Shulin Liu

Centromere repositioning refers to a de novo centromere formation at another chromosomal position without sequence rearrangement. This phenomenon was frequently encountered in both mammalian and plant species and has been implicated in genome evolution and speciation. To understand the dynamic of centromeres on soybean genome, we performed the pan-centromere analysis using CENH3-ChIP-seq data from 27 soybean accessions, including 3 wild soybeans, 9 landraces, and 15 cultivars. Building upon the previous discovery of three centromere satellites in soybean, we have identified two additional centromere satellites that specifically associate with chromosome 1. These satellites reveal significant rearrangements in the centromere structures of chromosome 1 across different accessions, consequently impacting the localization of CENH3. By comparative analysis, we reported a high frequency of centromere repositioning on 14 out of 20 chromosomes. Most newly emerging centromeres formed in close proximity to the native centromeres and some newly emerging centromeres were apparently shared in distantly related accessions, suggesting their emergence is independent. Furthermore, we crossed two accessions with mismatched centromeres to investigate how centromere positions would be influenced in hybrid genetic backgrounds. We found that a significant proportion of centromeres in the S9 generation undergo changes in size and position compared to their parental counterparts. Centromeres preferred to locate at satellites to maintain a stable state, highlighting a significant role of centromere satellites in centromere organization. Taken together, these results revealed extensive centromere repositioning in soybean genome and highlighted how important centromere satellites are in constraining centromere positions and supporting centromere function.

Drought has a serious impact on agricultural production, which can result in production losses ranging between 30% and 90%, depending on the crop species (Hussain et al., 2019; Lesk et al., 2016). Soybean [Glycine max (L.) Merr.] is an important crop that provides primary vegetable oil and protein as well as a supplement in livestock feed worldwide (Wilson, 2008). However, soybean is very sensitive to drought (Dong et al., 2019), and it has been revealed that from 1983 to 2009 approximately 67 Mha of harvested soybean areas experienced drought stress, resulting in a 7% total yield loss (Kim et al., 2019). To identify the genes and corresponding beneficial alleles conferring drought tolerance in soybean germplasms, we performed genome-wide association study (GWAS) using a panel of 585 soybean accessions, which had been genotyped in our previous work (Fang et al., 2017). The drought tolerance values of these 585 accessions were evaluated in the field in Shanxi Province, China (Figure S1, Table S1). GWAS identified one significant association locus on chromosome 16 ranging from 32 206 964 bp to 32 458 483 bp that covered 23 genes (Figure 1a, Table S2). Haplotype investigation showed that a C to G nonsynonymous SNP in Glyma.16G164400 (encoding a peroxidase, named as GmPrx16) was highly associated with the drought tolerance variation in soybean germplasm, suggesting that GmPrx16 might be the candidate gene in the association locus on chromosome 16 (Figure 1b). GmPrx16 was highly expressed in the root and mature leaf tissues (Figure S2a,b). Either dehydration stress treatment or withholding water treatment could induce the transcription of GmPrx16 (Figure S2c,d). A presence and absence variation (PAV) of a transposable element (TE) existed in the promoter region of GmPrx16, which was highly linked to the associated nonsynonymous SNP (Figure S2e). However, we determined that the PAV did not affect the expression of GmPrx16 in different accessions under normal and drought conditions (Figure S2f,g), indicating that the nonsynonymous SNP instead of the PAV was the causal polymorphism for the functional divergence of GmPrx16 in soybean. To validate the function of GmPrx16 in conferring drought tolerance in soybean, we performed overexpression (OE) and RNA interference (RNAi) on this gene in Dongnong No. 50 (DN50, an accession harbouring GmPrx16HapII) and obtained two independent transgenic lines for each construct (Figure S3a). Under well-watered condition, no obvious phenotypic differences were observed among DN50, OE lines and RNAi lines (Figure 1c, Figure S3b). When the 2-week-old seedling plants were subjected to drought treatment by withholding water for 12-day, the RNAi lines exhibited obvious drought-induced wilting compared with DN50 (Figure S3c); after withholding water for 14 days, the OE lines exhibited a higher drought-tolerant phenotype than DN50 (Figure 1d). Following a 14-day drought treatment, we rehydrated the plants and found that the survival rates of the OE lines were significantly higher than those of DN50, and the survival rates of the RNAi lines were significantly lower than those of DN50 (Figure 1e, Figure S3d). In consistent, malondialdehyde (MDA) content of DN50 was significantly higher than that of the OE lines, but lower than that of the RNAi lines (Figure 1f, Figure S3e). Interestingly, we also found that the GmPrx16 OE lines showed improved salt tolerance than DN50 (Figure S3f,g). These results demonstrated that GmPrx16 may play multiple roles besides drought tolerance in abiotic stress response. To test the functional divergence of GmPrx16HapI and GmPrx16HapII, we expressed the two GmPrx16 haplotypes in tobacco and observed that leaves expressing GmPrx16HapI exhibited higher peroxidase activity than that expressing GmPrx16HapII (Figure 1g). Furthermore, we compared the peroxidase activity of DN50 and the transgenic lines under drought conditions and found that the peroxidase activity in DN50 was significantly lower than that in the OE lines (Figure 1h) and higher than that in the RNAi lines (Figure 1i), consistent with the 3,3′-diaminobenzidine (DAB) staining assay (Figure S3h,i). To gain a better understanding how GmPrx16 conferred soybean drought tolerance, we performed RNA sequencing of GmPrx16 OE and RNAi lines with DN50 under drought conditions (Figure S4a,b). Gene ontology (GO) term enrichment analysis demonstrated GmPrx16 involved in multiple stress-responsive pathways (Figure S4c,d). It has been reported that peroxidases involve in lignin biosynthesis (Lee et al., 2007). Notably, pathways related to cell wall biosynthesis were also enriched (Figure S4c). We also found that the GmPrx16 OE lines had higher lignin content and the RNAi lines had lower lignin content than DN50 (Figure S4e). We randomly chose some reported and predicted genes participating in the above pathways and checking their expression levels using qRT-PCR (Figures S5 and S6). Consistent changing patterns to RNA-seq were obtained in the transgenic lines, suggesting a reliability of the RNA-seq data and also indicating that GmPrx16 influenced multiple pathways under drought stress. To determine the upstream regulator of GmPrx16, we screened a soybean root cDNA library through a one-hybrid assay (Y1H) and determined that two putative candidate regulators, Glyma.02G085900 (GmDRF1) and Glyma.07G171200 (GmDRF2), could specifically bind the promoter of GmPrx16 (Figure 1j). Transcriptional analysis showed that GmDRF1/2 were mainly expressed in leaves (Figure S7a) and either dehydration stress treatment or withholding water treatment could induce the transcription of GmDRF1/2 (Figure S7b,c). Transient transfection assays in Arabidopsis protoplasts and tobacco leaves indicated that GmDRF1/2 could significantly induce the expression of GmPrx16 (Figure 1k, Figure S7d). Therefore, we propose a model to illustrate the molecular mechanisms of GmPrx16 in modulating soybean drought tolerance (Figure 1l): GmDRF1/2 physically bind to the promoter of GmPrx16 and promote its expression, and drought stress induces the expression of GmDRF1/2, thereby influencing the accumulation of ROS and multiple stress response pathways. Taken together, we identified GmPrx16 as a key gene responsible for drought tolerance in soybean natural populations, providing insights into the development of drought-tolerant soybean cultivars by molecular design breeding. This work was supported by the National Key Research and Development Program of China (2021YFD1201101), the Taishan Scholars Program, the National Natural Science Foundation of China (32388201 and 32001501), Hainan Yazhou Bay Seed Laboratory Project (B21HJ0002 and B23YQ1501), Science and Technology Innovation Team of Soybean Modern Seed Industry in Hebei (21326313D), Support Plan for Innovation and Development of Key Industries in South Xinjiang (2022DB015), the Seed-Industrialized Development Program in Shandong Province (2021LZGC003) and Provincial Special Fund for Science and Technology Innovation and Development of Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta of Shandong Province (2022SZX15). The authors declare no conflicts of interest. Z.T. designed the research; Z.Z., J.M., X.L., S.L., X.Y., Y.L., Z.L., S.L., Z.D., Z.W., X.Y., L.Y., and M.Z. performed the research; Z.Z., S.L., and Z.T. analysed the data; Z.Z., S.L., and Z.T. wrote the manuscript. All authors reviewed the manuscript. Figure S1 Frequency distribution histogram of drought tolerance value. Figure S2 GmPrx16 is the causal gene on the chromosome 16 association locus for drought tolerance in soybean. Figure S3 GmPrx16 confers drought and salt tolerance through regulating peroxidase activity in soybean. Figure S4 GmPrx16 affects multiple signaling pathways under drought condition in soybean. Figure S5 Expression levels of reported genes participating in drought tolerance in soybean in GmPrx16 transgenic lines and DN50 under drought condition. Figure S6 Expression levels of representative genes participating in the hormone signaling pathway and cell wall biosynthesis in DN50 and GmPrx16 transgenic lines under drought condition. Figure S7 GmDRF1 and GmDRF2 regulate GmPrx16 transcription. Table S1 Information for the natural population used in the GWAS. Table S2 Candidate genes list in the locus located on chomosome 16. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.

