Functional characterisation of Dof gene family and expression analysis under abiotic stresses and melatonin-mediated tolerance in pitaya (Selenicereus undatus).

DNA binding proteins with one finger (Dof ) transcription factors are essential for seed development and defence against various biotic and abiotic stresses in plants. Genomic analysis of Dof has not been determined yet in pitaya (Selenicereus undatus ). In this study, we have identified 26 Dof gene family members, renamed as HuDof-1 to HuDof-26 , and clustered them into seven subfamilies based on conserved motifs, domains, and phylogenetic analysis. The gene pairs of Dof family members were duplicated by segmental duplications that faced purifying selection, as indicated by the K a /K s ratio values. Promoter regions of HuDof genes contain many cis -acting elements related to phytohormones including abscisic acid, jasmonic acid, gibberellin, temperature, and light. We exposed pitaya plants to different environmental stresses and examined melatonin's influence on Dof gene expression levels. Signifcant expression of HuDof -2 and HuDof -6 were observed in different developmental stages of flower buds, flowers, pericarp, and pulp. Pitaya plants were subjected to abiotic stresses, and transcriptome analysis was carried out to identify the role of Dof gene family members. RNA-sequencing data and reverse transcription quantitative PCR-based expression analysis revealed three putative candidate genes (HuDof -1, HuDof -2, and HuDof -8), which might have diverse roles against the abiotic stresses. Our study provides a theoretical foundation for functional analysis through traditional and modern biotechnological tools for pitaya trait improvement.

Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops.

The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson-Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits. DNA-free and off-target-free GEd crops with defined characteristics can help to achieve sustainable global food security under a changing climate, but need alignment of international regulations to operate in existing supply chains.

Distribution patterns and drivers of urban green space and plant diversity in Haikou, China.

Investigating historical and ongoing changes in urban green space (UGS) and urban plant diversity (UPD) provides critical insights into urban ecology and urban planning development. The present study illuminates some of the transformations which can occur in rapidly developing urban landscapes. In this work, we used 30 m resolution images from the Landsat 5 satellite from 2015 to investigate UGS patterns in Haikou City, China. Metrics of UPD were obtained using field surveys, allowing the proportion of UGS and UPD to be determined in each urban functional unit (UFU) of Haikou. The results revealed that leisure and entertainment areas (such as parks) had the highest diversity, whereas roads and transportation hubs had the lowest. More frequent anthropogenic maintenance had a positive effect on the total number of species, including cultivated, tree, and herb species. Similarly, increased watering frequency had a positive impact on the diversity of cultivated and shrub species. By providing demonstrating a crucial link between UGS and UPD, the results provide valuable information for planning sustainable urban development in Haikou City and other tropical regions. They highlight the important role of UGS in maintaining biodiversity and providing a range of ecosystem services. This research will inform policymakers and urban planners about the need to consider UGS and UPD in urban planning and management process, in order to promote sustainability and conservation of biodiversity.

New possibilities for trait improvement via mobile CRISPR-RNA.

CRISPR/Cas9 gene technology is transported as RNA from transgenic roots to distal parts of unmodified grafted scion, where it is translated into proteins to induce heritable mutagenesis at desired loci. This technique has the potential to produce transgene-free and genetically stable plants in difficult-to-propagate and near-extinct species.

Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae).

The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa, to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Nintooa were each polyphyletic. Based on the nuclear and chloroplast phylogenies, we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the mid Oligocene (26.45 Ma). The stem age of section Nintooa was estimated to be 17.09 Ma (95% HPD: 13.30-24.45). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 14.12-23.66). Ancestral area reconstruction analyses indicate that subgenus Chamaecerasus originated in East Asia and Central Asia. In addition, sections Coeloxylosteum and Nintooa originated in East Asia, with subsequent dispersals into other areas. The aridification of the Asian interior likely promoted the rapid radiation of sections Coeloxylosteum and Nintooa within this region. Moreover, our biogeographic analysis fully supports the Bering and the North Atlantic Land Bridge hypotheses for the intercontinental migrations in the Northern Hemisphere. Overall, this study provides new insights into the taxonomically complex lineages of subgenus Chamaecerasus and the process of speciation.

CAG (cytarabine, aclarubicin and granulocyte colony-stimulating factor) regimen for core binding factor acute myeloid leukaemia with measurable residual disease.

