Pan-Genome of Wild and Cultivated Soybeans.

Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.

Tandem duplication and sub-functionalization of clerodane diterpene synthase originate the blooming of clerodane diterpenoids in Scutellaria barbata.

Scutellaria barbata is a traditional Chinese herb medicine and a major source of bioactive clerodane diterpenoids. However, barely clerodanes have been isolated from the closely related S. baicalensis. Here we assembled a chromosome-level genome of S. barbata and identified three class II clerodane diterpene synthases (SbarKPS1, SbarKPS2 and SbaiKPS1) from these two organisms. Using in vitro and in vivo assays, SbarKPS1 was characterized as a monofunctional (-)-kolavenyl diphosphate synthases ((-)-KPS), while SbarKPS2 and SbaiKPS1 produced major neo-cleroda-4(18),13E-dienyl diphosphate with small amount of (-)-KPP. SbarKPS1 and SbarKPS2 shared a high protein sequence identity and formed a tandem gene pair, indicating tandem duplication and sub-functionalization probably led to the evolution of monofunctional (-)-KPS in S. barbata. Additionally, SbarKPS1 and SbarKPS2 were primarily expressed in the leaves and flowers of S. barbata, which was consistent with the distribution of major clerodane diterpenoids scutebarbatine A and B. In contrast, SbaiKPS1 was barely expressed in any tissue of S. baicalensis. We further explored the downstream class I diTPS by functional characterizing of SbarKSL3 and SbarKSL4. Unfortunately, no dephosphorylated product was detected in the coupled assays with SbarKSL3/KSL4 and four class II diTPSs (SbarKPS1, SbarKPS2, SbarCPS2 and SbarCPS4) when a phosphatase inhibitor cocktail was included. Co-expression of SbarKSL3/KSL4 with class II diTPSs in yeast cells did not increase the yield of the corresponding dephosphorylated products, either. Together, these findings elucidated the involvement of two class II diTPSs in clerodane biosynthesis in S. barbata, while the class I diTPS is likely not responsible for the subsequent dephosphorylation step.

Integrating spatial transcriptomics and single-cell RNA-sequencing reveals the alterations in epithelial cells during nodular formation in benign prostatic hyperplasia.

OBJECTIVE: Proliferative nodular formation represents a characteristic pathological feature of benign prostatic hyperplasia (BPH) and serves as the primary cause for prostate volume enlargement and consequent lower urinary tract symptoms (LUTS). Its specific mechanism is largely unknown, although several cellular processes have been reported to be involved in BPH initiation and development and highlighted the crucial role of epithelial cells in proliferative nodular formation. However, the technological limitations hinder the in vivo investigation of BPH patients. METHODS: The robust cell type decomposition (RCTD) method was employed to integrate spatial transcriptomics and single cell RNA sequencing profiles, enabling the elucidation of epithelial cell alterations during nodular formation. Immunofluorescent and immunohistochemical staining was performed for verification. RESULTS: The alterations of epithelial cells during the formation of nodules in BPH was observed, and a distinct subgroup of basal epithelial (BE) cells, referred to as BE5, was identified to play a crucial role in driving this progression through the hypoxia-induced epithelial-mesenchymal transition (EMT) signaling pathway. BE5 served as both the initiating cell during nodular formation and the transitional cell during the transformation from luminal epithelial (LE) to BE cells. A distinguishing characteristic of the BE5 cell subgroup in patients with BPH was its heightened hypoxia and upregulated expression of FOS. Histological verification results confirmed a significant association between c-Fos expression and key biological processes such as hypoxia and cell proliferation, as well as the close relationship between hypoxia and EMT in BPH tissues. Furthermore, a strong link between c-Fos expression and the progression of BPH was also been validated. Additionally, notable functional differences were observed in glandular and stromal nodules regarding BE5 cells, with BE5 in glandular nodules exhibiting enhanced capacities for EMT and cell proliferation characterized by club-like cell markers. CONCLUSIONS: This study elucidated the comprehensive landscape of epithelial cells during in vivo nodular formation in patients, thereby offering novel insights into the initiation and progression of BPH.

Global dissection of R2R3-MYB in Pogostemon cablin uncovers a species-specific R2R3-MYB clade.