Soybean [Glycine max (L.) Merr.] is one of the most important, but a drought-sensitive, crops. Identifying the genes controlling drought tolerance is important in soybean breeding. Here, through a genome-wide association study, we identified one significant association locus, located on chromosome 8, which conferred drought tolerance variations in a natural soybean population. Allelic analysis and genetic validation demonstrated that GmACO1, encoding for a 1-aminocyclopropane-1-carboxylate oxidase, was the causal gene in this association locus, and positively regulated drought tolerance in soybean. Meanwhile, we determined that GmACO1 expression was reduced after rhizobial infection, and that GmACO1 negatively regulated soybean nodule formation. Overall, our findings provide insights into soybean cultivars for future breeding.

The skin serves as a vital barrier, largely influenced by the commensal microbiota. Lawsonella clevelandensis, the currently recognized sole species in the genus Lawsonella, has gained increased attention as a cause of abscesses but is often overlooked due to its fastidious nature, which make its isolation and culture in the lab particularly challenging. Here, a comprehensive genomic investigation of Lawsonella was conducted using a cultivation-free metagenomic approach, focusing on 39 newly generated and 12 publicly available genomes. A novel species represented by 43 metagenome-assembled genomes (MAGs) was proposed based on mono-clade formation, 16S rDNA sequence similarity and genome-wide average nucleotide identity (ANI) values. All these MAGs were initially identified as L. clevelandensis A by GTDB-tk. Here, we designed them as 'Candidatus Lawsonella tjsk' sp. nov.. Distinct genomic characteristics between this newly proposed species and L. clevelandensis were observed. Significant fundamental functional differences between the two species were revealed by species-specific genes.