Acute myeloid leukaemia (AML) with t (8;21) or inv (16), called core binding factor (CBF) AML, has a favourable prognosis. However, some CBF-AML patients have persistent measurable residual disease (MRD) and are more likely to relapse after standard chemotherapy treatment. The CAG regimen, composed of cytarabine, aclarubicin and granulocyte colony-stimulating factor, has been proven to be effective and safe in treating refractory AML patients. We performed a retrospective study to evaluate the efficacy of the CAG regimen to eliminate MRD detected by RUNX1::RUNX1T1 and CBFß::MYH11 transcript levels by quantitative polymerase chain reaction (Q-PCR) among 23 patients. Molecular response was defined as the ratio of fusion transcript after treatment to that before treatment less than or equal to 0.5. The molecular response rate and median decrease ratio of fusion transcripts at the molecular level of the CAG regimen were 52% and 0.53, respectively. The median fusion transcripts before CAG treatment was 0.25% whereas after CAG was 0.11%. Among the 15 patients who had a poor molecular response to the high/intermediate-dose cytarabine regimen, the median decrease ratios of transcripts at the molecular level of high/intermediate-dose cytarabine and CAG were 1.55 and 0.53 (P = 0.028), respectively, and 6 of 15 patients achieved a molecular response to CAG (40%). The median disease-free survival was 18 months, and the overall survival rate at 3 years among all patients was 72.7% ± 10.7%. The common grades 3-4 adverse events were nausea (100%), thrombocytopenia (39%) and neutropenia (37.5%). The CAG regimen may have activity in CBF-AML patients and could provide a new option for patients who have a poor molecular response to high/intermediate-dose cytarabine.

How does spatial extent and environmental limits affect the accuracy of species richness estimates from ecological niche models? A case study with North American Pinaceae and Cactaceae.

Measuring species richness at varying spatial extents can be challenging, especially at large extents where exhaustive species surveys are difficult or impossible. Our work aimed at determining the reliability of species richness estimates from stacked ecological niche models at different spatial extents for taxonomic groups with vastly different environmental dependencies and interactions. To accomplish this, we generated ecological niche models for the species of Cactaceae and Pinaceae that occur within 180 published floras from North America north of Mexico. We overlaid or stacked the resulting species' potential distribution estimates over the bounding boxes representing each of the 180 floras to generate predictions of species richness. In general, our stacked models of Cactaceae and Pinaceae were poor predictors of species richness. The relationships between observed and predicted values improved noticeably with the size of spatial extents. However, the stacked models tended to overpredict the richness of Cactaceae and over- and underpredict the richness of Pinaceae. Cactaceae stacked models showed higher sensitivity and lower specificity than those for Pinaceae. We conclude that stacked ecological niche models may be somewhat poor predictors of species richness at smaller spatial extents and should be used with caution for this purpose. Perhaps more importantly, abilities to compensate for their limitations or apply corrections to their reliability may vary with taxonomic groups.

The complete plastome sequence of Artocarpus altilis (Parkinson ex F.A. Zorn) Fosberg, (Moraceae).

Artocarpus altilis (Parkinson ex F.A. Zorn) Fosberg is native to the Pacific Islands, India, and the Philippines. It is also cultivated in Taiwan and Hainan. The complete plastome of the species was assembled and annotated in this study. The circular genome was 160,184 bp in size, presenting a typical quadripartite structure including two inverted repeats (IRs) of 25,734 bp, a large single-copy (LSC) of 88,791 bp, and a small single-copy (SSC) of 19,925 bp. The genome contained 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The total G/C content of complete plastome was 36.0%, with the corresponding values of the LSC, SSC, and IR being 33.7%, 28.8%, and 42.7%, respectively. The complete plastome sequence of A. altilis (Parkinson ex F.A. Zorn) Fosberg will make contributions to the conservation genetics of this species as well as to phylogenetic studies of Moraceae.

Spatiotemporal Variation of Urban Plant Diversity and above Ground Biomass in Haikou, China.

Understanding the drivers of urban plant diversity (UPD) and above ground biomass (AGB) in urbanized areas is critical for urban ecosystem services and biodiversity protection. The relationships between UPD and AGB have been investigated simultaneously. However, the drivers of UPD and AGB have been explored independently in tropical coastal areas at different time points. To fill this gap, we conducted a remote sensing interpretation, field plant plot surveys, and compiled socioeconomic and urban greening management survey data. We conducted spatial analyses to investigate the relationships among UPD and socioeconomic variables across different primary and secondary urban functional units (UFUs) in the tropical urban ecosystems of the coastal city of Haikou, China. The primary UFUs with the highest AGB were the recreation and leisure districts in 2015 and 2021. In 2015, AGB was mainly correlated with the number of herb species in undeveloped land and the districts of industry, business, recreation, and leisure. In 2021, AGB was affected primarily by the frequency of fertilizing, maintenance, and watering. Our study found that the relationship between UPD and AGB varied across time and space in Haikou. The plant diversity and AGB's response to human activities and socioeconomics appear to have a time-lag effect. These results provide new insights in understanding how management decisions affect urban vegetation and could be used to guide future urban green space planning in Haikou.

