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Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton.Nature Genetics Nov 2023Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between...
Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.
Topics: Gossypium; Plant Breeding; Alleles; Domestication; Polyploidy; Transcriptome; Cotton Fiber; Gene Expression Regulation, Plant; Genome, Plant
PubMed: 37845354
DOI: 10.1038/s41588-023-01530-8 -
Trends in Plant Science May 2024Plants can program and reprogram their genomes to create genetic variation and epigenetic modifications, leading to phenotypic plasticity. Although consequences of... (Review)
Review
Plants can program and reprogram their genomes to create genetic variation and epigenetic modifications, leading to phenotypic plasticity. Although consequences of genetic changes are comprehensible, the basis for transgenerational inheritance of epigenetic variation is elusive. This review addresses contributions of external (environmental) and internal (genomic) factors to the establishment and maintenance of epigenetic memory during plant evolution, crop domestication, and modern breeding. Dynamic and pervasive changes in DNA methylation and chromatin modifications provide a diverse repertoire of epigenetic variation potentially for transgenerational inheritance. Elucidating and harnessing epigenetic inheritance will help us develop innovative breeding strategies and biotechnological tools to improve crop yield and resilience in the face of environmental challenges. Beyond plants, epigenetic principles are shared across sexually reproducing organisms including humans with relevance to medicine and public health.
PubMed: 38806375
DOI: 10.1016/j.tplants.2024.04.007 -
Kidney International Apr 2024Tubular epithelial cells (TCs) compose the majority of kidney parenchyma and play fundamental roles in maintaining homeostasis. Like other tissues, mostly immature TC...
Tubular epithelial cells (TCs) compose the majority of kidney parenchyma and play fundamental roles in maintaining homeostasis. Like other tissues, mostly immature TC with progenitor capabilities are able to replace TC lost during injury via clonal expansion and differentiation. In contrast, differentiated TC lack this capacity. However, as the kidney is frequently exposed to toxic injuries, evolution positively selected a response program that endows differentiated TC to maintain residual kidney function during kidney injury. Recently, we and others have described polyploidization of differentiated TC, a mechanism to augment the function of remnant TC after injury by rapid hypertrophy. Polyploidy is a condition characterized by >2 complete sets of chromosomes. Polyploid cells often display an increased functional capacity and are generally more resilient to stress as evidenced by being conserved across many plants and eukaryote species from flies to mammals. Here, we discuss the occurrence of TC polyploidy in different contexts and conditions and how this integrates into existing concepts of kidney cell responses to injury. Collectively, we aim at stimulating the acquisition of novel knowledge in the kidney field as well as accelerating the translation of this basic response mechanism to the clinical sphere.
Topics: Animals; Hepatocytes; Cell Differentiation; Epithelial Cells; Polyploidy; Kidney; Mammals
PubMed: 38199322
DOI: 10.1016/j.kint.2023.10.036 -
Zoological Letters Oct 2023Tissue-specific endopolyploidy is widespread among plants and animals and its role in organ development and function has long been investigated. In insects, the fat body...
Tissue-specific endopolyploidy is widespread among plants and animals and its role in organ development and function has long been investigated. In insects, the fat body cells of sexually mature females produce substantial amounts of egg yolk precursor proteins (vitellogenins) and exhibit high polyploid levels, which is considered crucial for boosting egg production. Termites are social insects with a reproductive division of labor, and the fat bodies of mature termite queens exhibit higher ploidy levels than those of other females. The fat bodies of mature termite queens are known to be histologically and cytologically specialized in protein synthesis. However, the relationship between such modifications and polyploidization remains unknown. In this study, we investigated the relationship among cell type, queen maturation, and ploidy levels in the fat body of the termite Reticulitermes speratus. We first confirmed that the termite fat body consists of two types of cells, that is, adipocytes, metabolically active cells, and urocytes, urate-storing cells. Our ploidy analysis using flow cytometry has shown that the fat bodies of actively reproducing queens had more polyploid cells than those of newly emerged and pre-reproductive queens, regardless of the queen phenotype (adult or neotenic type). Using image-based analysis, we found that not urocytes, but adipocytes became polyploid during queen differentiation and subsequent sexual maturation. These results suggest that polyploidization in the termite queen fat body is associated with sexual maturation and is regulated in a cell type-specific manner. Our study findings have provided novel insights into the development of insect fat bodies and provide a basis for future studies to understand the functional importance of polyploidy in the fat bodies of termite queens.
PubMed: 37821917
DOI: 10.1186/s40851-023-00217-6 -
Journal of Molecular and Cellular... Oct 2023Cardiomyocyte proliferation is a difficult phenomenon to capture and prove. Here we employ a retrospective analysis of single cell ventricular suspensions to...
Cardiomyocyte proliferation is a difficult phenomenon to capture and prove. Here we employ a retrospective analysis of single cell ventricular suspensions to definitively identify cardiomyocytes that have completed cell division. Through this analysis we determined that the capacity of cardiomyocytes to re-enter the cell cycle and complete cell division after injury are separate and variable traits. Further, we provide evidence that Tnni3k definitively influences both early and final stages of the cell cycle.