MYB family is one of the largest transcription factor families in plants and plays a crucial role in regulating plant biochemical and physiological processes. However, R2R3-MYBs in patchouli have not been systematically investigated. Here, based on the gene annotation of patchouli genome sequence, 484 R2R3-MYB transcripts were detected. Further in-depth analysis of the gene structure and expression of R2R3-MYBs supported the tetraploid hybrid origin of patchouli. When combined with R2R3-MYBs from Arabidopsis, a phylogenetic tree of patchouli R2R3-MYBs was constructed and divided into 31 clades. Interestingly, a patchouli-specific R2R3-MYB clade was found and confirmed by homologous from other Lamiaceae species. The syntenic analysis demonstrated that tandem duplication contributed to its evolution. This study systematically analysed the R2R3-MYB family in patchouli, providing information on its gene characterization, functional prediction, and species evolution.

Anisotropic Sensing Performance in a High-Sensitivity Surface Plasmon Resonance Sensor Based on Few-Layer Black Phosphorus.

Few-layer black phosphorus (FLBP) is a highly promising material for high sensitivity label-free surface plasmon resonance (SPR) sensors due to its exceptional electrical, optical, and mechanical properties. FLBP exhibits inherent anisotropy with different refractive indices along its two main crystal orientations, the zigzag and armchair axes. However, this anisotropic property is often overlooked in FLBP-based sensors. In this study, we conducted a comprehensive investigation of the SPR reflectivity and phase in a BK7-Ag-FLBP structure to understand the influence of the stacking sequence and the number of FLBP layers on the sensing performance. Clear resonant angle shifts caused by different stacking sequences of FLBP could be observed both theoretically and experimentally. In the theoretical study, the highest reflective and phase sensitivities were achieved with a 12-layer black phosphorus (BP) structure. The reflectivity sensitivity reached 287.9°/refractive index units (RIU) with the zz stacking 12-layer BP film exhibiting a sensitivity 76°/RIU higher than the ac stacking structure. Similarly, the phase sensitivity reached 1162°/RIU with the zz stacking 12-layer BP structure showing a sensitivity 276.9°/RIU higher than the ac stacking structure. The electric field distribution of the 12-layer BP structure with four different stacking sequences has also been analyzed. In the experiment study, the well-known Attenuated Total Reflection (ATR) θ-2θ SPR setup is utilized to detect the reflectivity and phase of BK7-Ag-FLBP structures. The FLBP samples with the same thickness but different stacking sequences show significant resonant angle shift (0.275°) and maximum phase difference variation (34.6°). The FLBP sample thickness and crystal orientations have been demonstrated using the angular-resolved polarized Raman spectroscopy (ARPRS). These theoretical and experimental results provide strong evidence that the stacking sequences of FLBP have a significant impact on the sensing performance of SPR sensors. By harnessing the anisotropic properties of materials like FLBP, novel structures of anisotropic-2D material-based SPR sensors could open up exciting possibilities for innovative applications.

Frontiers of soybean pan-genome studies.

Artificial domestication provided the original motivation to the blooming of agriculture, following with the dramatic change of the genetic background of crops and livestock. According to theory and technology upgradation that contributing to the omics, we appreciate using the pan-genome instead of single reference genome for crop study. By comparison and integration of multiple genomes under the guidance of pan-genome theory, we can estimate the genomic information range of a species, leading to a global understanding of its genetic diversity. Combining pan-genome with large size chromosomal structural variations, high throughput population resequencing, and multi-omics data, we can profoundly study the genetic basis behind species traits we focus on. Soybean is one of the most important commercial crops over the world. It is also essential to our food security. Dissecting the formation of genetic diversity and the causal loci of key agricultural traits of soybean will make the modern soybean breeding more efficiently. In this review, we summarize the core idea of pan-genome and clarified the characteristics of construction strategies of pan-genome such as de novo/mapping assembly, iterative assembly and graph-based genome. Then we used the soybean pan-genome work as a case study to introduce the general way to study pan-genome. We highlighted the contribution of structural variation (SV) to the evolution/domestication of soybean and its value in understanding the genetic bases of agronomy traits. By those, we approved the value of graph-based pan-genome for data integration and SV calculation. Future research directions are also discussed for crop genomics and data science.