Plastome structure, phylogenomic analyses and molecular dating of Arecaceae.

Arecaceae is a species-rich clade of Arecales, while also being regarded as a morphologically diverse angiosperm family with numerous species having significant economic, medicinal, and ornamental value. Although in-depth studies focused on the chloroplast structure of Arecaceae, as well as inferring phylogenetic relationships using gene fragments, have been reported in recent years, a comprehensive analysis of the chloroplast structure of Arecaceae is still needed. Here we perform a comprehensive analysis of the structural features of the chloroplast genome of Arecaceae, compare the variability of gene sequences, infer phylogenetic relationships, estimate species divergence times, and reconstruct ancestral morphological traits. In this study, 74 chloroplast genomes of Arecaceae were obtained, covering five subfamilies. The results show that all chloroplast genomes possess a typical tetrad structure ranging in size between 153,806-160,122 bp, with a total of 130-137 genes, including 76-82 protein-coding genes, 29-32 tRNA genes, and 4 rRNA genes. Additionally, the total GC content was between 36.9-37.7%. Analysis of the SC/IR boundary indicated that the IR region underwent expansion or contraction. Phylogenetic relationships indicate that all five subfamilies in Arecaceae are monophyletic and that Ceroxyloideae and Arecoideae are sister groups (BS/PP = 100/1). The results of molecular dating indicate that the age of the crown group of Arecaceae is likely to be 96.60 [84.90-107.60] Ma, while the age of the stem group is 102.40 [93.44-111.17] Ma. Reconstruction of ancestral traits indicate that the ancestral characteristics of the family include monoecious plants, one seed, six stamens, and a smooth pericarp.

The complete plastome of Spondias dulcis (Anacardiaceae): an edible deciduous tree species from South America.

Spondias dulcis is a deciduous tree in the family Anacardiaceae. The species originates in South America and now is widely cultivated in tropical areas due to its edible fruits. In this study, we find that the length of the complete plastome of S. dulcis is 162,256 bp. It includes 35 tRNA genes and eight rRNA genes, 86 protein-coding genes and totally 130 genes. The complete plastome of S. dulcis includes a small single-copy (SSC) region of 18,459 bp, a large single-copy (LSC) region of 89,353 bp, and two inverted repeats (IRs) regions of 27,222 bp. The total G/C content of S. dulcis is 37.7%. It shows that S. dulcis is closely related to S. mombin within Anacardiaceae. It will contribute to the conservation genetics of S. dulcis and the phylogenetic studies in Anacardiaceae.

Global patterns of vascular plant alpha diversity.

Global patterns of regional (gamma) plant diversity are relatively well known, but whether these patterns hold for local communities, and the dependence on spatial grain, remain controversial. Using data on 170,272 georeferenced local plant assemblages, we created global maps of alpha diversity (local species richness) for vascular plants at three different spatial grains, for forests and non-forests. We show that alpha diversity is consistently high across grains in some regions (for example, Andean-Amazonian foothills), but regional 'scaling anomalies' (deviations from the positive correlation) exist elsewhere, particularly in Eurasian temperate forests with disproportionally higher fine-grained richness and many African tropical forests with disproportionally higher coarse-grained richness. The influence of different climatic, topographic and biogeographical variables on alpha diversity also varies across grains. Our multi-grain maps return a nuanced understanding of vascular plant biodiversity patterns that complements classic maps of biodiversity hotspots and will improve predictions of global change effects on biodiversity.

A Recurrence Predictive Model for Node-negative Esophageal Squamous Cell Carcinoma After Upfront Esophagectomy.

The prognosis for pathologically node-negative (pN0) esophageal squamous cell carcinoma (ESCC) with surgery alone remains poor. We aimed to develop a model for a more precise prediction of recurrence, which will allow personalized management for pN0 ESCC after upfront complete resection. Clinical and pathological records of patients with completely resected pT1-3N0M0 ESCC were retrospectively analyzed between January 2014 and December 2019. A nomogram for the prediction of recurrence was established based on the Cox regression analysis and evaluated by C-index, AUC, and calibration curves. The model was further validated using bootstrap resampling and k-fold cross-validation and compared with the 8th edition of the AJCC TNM staging system using Td-ROC, NRI, IDI, and DCA. Two-hundred-and seventy cases were included in this study. The median follow-up was 45 months. Distant and/or loco-regional recurrences were noted in 89 (33.0%) patients. The predictive model revealed pT-category, differentiation, perineural invasion, examined lymph nodes (ELN), and prognostic nutritional index (PNI) as independent risk factors for recurrence, with a c-index of 0.725 in the bootstrapping cohort. Td-ROC, NRI, and IDI showed a better predictive ability than the AJCC 8th TNM staging system. Based on this model, patients in the low-risk group had a significantly lower recurrence incidence than those in the high-risk group (p < .001). The predictive model developed in this study may facilitate the precise prediction of recurrences for pN0 ESCC after upfront surgery. Stratifying management of those patients might bring significantly better survival benefits.

