Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae.

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance.

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

Arabidopsis AGAMOUS-LIKE16 and SUPPRESSOR OF CONSTANS1 regulate the genome-wide expression and flowering time.

Flowering transition is tightly coordinated by complex gene regulatory networks, in which AGAMOUS-LIKE 16 (AGL16) plays important roles. Here, we identified the molecular function and binding properties of AGL16 and demonstrated its partial dependency on the SUPPRESSOR OF CONSTANS 1 (SOC1) function in regulating flowering. AGL16 bound to promoters of more than 2,000 genes via CArG-box motifs with high similarity to that of SOC1 in Arabidopsis (Arabidopsis thaliana). Approximately 70 flowering genes involved in multiple pathways were potential targets of AGL16. AGL16 formed a protein complex with SOC1 and shared a common set of targets. Intriguingly, only a limited number of genes were differentially expressed in the agl16-1 loss-of-function mutant. However, in the soc1-2 knockout background, AGL16 repressed and activated the expression of 375 and 182 genes, respectively, with more than a quarter bound by AGL16. Corroborating these findings, AGL16 repressed the flowering time more strongly in soc1-2 than in the Col-0 background. These data identify a partial inter-dependency between AGL16 and SOC1 in regulating genome-wide gene expression and flowering time, while AGL16 provides a feedback regulation on SOC1 expression. Our study sheds light on the complex background dependency of AGL16 in flowering regulation, thus providing additional insights into the molecular coordination of development and environmental adaptation.

[The planting effect of cover crop in Sanjiang Plain, Northeast China]. / 东北三江平原覆盖作物种植效果.

The planting effect and the planting potential of 12 cover crops (Leguminous: alfalfa, smooth vetch, hairy vetch, red clover, white clover, common vetch; non-leguminous: sudangrass, green radish, Nitro radish, rape, kale, endive) in the Sanjiang Plain of Northeast China were comprehensively evaluated by soil penetration resistance, pre-winter biomass, root characteristics, and plant nitrogen accumulation. The results showed that all the 12 cover crops grew normally during the experimental sowing period. Compared with the control, all the cover crops successfully reduced soil compactness. The planting of green radish, nitro radish, and sudangrass decreased soil penetration resistance by 47.1%, 43.4% and 33.4%, respectively. The pre-winter total fresh biomass of cover crop populations was between 3.38 and 13.98 kg·m-2, and the total dry matter mass was between 0.78 and 2.43 kg·m-2. The biomass of non-leguminous cover crops was significantly higher than that of the leguminous cover crops. The group roots of radish, rape and endive had large volumes. In particular, the nitro radish roots had a vo-lume of 4018.5 cm3·m-2, and the root system of sudangrass extended over the widest horizontal range. The ash content of leguminous cover crops was significantly lower than that of non-leguminous species, which could provide more organic matter with high decomposability. The total nitrogen accumulation of cover crops varied from 18.72 to 53.09 g·m-2. Kale and endive accumulated the highest amount of nitrogen and large biomass, which could facilitate nitrogen fixation and accumulation. According to the type of main crops in Sanjiang Plain and canopy structure, planting leguminous (clover, vetch, and alfalfa) and non-leguminous (radish, kale and sudangrass) cover crops to plant inter-row or in a line mixed cropping pattern could regulate soil structure and promote nutrient cycing, with positive effects on the fertility of black soil in the Sanjiang Plain.

Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos.

MAIN CONCLUSION: CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) of woody bamboos were obviously decreased, which might regulate the internode elongation during rapid shoot growth, while CHH methylation was strongly associated with shoot developmental time or age. DNA methylation plays a critical role in the regulation of plant growth and development. Woody bamboos have a unique trait of rapid stem growth resulted from internode elongation at the shooting period. However, it is still unclear whether DNA methylation significantly controls the bamboo rapid stem growth. Here we present whole-genome DNA methylation profiles of the paleotropical woody bamboo Bonia amplexicaulis at five newly defined stages of shoot growth, named ST1-ST5. We found that CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) were significantly lower than in the incubation (ST1) and plateau stages (ST5). The changes in methylation levels mainly occurred in flanking regions of genes and gene body regions, and 23647 differentially methylated regions (DMRs) were identified between ST1 and rapid shoot growth stages (ST2-ST4). Combined with transcriptome analysis, we found that DMR-related genes enriched in the auxin and jasmonic acid (JA) signal transduction, and other pathways closely related to plant growth. Intriguingly, CHH methylation was not involved in the rapid shoot growth, but strongly associated with shoot developmental time by gradually accumulating in transposable elements (TEs) regions. Overall, our results reveal the importance of DNA methylation in regulating the bamboo rapid shoot growth and suggest a role of DNA methylation associated with development time or age in woody bamboos.