MnO2 nanoparticles decorated with Ag/Au nanotags for label-based SERS determination of cellular glutathione.

A novel stimulus-responsive surface-enhanced Raman scattering (SERS) nanoprobe has been developed for sensitive glutathione (GSH) detection based on manganese dioxide (MnO2) core and silver/gold nanoparticles (Ag/Au NPs). The MnO2 core is not only capable to act as a scaffold to amplify the SERS signal via producing "hot spots", but also can be degraded in the presence of the target and thus greatly enhance the nanoprobe sensitivity for sensing of GSH. This approach enables a wide linear range from 1 to 100 µM with a 2.95 µM (3σ/m) detection limit. Moreover, the developed SERS nanoprobe represents great possibility in both sensitive detection of intracellular GSH and even can monitor the change of intracellular GSH level when the stimulant occurs. This sensing system not merely offers a novel strategy for sensitive sensing of GSH, but also provides a new avenue for other biomolecules detection.

One-Pot Self-Assembly of Dual-Color Domes Using Mono-Sized Silica Nanoparticles.

Spots with dual structural colors on the skin of some organisms in nature are of tremendous interest due to the unique function of their dye-free colors. However, imitation of them requires complicated manufacturing processes, expensive equipment, and multiple predesigned building blocks. In this work, a one-pot strategy based on the phase-separation-assisted nonuniform self-assembly of monosized silica nanoparticles is developed to construct domes with dual structural colors. In drying poly(ethylene glycol)-dextran-based (PEG-DEX) droplets, monosized nanoparticles distribute nonuniformly in two compartments due to the droplet inner flow and different nanoparticle compatibility with the two phases. The dome colors are derived from the self-assembled nanoparticles and are programmable by regulating the assembly conditions. The one-pot strategy enables the preparation of multicolor using only one type of building block. With the dual-color domes, encrypted patterns with a high volume of contents are designed, showing promising applications in information delivery.

Whole-Genome Resequencing Reveals the Diversity of Patchouli Germplasm.

As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli's genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on them. In total, 402,650 single nucleotide polymorphisms (SNPs) and 153,233 insertions/deletions (INDELs) were detected. Based on these abundant genetic variants, patchouli accessions were primarily classified into the Chinese group and the Southeast Asian group. However, the accession SP (Shipai) collected from China formed a distinct subgroup within the Southeast Asian group. As SP has been used as a genuine herb in traditional Chinese medicine, its unique molecular markers have been subsequently screened and verified. For 26,144 specific SNPs and 16,289 specific INDELs in SP, 10 of them were validated using Polymerase Chain Reaction (PCR) following three different approaches. Further, we analyzed the effects of total genetic variants on genes involved in the sesquiterpene synthesis pathway, which produce the primary phytochemical compounds found in patchouli. Eight genes were ultimately investigated and a gene encoding nerolidol synthetase (PatNES) was chosen and confirmed through biochemical assay. In accession YN, genetic variants in PatNES led to a loss of synthetase activity. Our results provide valuable information for understanding the diversity of patchouli germplasm resources.

Senolytic therapy ameliorates renal fibrosis postacute kidney injury by alleviating renal senescence.

Acute kidney injury (AKI) is a common clinical problem, and patients who survive AKI have a high risk of chronic kidney disease (CKD). The mechanism of CKD post-AKI, characterized by progressive renal fibrosis, is still unclear. Maladaptive tubular epithelial cells (TECs) after AKI are considered a leading cause of renal fibrosis post-AKI. TECs under maladaptive repair manifest characteristics of senescence. Removing senescent TECs by genetic ablation has been proven effective in reducing renal fibrosis. Senolytics, which eliminate senescent cells by pharmacological intervention, have been studied in a series of degenerative diseases. To our knowledge, the effects of senolytics on renal fibrosis post-AKI have not been verified before. Here, we confirmed renal senescence in the unilateral ischemia/reperfusion injury murine model. Senescent TECs could activate fibroblasts and senolytics specifically induced apoptosis of senescent TECs. Next, we demonstrated that senolytics could reduce renal senescence and ameliorate renal fibrosis in both unilateral renal ischemia/reperfusion injury and multiple-cisplatin-treatment murine models. Our results indicate senescent TECs as a vital factor in renal fibrosis progression, and senolytic therapy might be promising for treating CKD post-AKI.

Twisted electromagnetic elliptical multi-Gaussian Schell-model beams and their transmission in random media.

We extend the scalar elliptical multi-Gaussian Schell-model (EMGSM) beams with twist phase to the electromagnetic domain and obtain the analytical expression for the propagation of the electromagnetic twisted EMGSM beams through random media. The twist phase-induced changes of the spectral density and degree of polarization of such beams on propagation are studied numerically. Results show that by adjusting the twist factor and the correlated parameters of the source, both the spectral density and degree of polarization not only rotate around the propagation axis but also exhibit diverse shapes. The flattopped ellipse-like and diamond-like shape maintain over a relatively long propagation distance and finally involve into Gaussian-like shape due to stronger atmospheric turbulence. The results will be useful in optical trapping and optical communication.

OsbHLH057 targets the AATCA cis-element to regulate disease resistance and drought tolerance in rice.

KEY MESSAGE: The AATCA motif was identified to respond pathogens infection in the promoter of defense-related gene Os2H16. OsbHLH057 bound to the motif to positively regulate rice disease resistance and drought tolerance. Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani, is a devastating disease in rice (Oryza sativa L.). The transcriptional regulation of host defense-related genes in response to R. solani infection is poorly understood. In this study, we identified a cis-element, AATCA, in the promoter of Os2H16, a previously identified multifaceted defense-related gene in rice that responded to fungal attack. Using a DNA pull-down assay coupled with mass spectrometry, a basic helix-loop-helix (bHLH) transcription factor OsbHLH057 was determined to interact with the AATCA cis-element. OsbHLH057 was rapidly induced by R. solani, Xanthomonas oryzae pv. oryzae (Xoo), and osmotic stress. Furthermore, overexpressing OsbHLH057 enhanced rice disease resistance and drought tolerance, while knocking out OsbHLH057 made rice more susceptible to pathogens and drought. Overall, our results uncovered an OsbHLH057 and AATCA module that synergistically regulates the expression of Os2H16 in response to R. solani, Xoo, and drought in conjunction with the previously identified stress-related OsASR2 and GT-1 module.

Colorimetric/SERS dual-channel nanoprobe for reactive oxygen species monitoring in elucidating the mechanism of chemotherapeutic drugs action on cancer cells.

Reactive oxygen species (ROS) are involved in drug-induced cytotoxicity by regulating cell signaling, inducing oxidative stress, and damaging the DNA and proteins. Examining ROS production in cells under the stimulation of chemotherapeutic drugs is of great importance for understanding the ROS roles and identifying the mechanism of drug-induced cytotoxicity. Here, a silver/gold (Ag/Au) nanoshell-based colorimetric and surface-enhanced Raman spectroscopy (SERS) dual-response nanoprobe was proposed for ROS sensing on the basis of Ag etching. In this study, as a kind of ROS, hydrogen peroxide (H2O2) was detected by the prepared nanoprobe. The linear ranges of 0.5-100 µM with a limit of detection (LOD) of 0.343 µM for the colorimetric determination and 1-50 µM with LOD of 0.294 µM for SERS determination were achieved. The detection of cellular ROS concentration after stimulation by cisplatin, paclitaxel, doxorubicin, and 5-fluorouracil was validated by the nanoprobe. The nanoprobe could also be used to detect the signal pathway of ROS production by cisplatin stimulation. This study provided a simple and novel dual-response nanoplatform for detecting and monitoring ROS in cells, which holds great potential for elucidating the mechanism of occurrence and treatment of ROS-involved diseases.

Diagnosis and genetic analysis of a case with Bardet-Biedl syndrome caused by compound heterozygous mutations in the BBS12 gene.

