Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.

Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.

Do red and yellow autumn leaves make use of different photoprotective strategies during autumn senescence?

Our goal was to determine whether anthocyanin-producing species (red) use different photoprotective strategies to cope with excess light during fall senescence compared with non-anthocyanin-producing species (yellow). In a previous study, we found that a yellow species retained the photoprotective PsbS protein in late autumn, while a red species did not. Specifically, we tested the hypothesis that red species make less use of zeaxanthin and PsbS-mediated thermal dissipation, as they rely on anthocyanins for photoprotection. We monitored four red (Acer ginnala, Rhus typhnia, Parenthocissus quinquefolia, Viburnum dentatum) and four yellow species (Acer negundo, Ostrya virginiana, Vitis riparia, Zanthoxylum americanum) throughout autumn senescence and analyzed pigments, protein content, and chlorophyll fluorescence. We found yellow species retained the PsbS protein at higher levels, and had higher dark retention of zeaxanthin in late autumn relative to red species. All species retained lutein and the pool of xanthophyll cycle pigments in higher amounts than other carotenoids in late autumn. Our data support the hypothesis that red species use anthocyanins as a photoprotective strategy during autumn senescence, and therefore make less use of PsbS and zeaxanthin-mediated thermal dissipation. We also found species-specific variation in the particular combination of photoprotective strategies used.

Cutting-edge plant natural product pathway elucidation.

Plant natural products (PNPs) play important roles in plant physiology and have been applied across diverse fields of human society. Understanding their biosynthetic pathways informs plant evolution and meanwhile enables sustainable production through metabolic engineering. However, the discovery of PNP biosynthetic pathways remains challenging due to the diversity of enzymes involved and limitations in traditional gene mining approaches. In this review, we will summarize state-of-the-art strategies and recent examples for predicting and characterizing PNP biosynthetic pathways, respectively, with multiomics-guided tools and heterologous host systems and share our perspectives on the systematic pipelines integrating these various bioinformatic and biochemical approaches.

Imprisonment for South Ethiopian people living with HIV presents a double health burden: lived experiences of prisoners.

BACKGROUND: Optimal adherence is crucial for ensuring both therapeutic and preventative benefits of antiretroviral therapy (ART). Sub-optimal adherence is common in prisoners and little information is available about its predisposing circumstances in resource-limited settings. We explored lived experiences of inmates living with HIV (ILWH) and experiential accounts of service providers in South Ethiopia to identify barriers to and facilitators of HIV care use in the prison context. METHODS: We conducted qualitative in-depth interviewing with eleven ILWH and eleven service providers. Audio recorded interview data were transcribed verbatim in Amharic language, translated into English and coded based on emerging concepts. We employed a descriptive phenomenological approach to abstract meaning attributed to the prisoners' lived experiences in relation to HIV care use and service providers' experiential account regarding care provision as presented to our consciousness. FINDINGS: Several concepts emerged as barriers to HIV care use amongst ILWH in South Ethiopia including: limited access to standard care, insufficient health staff support, uncooperative security system, loss of patient privacy, a lack of status disclosure due to social stigma, and food supply insufficiency. In addition to a unique opportunity offered by an imprisonment for some ILWH to refrain from health damaging behaviours, the presence of social support in the prison system facilitated care use. CONCLUSIONS: This study identified important structural and social contexts that can both hinder and enhance HIV care use amongst ILWH in South Ethiopia. Given the disproportionate burden of HIV in prisoners and the potential of transmission to others during and after incarceration, development of contextually-responsive strategies is required to address the barriers and to also strengthen the enablers.

The placebo effect in randomized-controlled trials of medical treatments for chronic rhinosinusitis: A systematic review and meta-analysis.