Lanthanide-Organic Frameworks with Uncoordinated Lewis Base Sites: Tunable Luminescence, Antibiotic Detection, and Anticounterfeiting.

Several new isostructural lanthanide metal-organic frameworks (Ln-MOFs), {[Ln2(L)3DMA4]·2DMA}n (1-Ln, where Ln = Eu, Tb, or EuxTb1-x), were first constructed via the solvothermal reactions of 4,6-di(4-carboxyphenyl)pyrimidine and Ln3+ ions. 1-Ln exhibits a 4-connected two-dimensional framework endowed with uncoordinated Lewis base sites. An exploration of luminescence sensing demonstrated 1-Eu can be used for the selectivity detection of dimetridazole and metronidazole antibiotics in other antibiotics, blood plasma, and urine, acting as an exceptional recyclable luminescent probe. More importantly, the luminescent inks of 1-Ln are invisible, color adjustable, and stabilized, which may greatly improve their anticounterfeiting applications.

Highly Efficient I2 Sorption, CO2 Capture, and Catalytic Conversion by Introducing Nitrogen Donor Sites in a Microporous Co(II)-Based Metal-Organic Framework.

Recently, the development of porous absorbents for efficient CO2 and I2 capture has attracted considerable attention because of severe global climate change and environmental issues with the nuclear energy. Hence, a unique porous metal-organic framework (MOF), {[Co(L)]·DMF·2H2O}n (1, DMF = N,N-dimethylformamide) with uncoordinated N atoms was rationally constructed via using a heterofunctional 4,6-bis(4'-carboxyphenyl)pyrimidine (H2L) linker. Interestingly, 1 exhibits exceptional properties for I2 sorption, CO2 capture, and catalytic conversion. Particularly, I2 can be efficiently removed in both vapor and solution forms, and the adsorption amount can reach 676.25 and 345.28 mg g-1, respectively. Furthermore, complex 1 displays high adsorption capacity for CO2 (53.78 cm3 g-1, 273 K). Consequently, 1 is expected to be a promising and practical material for environmental purification due to its excellent adsorption properties.

Porcine oviductal extracellular vesicles facilitate early embryonic development via relief of endoplasmic reticulum stress.

The key to successful in vitro embryo production (IVEP) is to mimic the natural in vivo oviductal microenvironment. Although the chemically defined media in extensive use for the in vitro culture of mammalian embryos is based on the composition of oviductal fluid, the IVEP systems in current use must still bypass the oviduct to produce embryos in vitro. Extracellular vesicles (EVs) in the oviduct are versatile intercellular delivery vehicles for maternal-embryo communication, and a lack of them can be associated with failed early embryonic development under in vitro culture conditions. Herein, we isolated EVs from porcine oviduct fluid and confirmed that oviductal EV supplementation improves the embryonic development of parthenogenetically activated (PA) embryos in terms of blastocyst formation rates and total cell numbers. Our experiments also revealed that a beneficial effect of oviductal EVs on PA embryos was achievable, at least in part, by relieving endoplasmic reticulum stress. These results suggest that the maternal-embryo communication mediated by oviductal EVs benefits early embryonic development. Given the contribution of oviductal EVs to early embryonic development, these findings offer novel insights for the optimization of current IVEP systems.

The Pharus latifolius genome bridges the gap of early grass evolution.