Bardet-Biedl syndrome (BBS) is a rare autosomal recessive ciliopathy, which is caused by mutations mainly in genes encoding BBSome complex and IFT complex. Here, we reported a 21-year-old female with BBS characterized by three primary features including obesity, retinitis pigmentosa sine pigmento and bilateral renal cysts. She also had some secondary features such as diabetes mellitus, nonalcoholic fatty liver disease, subclinical hypothyroidism and mild conductive hearing damage. Whole exome sequencing revealed two compound heterozygous mutations in exon 2 of the BBS12 gene (c.188delC, p.T63fs and c.1993_1995del, p.665_665del) in this patient. Sanger sequencing showed that her father and mother carried c.188delC (p.T63fs) and c.1993_1995del (p.665_665del) variants, respectively, while her parents were free of BBS-related symptoms. In conclusion, this case reported two novel mutations (c.188delC, p.T63fs and c.1993_1995del, p.665_665del) of the BBS12 gene in a girl presented with BBS, which provides novel genetic resources for studies of the disease. Meanwhile, the BBS case shows the entire development progress from her birth to adulthood, which helps facilitate clinicians' understanding of BBS.

Discovery and Functional Characterization of a Diverse Diterpene Synthase Family in the Medicinal Herb Isodon lophanthoides Var. gerardiana.

Isodon lophanthoides var. gerardiana (Lamiaceae), also named xihuangcao, is a traditional Chinese medicinal herb that exhibits a broad range of pharmacological activities. Abietane-type diterpenoids are the characteristic constituents of I. lophanthoides, yet their biosynthesis has not been elucidated. Although the aerial parts are the most commonly used organs of I. lophanthoides, metabolite profiling by gas chromatography-mass spectrometry showed the underground parts also contain large amounts of labdane diterpenoids including abietatriene, miltiradiene and ferruginol, which are distinct from the 13-hydroxy-8(14)-abietene detected in the aerial parts. Comparative transcriptome analysis of root and leaf samples identified a diverse diterpene synthase family including 6 copalyl diphosphate synthase (IlCPS1-6) and 5 kaurene synthase-like (IlKSL1-5). Here we report the functional characterization of six of these enzymes using yeast heterologous expression system. Both IlCPS1 and IlCPS3 synthesized (+)-copalyl diphosphate (CPP), in combination with IlKSL1 resulted in miltiradiene, precursor of abietane-type diterpenoids, while coupling with IlKSL5 led to the formation of hydroxylated diterpene scaffold nezukol. Expression profiling and phylogenetic analysis further support the distinct evolutionary relationship and spatial distribution of IlCPS1 and IlCPS3. IlCPS2 converted GGPP into labda-7,13E-dien-15-ol diphosphate. IlCPS6 was identified as ent-CPS, indicating a role in gibberellin metabolism. We further identified a single residue that determined the water addition of nezukol synthase IlKSL5. Substitution of alanine 513 with isoleucine completely altered the product outcome from hydroxylated nezukol to isopimara-7,15-diene. Together, these findings elucidated the early steps of bioactive abietane-type diterpenoid biosynthesis in I. lophanthoides and the catalytic mechanism of nezukol synthase.

Investigating Lysosomal Autophagy via Surface-Enhanced Raman Scattering Spectroscopy.

Autophagy plays a critical role in many vitally important physiological and pathological processes, such as the removal of damaged and aged organelles and redundant proteins. Although autophagy is mainly a protective process for cells, it can also cause cell death. In this study, we employed in situ and ex situ surface-enhanced Raman scattering (SERS) spectroscopies to obtain chemical information of lysosomes of HepG2 cells. Results reveal that the SERS profiles of the isolated lysosomes are different from the in situ spectra, indicating that lysosomes lie in different microenvironments in these two cases. We further investigated the molecular changes of isolated lysosomes according to the autophagy induced by starvation via ex situ SERS. During autophagy, the conformation of proteins and the structures of lipids have been affected, and autophagy-related molecular evidence is given for the first time in the living lysosomes. We expect that this study will provide a reference for understanding the cell autophagy mechanism.

Fluorescence-active and peroxidase-like expanded mesoporous silica-encapsulated ultrasmall Pt nanoclusters: a novel colorimetric/fluorescent dual-mode nanosensor for sensitive detection of mercury in medicinal and edible Pueraria lobata.