BACKGROUND: The placebo effect observed in clinical trials evaluating medical treatments for chronic rhinosinusitis (CRS) is not well understood. This systematic review and meta-analysis sought to characterize the placebo effect present within CRS outcomes. METHODS: A systematic review of PubMed, Scopus, and Cumulated Index in Nursing and Allied Health Nursing (CINAHL) was performed. Randomized controlled trials (RCTs) evaluating medical treatments for CRS versus placebo were included. We assessed patient-reported (sino-nasal outcome test 22 [SNOT-22], nasal obstruction, sense of smell, nasal obstruction visual analogue score [VAS], sense of smell VAS, anterior rhinorrhea, and postnasal drip) and objective (Lund-Mackay Computed tomography (CT) score, peak nasal inspiratory flow [PNIF], nasal polyp scores, 40-item Smell Identification Test, serum IgE, and blood eosinophil levels) outcomes. RESULTS: Twenty-one RCTs were included, comprising 1437 patients (mean age 49.2 years). Biologics were the most common treatment investigated (n = 9). Eleven studies administered background steroids along with placebo. Following placebo administration, multiple patient-reported outcomes significantly decreased, including SNOT-22 (mean difference -9.49, 95% confidence interval [CI] [-11.26, -7.73]), nasal obstruction (-0.33 [-0.54, -0.13]), sense of smell (-0.22 [-0.33, -0.11]), nasal obstruction VAS (-2.47 [-2.87, -2.06]), and loss of smell VAS (-2.31 [-4.14, -0.47]) scores. For objective measures, significant changes occurred in Lund-Mackay CT score (-0.82, [-1.48, -0.16]) and PNIF (4.70, [4.76, 24.64]) with placebo. Placebo arms had the greatest impact when no background medications were used. CONCLUSIONS: Placebo treatments have a statistically and potentially clinically significant effect on patient-reported and some objective CRS outcomes. Further investigation is required to fully understand placebo effect, which could improve assessment of RCTs and impact patient care.

Outcomes of Spontaneous Cerebrospinal Fluid Leak Repair With Concurrent Eustachian Tube Dysfunction.

OBJECTIVE: To compare the presentation and outcomes of patients with and without obstructive eustachian tube dysfunction (oETD) undergoing repair of lateral skull base spontaneous cerebrospinal fluid (sCSF) leaks. STUDY DESIGN: Retrospective chart review. SETTING: Tertiary referral center. PATIENTS: Adults with lateral skull base sCSF leaks who underwent repairs from January 1, 2011, to December 31, 2020, were collected. MAIN OUTCOME MEASURE: Comparative statistics and effect sizes were used to compare clinical features, operative findings, and outcomes between groups. RESULTS: Of 92 ears from 89 patients included, 51.1% (n = 47) had oETD. There were no differences in demographics between patients with and without oETD. Mean age was 60.7 ± 13.1 versus 58.5 ± 12.8 years ( d = -0.17 [-0.58 to 0.24]), mean body mass index was 33.8 ± 8.5 versus 36.0 ± 8.0 kg/m 2 ( d = 0.27 [-0.14 to 0.68]), and female sex preponderance was 59.6% (n = 28) versus 68.8% (n = 31; Φ = -0.09), respectively. There were no differences in the radiologic number, size, and locations of defects. Patients with oETD had less pneumatized mastoids than those without oETD ( p = 0.001; Φ = 0.43). Mean change from preoperative to postoperative air pure-tone average for those with and without oETD was -1.1 ± 12.6 versus 0.1 ± 17.2 dB ( d = 0.09 [-0.04 to 0.58]), respectively. Six ears (6.5%; three with and three without oETD) underwent revisions for rhinorrhea/otorrhea between 5 and 28 months postoperatively, during which four leaks were found, the two patients without leaks had oETD. CONCLUSIONS: The presentation of sCSF leaks and outcomes of repairs in patients with oETD do not differ from those without oETD. Although postoperative otorrhea might represent an inflammatory or infectious process in patients with oETD, reexploration is warranted if patients do not improve with conservative treatment.

Delayed Sublingual Edema Following Neonatal Mandibular Distraction Osteogenesis.

The authors aim to report a rare sequela following neonatal mandibular distraction osteogenesis (MDO) involving delayed onset sublingual swelling. They performed a retrospective chart review of 3 patients who presented with delayed onset sublingual edema following neonatal MDO. The 3 patients presented at 2, 4, and 12 months following MDO for micrognathia secondary to Robin sequence with intermittent sublingual swelling associated with sialorrhea and feeding difficulties. There was no associated recent illness, fevers, or purulent drainage. All 3 children underwent magnetic resonance imaging which demonstrated asymmetric sublingual gland edema. The edema was located on the left sublingual gland in 2 children and was bilateral in the third. The symptoms continue to recur 25.5±3.3 months (range, 22.3-28.9) postoperatively and all are being managed conservatively. Chronic delayed onset intermittent sublingual edema is a possible long-term complication following neonatal MDO and further studies should explore the incidence and management of this finding.

General practitioners' perceptions of the provision of direct-acting antivirals for hepatitis C within Australian private general practice: an exploratory qualitative study.

BACKGROUND: There is a need to increase the involvement of Australian general practitioners (GPs) working in private practice to realise the potential of direct-acting antiviral (DAA) treatments for people with the hepatitis C virus. METHODS: Semi-structured interviews were conducted in 2018 with seven GPs and two practice nurses working in private general practice to elicit the experiences and perceptions of their involvement in providing care for patients with hepatitis C virus in this setting. The interviews were recorded, transcribed and thematically analysed to inform interventions to maximise the provision of DAA in private general practice. RESULTS: Participants described individual GPs purposely limiting their scope of clinical practice (SOCP) and expressed an expectation that DAA provision would not be included in all GP's SOCP. When GPs delineate their SOCP, their confidence to competently provide quality health care to their patients and GPs' professional special interests are important considerations. CONCLUSION: Providing DAA training, skill development, support and resources to GPs is necessary, but may not ensure that individual private GPs will provide this care. Where GPs do not include DAA in their SOCP, care pathways need to be developed for patients who will benefit from DAA, including GP-to-GP referral. These findings may be applicable to other areas of unmet need that rely on GPs including provision of care in their SOCP.

Efficacy of mindfulness and goal setting interventions for increasing resilience and reducing smoking in lower socio-economic groups: randomised controlled trial protocol.

BACKGROUND: Smoking and resulting health problems disproportionately impact low socioeconomic status (SES) individuals. Building resilience presents an approach to 'closing the gap'. Mindfulness-based interventions and setting realistic goals are preferred in low socioeconomic communities. We aim to test if these interventions, delivered online and consolidated with peer support offered via ex-smokers, are successful in promoting smoking cessation and resilience. Our conceptualisation of resilience encompasses the inner capacity/skills and external resources (e.g., social support) which smokers utilise to bounce back from adversity. We include a process evaluation of barriers/facilitators to interventions and cost-effectiveness analysis (from health system perspective). METHODS: We plan a four-arm parallel 12-month RCT with a 6-month follow-up to test the efficacy of three group-based interventions each followed by peer support. Arm 1: mindfulness-integrated cognitive behavioural therapy; Arm 2: mindfulness training; Arm 3: setting realistic goals; Arm 4: active control group directed to quit services. All interventions will be administered online. Participants are adult smokers in Australia (N = 812) who have an average weekly household income less than $457AUD or receive welfare benefits. Group-based interventions will occur over 6 months, followed by 6 months of forum-based peer support. PRIMARY OUTCOME: self-reported 14-day period prevalence of smoking abstinence at 6 months, with remote biochemical verification of saliva cotinine (< 30 ng/mL). Secondary outcomes include: internal resilience (Connor-Davidson Resilience Scale-25); external resilience (ENRICHD social support tool); quality adjusted life years (EQ-5D-5L); self-efficacy for smoking abstinence (Smoking-Abstinence Self-Efficacy Questionnaire); motivation to quit smoking (Biener and Abrams Contemplation Ladder); nicotine dependence (Fagerstrom Test for Nicotine Dependency); equanimity (Equanimity Scale-16); stress (Perceived Stress Scale-10); goal assessment/attainment (Problems and Goals Assessment Scale). DISCUSSION: This study is the first to compare resilience interventions for low SES smokers which have been identified by them as acceptable. Our various repeated measures and process evaluation will facilitate exploration of mechanisms of impact. We intervene within the novel framework of the Psychosocial Model of Resilience, applying a promising paradigm to address a critical and inequitable public health problem. Trial registration Australian New Zealand Clinical Trials Registry ID: ACTRN12621000445875, registered 19 April 2021 ( https://anzctr.org.au/Trial/Registration/TrialReview.aspx?id=381007&isReview=true ). The Universal Trial Number is U1111-1261-8951.