The grass family (Poaceae) includes all commercial cereal crops and is a major contributor to biomass in various terrestrial ecosystems. The ancestry of all grass genomes includes a shared whole-genome duplication (WGD), named rho (ρ) WGD, but the evolutionary significance of ρ-WGD remains elusive. We sequenced the genome of Pharus latifolius, a grass species (producing a true spikelet) in the subfamily Pharoideae, a sister lineage to the core Poaceae including the (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) and Bambusoideae, Oryzoideae, and Pooideae (BOP) clades. Our results indicate that the P. latifolius genome has evolved slowly relative to cereal grass genomes, as reflected by moderate rates of molecular evolution, limited chromosome rearrangements and a low rate of gene loss for duplicated genes. We show that the ρ-WGD event occurred approximately 98.2 million years ago (Ma) in a common ancestor of the Pharoideae and the PACMAD and BOP grasses. This was followed by contrasting patterns of diploidization in the Pharus and core Poaceae lineages. The presence of two FRIZZY PANICLE-like genes in P. latifolius, and duplicated MADS-box genes, support the hypothesis that the ρ-WGD may have played a role in the origin and functional diversification of the spikelet, an adaptation in grasses related directly to cereal yields. The P. latifolius genome sheds light on the origin and early evolution of grasses underpinning the biology and breeding of cereals.

Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos.

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a clade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds, and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree, we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations. [Arundinarieae; ddRAD; paleopolyploid; genome skimming; rapid diversification; incongruence.].

Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae).

Shibataea is a genus of temperate bamboos (Poaceae: Bambusoideae) endemic to China, but little is known about its phylogenetic position and interspecific relationships. To elucidate the phylogenetic relationship of the bamboo genus Shibataea, we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing (ddRAD-seq) and whole plastid genomes generated using genome skimming. Our phylogenomic analyses based on ddRAD-seq and plastome data congruently recovered Shibataea as monophyletic. The nuclear data resolved S. hispida as the earliest diverged species, followed by S. chinensis, while the rest of Shibataea can be further divided into two clades. However, the plastid and nuclear topologies conflict significantly. By comparing the results of network analysis and topologies reconstructed from different datasets, we identify S. kumasasa as the most admixed species, which may be caused by incomplete lineage sorting (ILS) or interspecific gene flow with four sympatric species. This study highlights the power of ddRAD and plastome data in resolving complex relationships in the intractable bamboo genus.

Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos.

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics.

BACKGROUND: Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their extremely slow molecular evolutionary rates, supposedly caused by their mysterious monocarpic reproduction. However, the correlation between substitution rates and flowering cycles has not been formally tested. RESULTS: Here we present 15 newly sequenced plastid genomes of temperate woody bamboos, including the first genomes ever sequenced from Madagascar representatives. A data matrix of 46 plastid genomes representing all 12 lineages of Arundinarieae was assembled for phylogenetic and molecular evolutionary analyses. We conducted phylogenetic analyses using different sequences (e.g., coding and noncoding) combined with different data partitioning schemes, revealing conflicting relationships involving internodes among several lineages. A great difference in branch lengths were observed among the major lineages, and topological inconsistency could be attributed to long-branch attraction (LBA). Using clock model-fitting by maximum likelihood and Bayesian approaches, we furthermore demonstrated extensive rate variation among these major lineages. Rate accelerations mainly occurred for the isolated lineages with limited species diversification, totaling 11 rate shifts during the tribe's evolution. Using linear regression analysis, we found a negative correlation between rates of molecular evolution and flowering cycles for Arundinarieae, notwithstanding that the correlation maybe insignificant when taking the phylogenetic structure into account. CONCLUSIONS: Using the temperate woody bamboos as an example, we found further evidence that rate heterogeneity is universal in plants, suggesting that this will pose a challenge for phylogenetic reconstruction of bamboos. The bamboos with longer flowering cycles tend to evolve more slowly than those with shorter flowering cycles, in accordance with a putative generation time effect.

Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants.