A novel colorimetric/fluorescent dual-mode nanosensor for Hg2+ detection was constructed using expanded mesoporous silica (EMSN)-encapsulated ultrasmall platinum nanoclusters (EMSN@Pt NCs) with improved peroxidase-like and stable fluorescent activities. The sensing technique was based on the mechanism that the peroxidase mimetic activity and fluorescence intensity of EMSN@Pt NCs can be inhibited in the presence of Hg2+. In this sensing platform, a linear range of 5-50 nM with a detection limit of 1.78±0.38 nM and quantification limit of 5.93 nM was obtained via fluorescent analysis. A linear calibration curve from 0.25 to 200 nM with a detection limit of 8.25±0.51 nM and quantification limit of 27.47 nM was achieved via colorimetric analysis. The proposed dual-mode probe possesses excellent selectivity and reliability for Hg2+ detection, which can function as an efficient nanosensor for the quantitative determination of Hg2+ in Pueraria lobata.

Adsorption of Co(II) from aqueous solution using municipal sludge biochar modified by HNO3.

Here adsorption studies were proposed on a carboxylated sludge biochar (CSB) material modified by HNO3 to assess its capacity in the removal of cobalt from aqueous solution. The as-prepared sludge biochar material was characterized by Brunauer-Emmett-Teller (BET) analysis, Fourier transform infrared (FT-IR) spectroscopy, thermogravimetric analysis (TGA), energy-dispersive spectroscopy (EDS) and X-ray photoelectron spectroscopy (XPS). The isotherm process could be well described by the Langmuir isotherm model. The adsorption kinetics indicated that cobalt adsorption followed a pseudo-second-order kinetics model. The mechanism between Co(II) and biochar involved electrostatic interaction, ion exchange, surface complexation and physical function. The adsorption capacity on CSB was as high as 72.27 mg·g-1, surpassing original sludge biochar (SB) as CSB had abundant oxygen-containing functional groups and many hydroxyls, plus the BET surface areas increased when SB was modified by HNO3, which stimulated adsorption effect. Therefore, this work shows that CSB could be used as an efficient adsorbent to remove Co(II) in wastewater.

Revealing Mitochondrial Microenvironmental Evolution Triggered by Photodynamic Therapy.

Mitochondrion is one of the most important organelles and becomes a target in many cancer therapeutic strategies. Mitochondrial microenvironments in response to therapeutic methods are the key to understand therapeutic mechanisms. However, they are almost rarely studied. Herein, the mitochondrial microenvironments, including mitochondrial membrane potential (MMP) and reactive oxygen species (ROS) after different photodynamic therapy (PDT) dosages, were monitored by fluorescent imaging and compared among three cell lines (HepG2, MCF-7, and LO2). Furthermore, the fluctuations of intramitochondrial pHs were revealed via a plasmonic mitochondrion-targeting surface-enhanced Raman scattering (SERS) pH nanosensor. Results indicate that the MMP decreases gradually with the ROS generation and the cancerous cells exhibit less response to excess ROS relative to normal cells. On the other hand, the pH value in the mitochondria decreases initially and then increases when the amount of ROS increases. The LO2 cell is preliminarily evidenced to have a higher self-adjustment ability due to its better tolerance to differential intra/extracellular pHs. This study may provide a basis for an in-depth understanding of the mechanisms of the mitochondrial targeting-based PDT therapeutic processes. It is also helpful for more accurate and useful diagnosis according to intramitochondrial microenvironments and improvement on therapy efficiency of cancers.

Polarization state dependence of laser-induced domain nucleation in lithium niobate crystals investigated by digital holography.

This paper systematically investigates the influences of polarization states on laser-induced domain nucleation in z-cut LiNbO3 crystals. The real-time 2D and 3D phase distributions at the focus during laser-induced domain nucleation were reconstructed by digital holography. The different LiNbO3 samples, including undoped congruent LiNbO3, Mg-doped congruent LiNbO3, Hf-doped congruent LiNbO3, and stoichiometric LiNbO3, were tested. The systematical comparisons of phase mapping and nucleation fields with different polarization states, including linear polarization, circular polarization, and elliptical polarization, have been carried out. The polarization states proved to be a key influence factor for the laser-induced domain nucleation. It was demonstrated that the generated bulk photovoltaic field along the -z direction was an important mechanism for laser-induced preferential domain nucleation. This work is of great significance for the future development of ferroelectric domain engineering of LiNbO3 crystals.