A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination.

Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.

Dual Domestication, Diversity, and Differential Introgression in Old World Cotton Diploids.

Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and Gossypium arboreum, due to the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we provide support for their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 6 × 10-3) within species is similar, and that divergence between species is modest (FST = 0.413). Individual accessions were homozygous for ancestral single-nucleotide polymorphisms at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated as having experienced high levels of introgression. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces that shape diversity and divergence in the diploid cultivated species and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species.

The Marine Compound Tartrolon E Targets the Asexual and Early Sexual Stages of Cryptosporidium parvum.

New therapeutic agents for cryptosporidiosis are a critical medical need. The marine organic compound, tartrolon E (trtE), is highly effective against multiple apicomplexan parasites, including Cryptosporidium. Understanding the mechanism of action of trtE is required to advance in the drug development pipeline. Here, we validate using Nluc C. parvum parasites for the study of trtE and pinpoint the life stage targeted by trtE. Results show that trtE kills Nluc and wild type C. parvum with equal efficiency, confirming the use of the Nluc C. parvum to study this compound. Results revealed that trtE kills the parasite within an hour of treatment and while the compound has no effect on viability of sporozoites, trtE does inhibit establishment of infection. Targeting treatment at particular life cycle stages demonstrated that trtE is effective against asexual of the parasite but has reduced efficacy against mature sexual stages. Gene expression analysis shows that trtE inhibits the early sexual stage of the parasite. Results from these studies will aid the development of trtE as a therapeutic for cryptosporidiosis.

Analysis of two cooperating antibodies unveils immune pressure imposed on HIV Env to elicit a V3-glycan supersite broadly neutralizing antibody lineage.

Elicitation of broadly neutralizing antibodies (bnAbs) is a goal of vaccine design as a strategy for targeting highly divergent strains of HIV-1. Current HIV-1 vaccine design efforts seek to elicit bnAbs by first eliciting their precursors through prime-boost regimens. This requires an understanding of the co-evolution between viruses and antibodies. Towards this goal, we have analyzed two cooperating antibodies, DH475 and DH272, which exerted pressure on the HIV population in an infected donor, called CH848, to evolve in such a way that it became sensitive to the V3-glycan supersite DH270 bnAb lineage. We obtained a 2.90Å crystal structure of DH475 in complex with the Man9 glycan and a negative stain EM model of DH272 in complex with the HIV-1 spike trimer, Env. Coupled with additional modeling studies and biochemical data, our studies reveal that DH475 contacts a V3- and V4-glycan dependent epitope accessible on an open or shed Env and that DH272 makes critical contacts with the V1V2 and V3 loops on HIV-1 Env. Using these data, we suggest a prime-boost regimen that may facilitate the initiation of DH270-like bnAb precursors.

Assessing the health impacts of transnational corporations: a case study of Carlton and United Breweries in Australia.

