Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive genome elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant genomes, we draw comparisons with animal and fungal centromeres to derive a eukaryote-wide perspective of centromere structure and function.

The structure, function, and evolution of plant centromeres.

Abstract Coffea arabica , an allotetraploid hybrid of Coffea eugenioides and Coffea canephora , is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora . The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora , highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica . 

pdf/the-genome-and-population-genomics-of-allopolyploid-coffea-2w2da9dep0.pdf

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide. Cultivated accessions have undergone several population bottlenecks resulting in low genetic diversity. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, which show a mosaic pattern of dominance, similar to other polyploid crop species. Resequencing of 39 wild and cultivated accessions suggests a founding polyploidy event ∼610,000 years ago, followed by several subsequent bottlenecks, including a population split ∼30.5 kya and a period of migration between Arabica populations until ∼8.9 kya. Analysis of lines historically introgressed with C. canephora highlights loci that may contribute to their superior pathogen resistance and lay the groundwork for future genomics-based breeding of C. arabica.

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021–2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing. This study collected and analysed 3,517 de novo assemblies from 1,575 plant species sequenced since 2000, including 793 newly sequenced species in the past three years. A database named N3: plants, genomes, technologies was developed to accommodate the metadata associated with the sequenced genomes.

Technology-enabled great leap in deciphering plant genomes.

Aeromonas species (spp.) are well-known fish pathogens, several of which have been recognized as emerging human pathogens. The organism is capable of causing a wide spectrum of diseases in humans, ranging from gastroenteritis, wound infections, and septicemia to devastating necrotizing fasciitis. The systemic form of infection is often fatal, particularly in patients with underlying chronic diseases. Indeed, recent trends demonstrate rising numbers of hospital-acquired Aeromonas infections, especially in immuno-compromised individuals. Additionally, Aeromonas-associated antibiotic resistance is an increasing challenge in combating both fish and human infections. The acquisition of antibiotic resistance is related to Aeromonas' innate transformative properties including its ability to share plasmids and integron-related gene cassettes between species and with the environment. As a result, alternatives to antibiotic treatments are desperately needed. In that vein, many treatments have been proposed and studied extensively in the fish-farming industry, including treatments that target Aeromonas quorum sensing. In this review, we discuss current strategies targeting quorum sensing inhibition and propose that such studies empower the development of novel chemotherapeutic approaches to combat drug-resistant Aeromonas spp. infections in humans. KEY POINTS: • Aeromonas notoriously acquires and maintains antimicrobial resistance, making treatment options limited. • Quorum sensing is an essential virulence mechanism in Aeromonas infections. • Inhibiting quorum sensing can be an effective strategy in combating Aeromonas infections in animals and humans. 

Antimicrobial resistance in aeromonads and new therapies targeting quorum sensing

A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus

The Lysine Acetylation Modification in the Porin Aha1 of Aeromonas hydrophila Regulates the Uptake of Multidrug Antibiotics

Simple Summary Aeromonas hydrophila is a major pathogen with human–animal–fish comorbidity that causes many diseases. To better investigate the roles of different genes in Aeromonas hydrophila, our aim is to knock out a gene in A. hydrophila and study whether the gene affects the physiological phenotypes or not. We found that AHA_2124, encoding a multiple antibiotic resistance regulator (MarR) family regulator, affected the extracellular protease activity, hemolytic activity, and motility of the phytopathogenic bacterium Aeromonas hydrophila. The MarR family of the transcriptional regulators of bacteria are mainly involved in the regulation of various cellular processes. In this work, we call for further research on the bioinformatics analysis based on the comparison of the ΔAHA_2124 strain and wild type. Abstract The transcriptional regulators of the MarR family play an important role in diverse bacterial physiologic functions, whereas their effect and intrinsic regulatory mechanism on the aquatic pathogenic bacterium Aeromonas hydrophila are, clearly, still unknown. In this study, we firstly constructed a deletion strain of AHA_2124 (ΔAHA_2124) of a MarR family transcriptional regulator in Aeromonas hydrophila ATCC 7966 (wild type), and found that the deletion of AHA_2124 caused significantly enhanced hemolytic activity, extracellular protease activity, and motility when compared with the wild type. The differentially abundant proteins (DAPs) were compared by using data-independent acquisition (DIA), based on a quantitative proteomics technology, between the ΔAHA_2124 strain and wild type, and there were 178 DAPs including 80 proteins up-regulated and 98 proteins down-regulated. The bioinformatics analysis showed that the deletion of gene AHA_2124 led to some changes in the abundance of proteins related to multiple biological processes, such as translation, peptide transport, and oxidation and reduction. These results provided a theoretical basis for better exploring the regulatory mechanism of the MarR family transcriptional regulators of Aeromonas hydrophila on bacterial physiological functions.

Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila

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A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus

The Lysine Acetylation Modification in the Porin Aha1 of Aeromonas hydrophila Regulates the Uptake of Multidrug Antibiotics

Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila