroups \(S_{\alpha}=I_{\alpha}\times G_{\alpha}\times \Lambda_{\alpha}\), \(\alpha\in Y\), where \(I_{\alpha ...
openaire   +2 more sources

Integrative transcriptomic and machine learning approaches reveal candidate genes for silk and venom production in Bibionomorpha (Diptera)

Insect Molecular Biology, EarlyView.
Multi‐species transcriptomics and deep learning identified candidate genes associated with silk and venom production in Bibionomorpha. Venom‐associated genes were enriched in proteases, inhibitors and pore‐forming proteins, whereas silk‐related genes showed chitin‐binding and peritrophin domains. Integrating co‐expression networks, machine learning and
Daniel Kenji Matuo, João Alfredo Teodoro, Danilo T. Amaral   +2 more
wiley   +1 more source

High‐quality genome of elite peanut cultivar ZH05 reveals subgenome asymmetry, pan‐genome diversity, and breeding insights

Journal of Integrative Plant Biology, EarlyView.
A high‐quality reference genome for the elite peanut cultivar Zhonghua No. 5 revealed differing evolutionary paths between the two peanut subgenomes. SubA has higher overall gene expression and more open chromatin, whereas SubB has stronger structural organization, higher DNA methylation, and greater adaptive diversity associated with peanut evolution ...
Taihua Yang, Nian Liu, Li Huang, Jianbin Guo, Xiaomeng Xue, Mingjun Wang, Xiaohan Zhang, Chengtao Quan, Enyou Feng, Jiazhuang Tan, Zhenzhen Zhang, Yu You, Youlin Xia, Dongxin Huai, Yuning Chen, Liyin Yan, Kede Liu, Huifang Jiang, Yong Lei, Boshou Liao   +19 more
wiley   +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