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1. A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species

   https://doi.org/10.1371/journal.pone.0314509  

   Coomber, Allison L; Saville, Amanda C; Carbone, Ignazio; Martin, Michael; Bieker, Vanessa C; Ristaino, Jean Beagle (January 2025, PLOS ONE)

   Blair, Jaime E (Ed.)

   We examined the evolutionary history ofPhytophthora infestansand its close relatives in the 1c clade. We used whole genome sequence data from 69 isolates ofPhytophthoraspecies in the 1c clade and conducted a range of genomic analyses including nucleotide diversity evaluation, maximum likelihood trees, network assessment, time to most recent common ancestor and migration analysis. We consistently identified distinct and later divergence of the two MexicanPhytophthoraspecies,P.mirabilisandP.ipomoeae, fromP.infestansand other 1c clade species.Phytophthora infestansexhibited more recent divergence from other 1c clade species ofPhytophthorafrom South America,P.andinaandP.betacei. Speciation in the 1c clade and evolution ofP.infestansoccurred in the Andes.P.andina–P.betacei–P.infestansformed a species complex with indistinct species boundaries, hybridizations between the species, and short times to common ancestry. Furthermore, the distinction between modern Mexican and South AmericanP.infestansproved less discrete, suggesting gene flow between populations over time. Admixture analysis indicated a complex relationship among these populations, hinting at potential gene flow across these regions. HistoricP.infestans, collected from 1845–1889, were the first to diverge from all otherP.infestanspopulations. Modern South American populations diverged next followed by Mexican populations which showed later ancestry. Both populations were derived from historicP.infestans. Based on the time of divergence ofP.infestansfrom its closest relatives,P.andinaandP.betaceiin the Andean region, we consider the Andes to be the center of origin ofP.infestans, with modern globalization contributing to admixture betweenP.infestanspopulations today from Mexico, the Andes and Europe. 

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2. Bounding p-Brauer characters in finite groups with two conjugacy classes of p-elements

   https://doi.org/10.1007/s11856-024-2613-1  

   Hung, Nguyen Ngoc; Sambale, Benjamin; Tiep, Pham Huu (September 2024, Israel Journal of Mathematics)

   Abstract Letk(B₀) andl(B₀) respectively denote the number of ordinary andp-Brauer irreducible characters in the principal blockB₀of a finite groupG. We prove that, ifk(B₀)−l(B₀) = 1, thenl(B₀) ≥p− 1 or elsep= 11 andl(B₀) = 9. This follows from a more general result that for every finite groupGin which all non-trivialp-elements are conjugate,l(B₀) ≥p− 1 or elsep= 11 and$$G/{{\bf{O}}_{{p^\prime }}}(G) \cong C_{11}^2\, \rtimes\,{\rm{SL}}(2,5)$$ $G/O_{p^{\prime }}\left(G\right)\cong C_{11}^2⋊\text{SL}(2,5)$. These results are useful in the study of principal blocks with few characters. We propose that, in every finite groupGof order divisible byp, the number of irreducible Brauer characters in the principalp-block ofGis always at least$$2\sqrt {p - 1} + 1 - {k_p}(G)$$ $2\sqrt{p-1}+1-k_p\left(G\right)$, wherek_p(G) is the number of conjugacy classes ofp-elements ofG. This indeed is a consequence of the celebrated Alperin weight conjecture and known results on bounding the number ofp-regular classes in finite groups. 

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3. Relationship between local-scale topography and vegetation on the invasive C ₄ perennial bunchgrass buffelgrass ( Pennisetum ciliare ) size and reproduction

   https://doi.org/10.1017/inp.2023.9  

   Hovanes, Katherine A.; Lien, Aaron M.; Baldwin, Elizabeth; Li, Yue M.; Franklin, Kim; Gornish, Elise S. (March 2023, Invasive Plant Science and Management)