BACKGROUND: The double digest restriction-site associated DNA sequencing technology (ddRAD-seq) is a reduced representation sequencing technology by sampling genome-wide enzyme loci developed on the basis of next-generation sequencing. ddRAD-seq has been widely applied to SNP marker development and genotyping on animals, especially on marine animals as the original ddRAD protocol is mainly built and trained based on animal data. However, wide application of ddRAD-seq technology in plant species has not been achieved so far. Here, we aim to develop an optimized ddRAD library preparation protocol be accessible to most angiosperm plant species without much startup pre-experiment and costs. RESULTS: We first tested several combinations of enzymes by in silico analysis of 23 plant species covering 17 families of angiosperm and 1 family of bryophyta and found AvaII + MspI enzyme pair produced consistently higher number of fragments in a broad range of plant species. Then we removed two purifying and one quantifying steps of the original protocol, replaced expensive consumables and apparatuses by conventional experimental apparatuses. Besides, we shortened P1 adapter from 37 to 25 bp and designed a new barcode-adapter system containing 20 pairs of barcodes of varying length. This is an optimized ddRAD strategy for angiosperm plants that is economical, time-saving and requires little technical expertise or investment in laboratory equipment. We refer to this simplified protocol as MiddRAD and we demonstrated the utility and flexibility of our approach by resolving phylogenetic relationships of two genera of woody bamboos (Dendrocalamus and Phyllostachys). Overall our results provide empirical evidence for using this method on different model and non-model plants to produce consistent data. CONCLUSIONS: As MiddRAD adopts an enzyme pair that works for a broad range of angiosperm plants, simplifies library constructing procedure and requires less DNA input, it will greatly facilitate designing a ddRAD project. Our optimization of this method may make ddRAD be widely used in fields of plant population genetics, phylogenetics, phylogeography and molecular breeding.

Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids.

The Rosids is one of the largest groups of flowering plants, with 140 families and ∼70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from nuclear genes. To better understand the evolutionary history of rosids, it is necessary to investigate their phylogenetic relationships using nuclear genes. Here, we employed large-scale phylogenomic datasets composed of nuclear genes, including 891 clusters of putative orthologous genes. Combined with comprehensive taxon sampling covering 63 species representing 14 out of the 17 orders, we reconstructed the rosids phylogeny with coalescence and concatenation methods, yielding similar tree topologies from all datasets. However, these topologies did not agree on the placement of Zygophyllales. Through comprehensive analyses, we found that missing data and gene tree heterogeneity were potential factors that may mislead concatenation methods, in particular, large amounts of missing data under high gene tree heterogeneity. Our results provided new insights into the deep phylogenetic relationships of the rosids, and demonstrated that coalescence methods may effectively resolve the phylogenetic relationships of the rosids with missing data under high gene tree heterogeneity.

Multi-locus plastid phylogenetic biogeography supports the Asian hypothesis of the temperate woody bamboos (Poaceae: Bambusoideae).

In this paper we investigate the biogeography of the temperate woody bamboos (Arundinarieae) using a densely-sampled phylogenetic tree of Bambusoideae based on six plastid DNA loci, which corroborates the previously discovered 12 lineages (I-XII) and places Kuruna as sister to the Chimonocalamus clade. Biogeographic analyses revealed that the Arundinarieae diversified from an estimated 12 to 14Mya, and this was followed by rapid radiation within the lineages, particularly lineages IV, V and VI, starting from c. 7-8Mya. It is suggested that the late Miocene intensification of East Asian monsoon may have contributed to this burst of diversification. The possibilities of the extant Sri Lankan and African temperate bamboo lineages representing 'basal elements' could be excluded, indicating that there is no evidence to support the Indian or African route for migration of temperate bamboo ancestors to Asia. Radiations from eastern Asia to Africa, Sri Lanka, and to North America all are likely to have occurred during the Pliocene, to form the disjunct distribution of Arundinarieae we observe today. The two African lineages are inferred as being derived independently from Asian ancestors, either by overland migrations or long-distance dispersals. Beringian migration may explain the eastern Asian-eastern North American disjunction.

Development of porcine tetraploid somatic cell nuclear transfer embryos is influenced by oocyte nuclei.

