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Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species. [ABSTRACT FROM AUTHOR]

Due to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations, and small variations including single nucleotide polymorphisms and insertions/deletions. A simple linear pan-genome does not allow these structural variations to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and structural variation information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genomes is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding. [ABSTRACT FROM AUTHOR]

Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments. [ABSTRACT FROM AUTHOR]

Summary: Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single‐nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small‐ (30–10 000 bp) to mid‐scale (10 000–30 000 bp) SV and their impact on evolution and adaptation‐related traits in plants. This might be attributed to complex and highly duplicated nature of plant genomes, which makes them difficult to assess using high‐throughput genome screening methods. Here, we describe how long‐read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small‐ to mid‐scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small‐ to mid‐scale SV events. Nearly half of these SV events ranged between 100 bp and 1000 bp, which makes them challenging to detect using short‐read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco‐geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium‐coverage long‐read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement. [ABSTRACT FROM AUTHOR]

Similar to the method proposed in rice pan-genome (Wang I et al i ., 2018a, 2018b), we constructed the pan-genome of I B. napus i by "PVs + map-to-pan" strategy based on well-assembled ZS11 reference genome (Figure 1a, Song I et al i ., 2020). Keywords: Brassica napus; pan-genome; rapeseed population; presence/absence variations (PAVs); homolog; gene index EN Brassica napus pan-genome rapeseed population presence/absence variations (PAVs) homolog gene index 412 414 3 03/15/21 20210301 NES 210301 I Brassica napus i ( I B. napus i ) was originally formed ~7500 years ago by interspecific hybridization between I B. rape i and I B. oleracea i (Chalhoub I et al i ., 2014), which supplies approximately 13%-16% of the vegetable oil globally. (l) Literature of rapeseed. gl Compared with ZS11 reference genome, the I B. napus i pan-genome adds 781.9 Mb sequences and 21 020 protein-coding genes, which are classified into "core genes" (exist in >=95% of all rapeseed accessions) and "distributed genes" (exist in <95% of all accessions) by their presence in each variety. Based on the above eight I B. napus i reference genomes, and a collection of 1688 rapeseed re-sequencing data, we constructed a comprehensive database, I B. napus i pan-genome information resource (BnPIR, http://cbi.hzau.edu.cn/bnapus), which is based on gene information module, with Pan-genome Browser and Gbrowse Synteny as the core, and containing multi-omics data and common bioinformatics tools. [Extracted from the article]

The updated genome of Bacillus licheniformis WX-02 comprises a circular chromosome of 4 286 821 base-pairs containing 4512 protein-coding genes. We applied strand-specific RNA-sequencing to explore the transcriptome profiles of B. licheniformis WX-02 under normal and high-salt conditions (NaCl 6%). We identified 2381 co-expressed gene pairs constituting 871 operon structures. In addition, 1169 antisense transcripts and 90 small RNAs were detected. Systematic comparison of differentially expressed genes under different conditions revealed that genes involved in multiple functions were significantly repressed in long-term high salt adaptation process. Genes related to promotion of glutamic acid synthesis were activated by 6% NaCl, potentially explaining the high yield of γ-PGA under salt condition. This study will be useful for the optimization of crucial metabolic activities in this bacterium. [ABSTRACT FROM AUTHOR]

We report two novel titanium-based pnictide oxide compounds (EuF) 2 Ti 2 Pn 2 O (Pn = Sb, Bi), which are synthesized by replacing Sr 2+ in (SrF) 2 Ti 2 Pn 2 O [Liu, R. H. Structure and Physical Properties of the Layered Pnictide-Oxides: (SrF) 2 Ti 2 Pn 2 O ( Pn = As, Sb) and (SmO) 2 Ti 2 Sb 2 O. Chem. Mater. 2010, 22, 1503-1508] with Eu 2+ using a solid-state reaction. (EuF) 2 Ti 2 Sb 2 O exhibits an obvious anomaly in resistivity and heat capacity at T ∼ 195 K, which may arise from the spin-density wave/charge-density wave instability. Similar features are also observed in BaTi 2 Pn 2 O, (SrF) 2 Ti 2 Pn 2 O, and Na 2 Ti 2 Pn 2 O (Pn = As and Sb) [Liu, R. H. Structure and Physical Properties of the Layered Pnictide-Oxides: (SrF) 2 Ti 2 Pn 2 O ( Pn = As, Sb) and (SmO) 2 Ti 2 Sb 2 O. Chem. Mater. 2010, 22, 1503-1508, Ozawa, T. C. Chemistry of layered d-metal pnictide oxides and their potential as candidates for new superconductors. Sci. Technol. Adv. Mater. 2008, 9, 033003, Wang, X. F. Structure and physical properties for a new layered pnictide-oxide: BaTi 2 As 2 O. J. Phys.: Condens. Matter. 2010, 22, 075702, and Xu, H. C. Electronic structure of the BaTi 2 As 2 O parent compound of the titanium-based oxypnictide superconductor. Phys. Rev. B 2014, 89, 155108]. Magnetic susceptibility measurements indicate an antiferromagnetic transition at T ∼ 2.5 K for (EuF) 2 Ti 2 Sb 2 O. In particular, the electronic specific heat coefficients of both (EuF) 2 Ti 2 Sb 2 O and (EuF) 2 Ti 2 Bi 2 O are significantly enhanced compared to those of (SrF) 2 Ti 2 Pn 2 O, Na 2 Ti 2 Pn 2 O, and BaTi 2 Pn 2 O, 1,5,6 which may be due to a strong electron correlation effect in this system. Thus, (EuF) 2 Ti 2 Pn 2 O (Pn = Sb, Bi) may provide new platforms for studying density wave, magnetic ordering, and electron correlation effects.