   Abstract Buffelgrass [Pennisetum ciliare(L.) Link] is an invasive C₄perennial bunchgrass that is a threat to biodiversity in aridlands in the Americas and Australia. Topography influencesP. ciliareoccurrence at large spatial scales, but further investigation into the relationship between local-scale topography andP. ciliaregrowth and reproduction would be beneficial. Further, density-dependent effects onP. ciliaregrowth and reproduction have been demonstrated in greenhouse experiments, but the extent to which density dependence influencesP. ciliarein natural populations warrants further investigation. Here we present a study on the relationships between local-scale topography (aspect and slope gradient) and vegetation characteristics (shrub cover,P. ciliarecover, andP. ciliaredensity) and their interactions on individualP. ciliareplant size and reproduction. We measured slope gradient, aspect, shrub cover,P. ciliarecover,P. ciliaredensity, and the total number of live culms and reproductive culms of 10P. ciliareplants in 33 4 by 4 m plots located in 11 transects at the Desert Laboratory at Tumamoc Hill, Tucson, AZ, USA. We modeled the relationships at the local scale of (1)P. ciliarecover and density with aspect and slope gradient and (2)P. ciliaresize and reproduction with abiotic (slope gradient and aspect) and biotic (P. ciliarecover and density and native shrub and cacti cover) characteristics. Aspect and slope gradient were poor predictors ofP. ciliarecover and density in already invaded sites at the scale of our plots. However, aspect had a significant relationship withP. ciliareplant size and reproduction.Pennisetum ciliareplants on south-facing aspects were larger and produced more reproductive culms than plants on other aspects. Further, we found no relationship betweenP. ciliaredensity andP. ciliareplant size and reproduction. Shrub cover was positively correlated withP. ciliarereproduction. South-facing aspects are likely most vulnerable to fast spread and infilling by newP. ciliareintroductions. 

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4. DEK domain‐containing proteins control flowering time in Arabidopsis

   https://doi.org/10.1111/nph.17366  

   Zong, Wei; Zhao, Bo; Xi, Yanpeng; Bordiya, Yogendra; Mun, Hyungwon; Cerda, Nicholas A.; Kim, Dong‐Hwan; Sung, Sibum (May 2021, New Phytologist)

   Summary Evolutionarily conserved DEK domain‐containing proteins have been implicated in multiple chromatin‐related processes, mRNA splicing and transcriptional regulation in eukaryotes.Here, we show that two DEK proteins, DEK3 and DEK4, control the floral transition inArabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors,FLOWERING LOCUS C(FLC), and its two homologs,MADS AFFECTING FLOWERING4(MAF4) andMAF5, to promote their expression.The binding of DEK3 and DEK4 to a histone octamerin vivoaffects histone modifications atFLC,MAF4andMAF5loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II withFLC,MAF4andMAF5chromatin to promote their expression.Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering inArabidopsis. 

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5. Ranked Document Retrieval in External Memory

   https://doi.org/10.1145/3559763  

   Shah, Rahul; Sheng, Cheng; Thankachan, Sharma; Vitter, Jeffrey (January 2023, ACM Transactions on Algorithms)

   The ranked (or top-k) document retrieval problem is defined as follows: preprocess a collection{T₁,T₂,… ,T_d}ofdstrings (called documents) of total lengthninto a data structure, such that for any given query(P,k), wherePis a string (called pattern) of lengthp ≥ 1andk ∈ [1,d]is an integer, the identifiers of thosekdocuments that are most relevant toPcan be reported, ideally in the sorted order of their relevance. The seminal work by Hon et al. [FOCS 2009 and Journal of the ACM 2014] presented anO(n)-space (in words) data structure withO(p+klogk)query time. The query time was later improved toO(p+k)[SODA 2012] and further toO(p/log_σn+k)[SIAM Journal on Computing 2017] by Navarro and Nekrich, whereσis the alphabet size. We revisit this problem in the external memory model and present three data structures. The first one takesO(n)-space and answer queries inO(p/B+ log_Bn + k/B+log^*(n/B)) I/Os, whereBis the block size. The second one takesO(nlog^*(n/B)) space and answer queries in optimalO(p/B+ log_Bn + k/B)I/Os. In both cases, the answers are reported in the unsorted order of relevance. To handle sorted top-kdocument retrieval, we present anO(nlog(d/B))space data structure with optimal query cost. 

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