Cloning efficiency in mammalian systems remains low because reprogramming of donor cells is frequently incomplete. Nuclear factors in the oocyte are removed by enucleation, and this removal may adversely affect reprogramming efficiency. Here, we investigated the role of porcine oocyte nuclear factors during reprogramming. We introduced somatic cell nuclei into intact MII oocytes to establish tetraploid somatic cell nuclear transfer (SCNT) embryos containing both somatic nuclei and oocyte nuclei. We then examined the influence of the oocyte nucleus on tetraploid SCNT embryo development by assessing characteristics including pronucleus formation, cleavage rate, and blastocyst formation. Overall, tetraploid SCNT embryos have a higher developmental competence than do standard diploid SCNT embryos. Therefore, we have established an embryonic model in which a fetal fibroblast nucleus and an oocyte metaphase II plate coexist. Tetraploid SCNT represents a new research platform that is potentially useful for examining interactions between donor nuclei and oocyte nuclei. This platform should facilitate further understanding of the roles played by nuclear factors during reprogramming.

Using a nano-flare probe to detect RNA in live donor cells prior to somatic cell nuclear transfer.

Many transgenes are silenced in mammalian cells (donor cells used for somatic cell nuclear transfer [SCNT]). Silencing correlated with a repressed chromatin structure or suppressed promoter, and it impeded the production of transgenic animals. Gene transcription studies in live cells are challenging because of the drawbacks of reverse-transcription polymerase chain reaction and fluorescence in situ hybridization. Nano-flare probes provide an effective approach to detect RNA in living cells. We used 18S RNA, a housekeeping gene, as a reference gene. This study aimed to establish a platform to detect RNA in single living donor cells using a Nano-flare probe prior to SCNT and to verify the safety and validity of the Nano-flare probe in order to provide a technical foundation for rescuing silenced transgenes in transgenic cloned embryos. We investigated cytotoxic effect of the 18S RNA-Nano-flare probe on porcine fetal fibroblasts, characterized the distribution of the 18S RNA-Nano-flare probe in living cells and investigated the effect of the 18S RNA-Nano-flare probe on the development of cloned embryos after SCNT. The cytotoxic effect of the 18S RNA-Nano-flare probe on porcine fetal fibroblasts was dose-dependent, and 18S RNA was detected using the 18S RNA-Nano-flare probe. In addition, treating donor cells with 500 pM 18S RNA-Nano-flare probe did not have adverse effects on the development of SCNT embryos at the pre-implantation stage. In conclusion, we established a preliminary platform to detect RNA in live donor cells using a Nano-flare probe prior to SCNT.

Subcellular Characterization of Porcine Oocytes with Different Glucose-6-phosphate Dehydrogenase Activities.

The in vitro maturation (IVM) efficiency of porcine embryos is still low because of poor oocyte quality. Although brilliant cresyl blue positive (BCB+) oocytes with low glucose-6-phosphate dehydrogenase (G6PDH) activity have shown superior quality than BCB negative (-) oocytes with high G6PDH activity, the use of a BCB staining test before IVM is still controversial. This study aimed to shed more light on the subcellular characteristics of porcine oocytes after selection using BCB staining. We assessed germinal vesicle chromatin configuration, cortical granule (CG) migration, mitochondrial distribution, the levels of acetylated lysine 9 of histone H3 (AcH3K9) and nuclear apoptosis features to investigate the correlation between G6PDH activity and these developmentally related features. A pattern of chromatin surrounding the nucleoli was seen in 53.0% of BCB+ oocytes and 77.6% of BCB+ oocytes showed peripherally distributed CGs. After IVM, 48.7% of BCB+ oocytes had a diffused mitochondrial distribution pattern. However, there were no significant differences in the levels of AcH3K9 in the nuclei of blastocysts derived from BCB+ and BCB- oocytes; at the same time, we observed a similar incidence of apoptosis in the BCB+ and control groups. Although this study indicated that G6PDH activity in porcine oocytes was correlated with several subcellular characteristics such as germinal vesicle chromatin configuration, CG migration and mitochondrial distribution, other features such as AcH3K9 level and nuclear apoptotic features were not associated with G6PDH activity and did not validate the BCB staining test. In using this test for selecting porcine oocytes, subcellular characteristics such as the AcH3K9 level and apoptotic nuclear features should also be considered. Adding histone deacetylase inhibitors or apoptosis inhibitors into the culture medium used might improve the efficiency of IVM of BCB+ oocytes.