BACKGROUND: The practices of transnational corporations (TNCs) affect population health through unhealthy products, shaping social determinants of health, or influencing the regulatory structures governing their activities. There has been limited research on community exposures to TNC policies and practices. The aim of this paper was to adapt existing Health Impact Assessment methods that were previously used for both a fast food and an extractives industry corporation in order to assess Carlton and United Breweries (CUB) operations within Australia. CUB is an Australian alcohol company owned by a large transnational corporation Asahi Group Holdings. Data identifying potential impacts were sourced through document analysis, including corporate literature; media analysis, and 12 semi-structured interviews. The data were mapped against a corporate health impact assessment framework which included CUB's political and business practices; products and marketing; workforce, social, environmental and economic conditions; and consumers' adverse health impacts. We also conducted an ecological study for estimating alcohol attributable fractions and burdens of death due to congestive heart disease, diabetes mellitus, stroke, breast cancer, bowel cancer and injury in Australia. Beer attributable fractions and deaths and CUB's share were also estimated. RESULTS: We found both positive and adverse findings of the corporation's operations across all domains. CUB engage in a range of business practices which benefit the community, including sustainability goals and corporate philanthropy, but also negative aspects including from taxation arrangements, marketing practices, and political donations and lobbying which are enabled by a neoliberal regulatory environment. We found adverse health impacts including from fetal alcohol spectrum disorder and violence and aggression which disproportionately affect Indigenous and other disadvantaged populations. CONCLUSION: Our research indicates that studying a TNC in a rapidly changing global financialised capitalist economy in a world which is increasingly being managed by TNCs poses methodological and conceptual challenges. It highlights the need and opportunity for future research. The different methods revealed sufficient information to recognise that strong regulatory frameworks are needed to help to avoid or to mediate negative health impacts.

'I have a healthy relationship with alcohol': Australian midlife women, alcohol consumption and social class.

Alcohol consumption by Australian women during midlife has been increasing. Health promotion efforts to reduce alcohol consumption in order to reduce alcohol-related disease risk compete with the social contexts and value of alcohol in women's lives. This paper draws on 50 qualitative interviews with midlife women (45-64 years of age) from different social classes living in South Australia in order to gain an understanding of how and why women might justify their relationships with alcohol. Social class shaped and characterized the different types of relationships with alcohol available to women, structuring their logic for consuming alcohol and their ability to consider reducing (or 'breaking up with') alcohol. We identified more agentic relationships with alcohol in the narratives of affluent women. We identified a tendency for less control over alcohol-related decisions in the narratives of women with less privileged life chances, suggesting greater challenges in changing drinking patterns. If classed differences are not attended to in health promotion efforts, this might mitigate the effectiveness of alcohol risk messaging to women.

Variation in cytonuclear expression accommodation among allopolyploid plants.

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e. cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for 6 allopolyploid lineages that represent 4 genera (i.e. Arabidopsis, Arachis, Chenopodium, and Gossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression-level dominance in cytonuclear genes relative to the background of noncytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression evolution may be subtle and variable among genera and genes, likely reflecting a diversity of mechanisms to resolve nuclear-cytoplasmic incompatibilities in allopolyploid species.

Risk factors for late linkage to care and delayed antiretroviral therapy initiation among adults with HIV in sub-Saharan Africa: a systematic review and meta-analyses.

OBJECTIVES: Late treatment initiation threatens the clinical and public health benefits of antiretroviral therapy (ART). Quantitative synthesizes of the existing evidence related to this are lacking in sub-Saharan Africa (SSA), which would help ascertain the best evidence-based interventions. This review aimed to systematically synthesize the available literature on factors affecting linkage to care and ART initiation among adults with HIV in SSA. METHODS: Systematic searches were undertaken on four databases to identify observational studies investigating factors affecting both HIV care outcomes among adults (age ≥19 years) in SSA and were published between January 1, 2015 and June 1, 2021. RevMan-5 software was used to conduct meta-analyses and Mantel-Haenszel statistics to pool outcomes with a 95% confidence interval and <0.05 level of significance. RESULTS: A total of 46 studies were included in the systematic review, of which 18 fulfilled requirements for the meta-analysis. In both narrative review and meta-analyses, factors related to health care delivery, individual perception, and sociodemographic circumstances were associated with late linkage to care and delays in ART initiation. CONCLUSION: This review identified a range of risk factors for late linkage to care and delayed ART initiation among adults with HIV in SSA. We recommend implementation of patient-centered intervention approaches to alleviate these barriers.

Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels.

Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA sequencing (RNA-seq) to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9 to 82.3%) of messenger RNA (mRNA) transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3 to 3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than 10-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.

Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species.

Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.