Topics: Cell Cycle; Cell Division; Cell Proliferation; Heart; Heart Ventricles; Myocytes, Cardiac; Retrospective Studies; Animals; Mice
PubMed: 37597489
DOI: 10.1016/j.yjmcc.2023.08.004 -
BMC Biology Jul 2023Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a...
BACKGROUND
Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation.
RESULTS
Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum.
CONCLUSIONS
Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.
Topics: Pennisetum; Biomass; Genome, Plant; Polyploidy; Gene Expression Profiling
PubMed: 37480118
DOI: 10.1186/s12915-023-01643-w -
BMC Plant Biology Dec 2023Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However,...
BACKGROUND
Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples.
RESULTS
In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data.
CONCLUSIONS
This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.
Topics: In Situ Hybridization, Fluorescence; Karyotyping; Polyploidy; Karyotype; Aneuploidy
PubMed: 38062348
DOI: 10.1186/s12870-023-04650-9 -
Annals of Botany Aug 2023Cultivated bananas resulted from inter(sub)specific hybridizations involving Musa species and subspecies (M. acuminata subspecies, M. schizocarpa, M. balbisiana) and the...
BACKGROUND AND AIMS
Cultivated bananas resulted from inter(sub)specific hybridizations involving Musa species and subspecies (M. acuminata subspecies, M. schizocarpa, M. balbisiana) and the subsequent selection, centuries ago, of hybrids with parthenocarpic, seedless fruits. Cultivars have low fertility and are vegetatively propagated, forming groups of somaclones. Relatively few of them, mainly triploids, are grown on a large scale and characterization of their parental relationships may be useful for breeding strategies. Here we investigate parental relationships and gamete-type contributions among diploid and polyploid banana cultivars.
METHODS
We used SNP genotyping data from whole-genome sequencing of 178 banana individuals, including 111 cultivars, 55 wild bananas and 12 synthetic F1 hybrids. We analysed the proportion of SNP sites in accordance with direct parentage with a global statistic and along chromosomes for selected individuals.
KEY RESULTS
We characterized parentage relationships for 7 diploid cultivars, 11 triploid cultivars and 1 tetraploid cultivar. Results showed that both diploid and triploid cultivars could have contributed gametes to other banana cultivars. Diploids may have contributed 1x or 2x gametes and triploids 1x to 3x gametes. The Mchare diploid cultivar group, nowadays only found in East Africa, was found as parent of two diploid and eight triploid cultivars. In five of its identified triploid offspring, corresponding to main export or locally popular dessert bananas, Mchare contributed a 2x gamete with full genome restitution without recombination. Analyses of remaining haplotypes in these Mchare offspring suggested ancestral pedigree relationships between different interspecific banana cultivars.
CONCLUSIONS
The current cultivated banana resulted from different pathways of formation, with implication of recombined or un-recombined unreduced gametes produced by diploid or triploid cultivars. Identification of dessert banana's parents and the types of gametes they contributed should support the design of breeding strategies.
Topics: Triploidy; Musa; Diploidy; Hybridization, Genetic; Germ Cells
PubMed: 37267450
DOI: 10.1093/aob/mcad065 -
Nature Genetics May 2024
Topics: Polyploidy; Genome, Plant; Saccharum
PubMed: 38750321
DOI: 10.1038/s41588-024-01774-y -
Developmental Dynamics : An Official... Jan 2024Cardiovascular disease is a leading cause of death worldwide. Due to the limited proliferative and regenerative capacity of adult cardiomyocytes, the lost myocardium is... (Review)
Review
Cardiovascular disease is a leading cause of death worldwide. Due to the limited proliferative and regenerative capacity of adult cardiomyocytes, the lost myocardium is not replenished efficiently and is replaced by a fibrotic scar, which eventually leads to heart failure. Current therapies to cure or delay the progression of heart failure are limited; hence, there is a pressing need for regenerative approaches to support the failing heart. Cardiomyocytes undergo a series of transcriptional, structural, and metabolic changes after birth (collectively termed maturation), which is critical for their contractile function but limits the regenerative capacity of the heart. In regenerative organisms, cardiomyocytes revert from their terminally differentiated state into a less mature state (ie, dedifferentiation) to allow for proliferation and regeneration to occur. Importantly, stimulating adult cardiomyocyte dedifferentiation has been shown to promote morphological and functional improvement after myocardial infarction, further highlighting the importance of cardiomyocyte dedifferentiation in heart regeneration. Here, we review several hallmarks of cardiomyocyte maturation, and summarize how their reversal facilitates cardiomyocyte proliferation and heart regeneration. A detailed understanding of how cardiomyocyte dedifferentiation is regulated will provide insights into therapeutic options to promote cardiomyocyte de-maturation and proliferation, and ultimately heart regeneration in mammals.
Topics: Animals; Adult; Humans; Myocytes, Cardiac; Regeneration; Heart; Myocardium; Heart Failure; Cell Proliferation; Mammals
PubMed: 36502296
DOI: 10.1002/dvdy.557