Complete plastome sequence of Lonicera gynochlamydea Hemsl. (Caprifoliaceae).

We report and characterize the complete plastome of Lonicera gynochlamydea Hemsl. L. gynochlamydea is a shrub, belonging to the family Caprifoliaceae. Our results show that the length of the complete plastome is 154,643 bp, including 131 genes consisting of 84 protein-coding genes, 39 tRNA genes, and eight rRNA genes. The plastome exhibits the typical quadripartite structure and gene content of angiosperms, composed of two inverted repeats (IRs) regions of 23,846 bp, a large single-copy (LSC) region of 88,298 bp, and a small single-copy (SSC) region of 18,653 bp. The total G/C content in L. gynochlamydea plastome is 38.4%. The complete plastome sequence of L. gynochlamydea will make contributions to the conservation genetics of this species as well as to phylogenetic studies in Caprifoliaceae.

Complete plastome sequence from a cultivar of Diospyros nigra (J.F.Gmel.) M.R. Almeida (Ebenaceae): a nutritious fruit tree with high economic value cultivated in Hainan province, China.

Diospyros nigra (J.F.Gmel.) M.R.Almeida is a rare tree in the family Ebenaceae. The species is native to South America, while having been introduced to Florida and Texas (USA), India, Java and Madagascar. Additionally, this species is distributed in Guangdong Province and the southwest portion of Hainan Province, China. Here, we report and characterize the complete plastome of a cultivar of D. nigra. The length of the complete plastome is 157,168 bp, including 131 genes consisting of 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The plastome has the typical structure and gene content of angiosperms, including two inverted repeat (IR) regions of 26,095 bp, a large single copy (LSC) region of 86,610 bp and a small single-copy (SSC) region of 18,386 bp. The total G/C content of the plastome in D. nigra is 37.4%. The complete plastome sequence of D. nigra will make contributions to the conservation genetics of the species, as well as to phylogenetic studies in Ebenaceae.

The complete plastome of Syzygium odoratum (Lour.) DC. 1928 (Myrtaceae).

Syzygium odoratum (Lour.) DC. 1828 is a deciduous shrub in the family Myrtaceae. This species grows in sparse forests, especially in mountains, valleys, and broad-leaved evergreen forests along streams from 100 to 400 m above sea level. The primary distribution is in southern China (e.g. Guangdong, Guangxi, Hainan, etc.) and other south Asian countries (e.g. Vietnam). Here, we report and characterize the complete plastome from a cultivar of S. odoratum (Lour.) DC. 1828. The complete plastome is 159,352 bp in length with a typical structure and gene content found in angiosperms, including two inverted repeat regions (IRs) of 26,472 bp, a large single-copy (LSC) region of 87,993 bp, and a small single-copy (SSC) region of 18,415 bp. The plastome contains 132 genes, consisting of 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall G/C content in the plastome of S. odoratum is 36.9%. By inferring phylogenetic relationships based on the existing data of related taxa, we find that S. odoratum is most closely related to Syzygium acuminatissimum, (Blume) DC. 1828 given the current sampling. The complete plastome sequence of S. odoratum will provide a useful resource for conservation genetics of this species, as well as for phylogenetic studies involving Myrtaceae.

The complete plastome of Garcinia subelliptica, Merr. 1909 (Clusiaceae).

The complete plastome of G. subelliptica, Merr. 1909. The complete length is 158,356 bp, with the typical structure and gene content of angiosperm plastomes, including a large single-copy region (LSC) of 86,220 bp, a repeat region (IRB), and a reverse repeat region (IRA) of 27,399 bp, respectively, and a small single-copy region (SSC) of 17,338 bp. The plastome contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The total G/C content of the plastome is 36.1%.

The complete chloroplast genome sequence of a Citrus australasica cultivar (Rutaceae）.

Citrus australasica (F. Muell.) Swingle belongs to the family Rutaceae. Citrus australasica is native to eastern Australia and southeastern New Guinea, and is mainly concentrated in a small region of northern New South Wales and tropical rainforest areas in southern Queensland. The complete plastome length of C. australasica is 160,335 bp, with the typical structure and gene content of angiosperm plastids, including a 26,592 bp repeat B (IRB) region, 26,952 bp IRA, 87,678 bp large single copy (LSC) region and 18,756 bp small single copy (SSC) region. The plastid contains 135 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The total G/C content of the C. australasica plastome is 38.4%. The complete plastome sequence of C. australasica will provide useful resources for conservation genetics research of this species and phylogenetic research of Rutaceae.