Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.

Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.

Deferoxamine/magnesium modified ß-tricalcium phosphate promotes the bone regeneration in osteoporotic rats.

Recently, Deferoxamine (DFO) and magnesium (Mg) have been identified as critical factors for angiogenesis and bone formation. However, in current research studies, there is a lack of focus on whether DFO plus Mg can affect the regeneration of ß-tricalcium phosphate (ß-TCP) in osteoporosis and through what biological mechanisms. Therefore, the present work was aimed to preparation and evaluate the effect of Deferoxamine/magnesium modified ß-tricalcium phosphate promotes (DFO/Mg-TCP) in ovariectomized rats model and preliminary exploration of possible mechanisms. The MC3T3-E1 cells were co-cultured with the exudate of DFO/Mg-TCP and induced to osteogenesis, and the cell viability, osteogenic activity were observed by Cell Counting Kit-8(CCK-8), Alkaline Phosphatase (ALP) staining, Alizarin Red Staining (RES) and Western Blot. In vitro experiments, CCK-8, ALP and ARS staining results show that the mineralization and osteogenic activity of MC3T3-E1increased significantly after intervention by DFO/Mg-TCP, as well as a higher levels of protein expressions including VEGF, OC, Runx-2 and HIF-1α. In vivo experiment, Micro-CT and Histological analysis evaluation show that DFO/Mg-TCP treatment presented the stronger effect on bone regeneration, bone mineralization and biomaterial degradation, when compared with OVX+Mg-TCP group and OVX+TCP group, as well as a higher VEGF, OC, Runx-2 and HIF-1α gene expression. The present study indicates that treatment with DFO/Mg-TCP was associated with increased regeneration by enhancing the function of osteoblasts in an OVX rat.

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia.

Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation throughout the genus. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n = 2x = 38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.

Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance.

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome.

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

Sphingomonas floccifaciens sp. nov., isolated from subterranean sediment.

A Gram-stain-negative, non-motile, non-sporulating, rod-shaped, orange-pigmented bacterium, designated strain FQM01T, was isolated from a subterranean sediment sample in the Mohe permafrost area, China. Strain FQM01T grew optimally at 25 °C, pH 7.0 and NaCl concentration of 0 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FQM01T belonged to the genus Sphingomonas. The closest phylogenetic relative was Sphingomonas spermidinifaciens GDMCC 1.657T (97.6 %), followed by Sphingomonas mucosissima DSM 17494T (97.2 %). The DNA G+C content of the isolate was 66.9 mol%. Strain FQM01T contained Q-10 as the predominant ubiquinone, and C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C16 : 0, C14 : 0 2-OH and C18 : 1ω7c 11 methyl as the major fatty acids. Major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified glycolipid. Only sym-homospermidine was detected as the polyamine. On the basis of phylogenetic and phenotypic data, strain FQM01T is considered to represent a novel species of Sphingomonas for which the name Sphingomonasfloccifaciens sp. nov. is proposed. The type strain is FQM01T (=CGMCC 1.15797T=KCTC 52630T).

Description of Sphingomonas mohensis sp. nov., Isolated from Sediment.

An aerobic, gram-reaction-negative, rod-shaped bacterium, designated strain Z6(T), was isolated from sediment collected at Mohe Basin, China. And its taxonomic position was investigated by applying a polyphasic approach. Growth occurs at 10-45 °C (optimum, 30 °C), at pH 6.0-11.0 (optimum, pH 7.0) and in the presence of 0-3.0 % (w/v) NaCl (optimum, 0 %). The polar lipid profile of strain Z6(T) revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and two unidentified phospholipids, and the major quinone was Q-10. The major fatty acids were C18:1 ω7c and/or C18:1 ω6c (summed feature 8) and C16:1 ω6c and/or C16:1 ω7c (summed feature 3). The predominant polyamine was homospermidine. The DNA G + C content of strain Z6(T) is 65.2 mol%. On the basis of the polyphasic evidence presented, strain Z6(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas mohensis sp. nov. is proposed. The type strain is Z6(T) (=CGMCC 1.12891(T) = JCM 19983(T)).

[Molecular cloning and localization of Leishmania donovani expression site associated genes-like protein].

OBJECTIVE: To clone the novel gene that specifically expressed in the amastigotes of Leishmania donovani, and observe subcellular localization of the gene encoding protein. METHODS: mRNA from promastigotes and amastigotes of L. donovani were prepared. The novel expressed sequence tag of amastigotes was selected by suppression subtractive hybridization. The expression of the novel gene in different stages of L. donovani was detected by Northern hybridization and semi-quantitative RT-PCR. The subcellular localization of the novel gene encoding protein was observed. RESULTS: The subtractive library of the specifically expressed sequence tag of amastigotes was constructed, and a novel gene designated as expression site associated genes-like protein (ESAGLP) gene was cloned. The full length of ESAGLP cDNA was 2,258 bp. The open-reading frame encoded a polypeptide of 620 amino acid residues. ESAGLP gene expressed only in amastigotes, the encoding protein was localized in the mitochondria. CONCLUSION: The ESAGLP gene is identified as a novel gene which specifically expressed in Leishmania donovani amastigotes, and its encoding protein is localized in the mitochondria.

[Virulence-associated gene profiling of different Leishmania spp].

OBJECTIVE: To investigate the expression level of virulence-associated genes in promastigotes and amastigotes of different Leishmania spp. METHODS: Total RNA was extracted from the promastigotes and amastigotes of Leishmania donovani, L. infantum, L. tropica, L. major and L. mexicana, and relevant strains. According to the reported gene sequences in GenBank, primers were designed in relation to the virulence-associated genes [GDP-mannose pyrophosphorylase (GDPMP), 3'a2rel-related protein (A2rel), beta-galactofuranosyl transferase (LPG1), lipophosphoglycan biosynthetic protein (LPG2), kinetoplast membrane protein 11 (KMP-11), cpc gene for cysteine proteinase (CPC), hydrophilic acylated surface protein (HASPB1), cathepsin L-like cysteine protease (CPB2), cathepsin L-like cysteine proteinase lmcpb2.8 (CPB2.8), Mr 100 000 heat shock protein (CLP b)], and control genes (alpha tubulin gene and GAPDH). Semi-quantitative RT-PCR was performed to detect expression level of these genes in promastigotes and amastigotes of different Leishmania spp. RESULTS: There was a significant difference in the expression profiles of the genes among the promastigotes and amastigotes of different Leishmania spp. The HASPB1 was detected in the amastigotes of all strains and promastigotes of L. donovani, the GDPMP, LPG1, LPG2, CPB2.8, CPB2, CPC, A2rel and CLP b were expressed in the promastigotes and/or amastigotes of the specific Leishmania spp, respectively. None of the stains carried the KMP-11 gene, whereas the amastigotes of L. donovani SC10 strain and L. major 5ASKH strain possessed CPC. CONCLUSION: The expression profile of the virulence-associated genes shows species-specific and stage-specific differences.