Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution

The telomere-to-telomere genome of Pucai () (Typha angustifolia L.): a distinctive semiaquatic vegetable with lignin and chlorophyll as quality characteristics

Pucai () (Typha angustifolia L.), within the Typha spp., is a distinctive semiaquatic vegetable. Lignin and chlorophyll are two crucial traits and quality indicators for Pucai. In this study, we assembled a 207.00-Mb high-quality gapless genome of Pucai, telomere-to-telomere (T2T) level with a contig N50 length of 13.73 Mb. The most abundant type of repetitive sequence, comprising 16.98% of the genome, is the long terminal repeat retrotransposons (LTR-RT). A total of 30 telomeres and 15 centromeric regions were predicted. Gene families related to lignin, chlorophyll biosynthesis, and disease resistance were greatly expanded, which played important roles in the adaptation of Pucai to wetlands. The slow evolution of Pucai was indicated by the σ whole-genome duplication (WGD)-associated Ks peaks from different Poales and the low activity of recent LTR-RT in Pucai. Meanwhile, we found a unique WGD event in Typhaceae. A statistical analysis and annotation of genomic variations were conducted in interspecies and intraspecies of Typha. Based on the T2T genome, we constructed lignin and chlorophyll metabolic pathways of Pucai. Subsequently, the candidate structural genes and transcription factors that regulate lignin and chlorophyll biosynthesis were identified. The T2T genomic resources will provide molecular information for lignin and chlorophyll accumulation and help to understand genome evolution in Pucai.

Characterization of DnaJ gene family in Castanea mollissima and functional analysis of CmDnaJ27 under cold and heat stresses

BACKGROUND

The DnaJ gene family plays crucial roles in the plant abiotic stress response. Although the DnaJ gene family has been extensively characterized in various plants, its distribution in the Castanea mollissima genome is still unclear.

RESULTS

In this study, 78 CmDnaJ genes were identified and characterized in the C. mollissima genome, divided into three subfamilies based on the phylogeny analysis. The abundance of cis-acting elements related to temperature stress in the promoter regions of the CmDnaJ genes suggested a close relationship between this family and temperature stress response. Dispersed duplication was identified as the main driving force behind the expansion of the CmDnaJ family. RNA-seq data from 192 runs across nine projects were analyzed, revealing the potential roles of CmDnaJ genes in the growth, development, and environmental stress response of C. mollissima. Weighted gene co-expression network analysis showed that CmDnaJ27 and CmDnaJ34 were located in the red module and significantly correlated with temperature stimulus-response. RT-qPCR experiments and subcellular localization validated the expression levels and specific locations of CmDnaJ genes under cold and heat stresses. Overexpression of CmDnaJ27 in Nicotiana tabacum significantly reduces its tolerance to cold and heat stresses.

CONCLUSIONS

This study provides insights into the important roles of the DnaJ gene family in C. mollissima growth, development, and response to environmental stress, and provides reference to the research of CmDnaJs in cold and heat stresses response.

The complete reference genome of Tartary buckwheat and its mutation library provide important resources for genetic studies and breeding

Tartary buckwheat (TB), Fagopyrum tataricum, is an important medicinal and edible crop with a worldwide distribution. However, reference genomes with gaps and mutant population scarcity have hindered functional genomics and genetic improvement of TB. Here, we present a telomere-to-telomere (T2T) gap-free genome assembly of the elite TB inbred line Guiku1 and its ethyl-methyl-sulfonate (EMS)-induced phenotypically rich mutation library. The Guiku1 gap-free genome spans 453.83 Mb, containing 43,441 predicted protein-coding genes. The mutation library includes 751 mutants with stably heritable phenotypes. Whole-genome resequencing of 320 mutants identified 105,682 single-nucleotide polymorphisms (SNPs) and 21,461 insertions/deletions (indels), affecting the protein-coding sequences of 25,986 genes. Genes responsible for the pink stem and petiole mutant trait and flavonoid content variation were identified using forward- and reverse-genetics approaches, respectively. Collectively, the T2T gap-free genome of Guiku1 and its EMS mutation library provide important resources for functional genomics studies and the genetic improvement of TB.

Gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH zinc finger protein as a key regulator of stone cell formation in pear fruit

The Chinese white pear (Pyrus bretschneideri) is an economically significant fruit crop worldwide. Previous versions of the P. bretschneideri genome assembly contain numerous gaps and unanchored genetic regions. Here, we generated two high-quality, gap-free genome assemblies for 'Dangshansu' (DS; 503.92 Mb) and 'Lianglizaosu' (ZS; 509.01 Mb), each anchored to 17 chromosomes, achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%. Our genome-wide association studies explored the associations between genetic variations and stone cell traits, revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene, designated PbdsZF. Through genetic transformation, we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation, as it transcriptionally activates multiple genes involved in these processes. By binding to the CT-rich motifs CT1 (CTTTTTTCT) and CT2 (CTCTTTTT), PbdsZF significantly influences the transcription of genes essential for lignin production, underscoring its regulatory importance in plant lignin metabolism. Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation, thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.

Genome-wide identification, phylogeny, evolutionary expansion, and expression analyses of ABC gene family in Castanea mollissima under temperature stress

The ATP-binding cassette (ABC) gene family comprises some of the most critical transporter proteins in plants, playing vital roles in maintaining cellular homeostasis and adapting to environmental changes. While ABC transporters have been extensively characterized in various plant species, their profile in C. mollissima remains less understood. In this study, 164 ABC genes were identified and characterized within the C. mollissima genome, and subsequently classified into eight subfamilies. Collinear analysis suggested that dispersed duplication was the primary mechanism driving the expansion of the CmABC gene family. The study also examined morphological and physiological changes in C. mollissima under temperature stress, highlighting significant decreases in photosynthetic indicators and SOD enzyme activity, while other indicators varied. Transcriptome analysis revealed distinct expression patterns of various CmABC genes under temperature stress, identifying CmABCG29c and CmABCB11e as key candidates for responding to temperature stress. This was based on their expression patterns, correlation with physiological indicators, and WGCNA analysis. The expression levels of CmABC genes measured in RT-qPCR experiments were consistent with those observed in RNA-seq analysis. This research provides a theoretical foundation for understanding the physiological and gene expression responses of C. mollissima to temperature stress.

Multi-omics analysis reveals the role of UGT72 family genes in arbutin biosynthesis in Pyrus and evolution driven by whole genome duplication

The UGT72 gene family encodes proteins that glycosylate phenylpropanoids, and thus contribute to the synthesis of various phenolic substances. However, their functional role and evolutionary history in Pyrus spp. remains poorly understood. Here we explored the evolution, amplification, coding region structural variation, and functional divergence of the UGT72 gene family and its subfamilies. Further, we identified functional genes involved in arbutin synthesis and functionally validated the key genes. 15 UGT72 genes were identified in the complete genome sequence and classified into two subfamilies of Pyrus betulifolia. Significant expansion of the UGT72 gene family occurred after genome duplication in P. betulifolia. 53.33 % of all UGT72 family genes were found to have undergone expansion via WGD/segmental duplication. A noteworthy discovery was that the amplification of functional genes such as PbUGT72B1714 during polyploidization, combined with the loss of vital motifs and variations at important sites within these genes, significantly impacted the diversification of arbutin metabolism. These findings offer novel insights into how gene gains and losses caused by WGDs have contributed to metabolic diversification and evolutionary adaptation in Pyrus, as well as a groundwork for more detailed investigations into the mechanisms of arbutin metabolism.

Unlocking diversity from wild relatives of perennial fruit crops in the pan-genomics era

Crop wild relatives of perennial fruit crops have a wealth of untapped genetic diversity that can be utilized for cultivar development. However, barriers such as linkage drag, long juvenility, and high heterozygosity have hindered their utilization. Advancements in genome sequencing technologies and assembly methods, combined with the integration of chromosome conformation capture have made it possible to construct high-quality reference genomes. These genome assemblies can be combined into pan-genomes, capturing inter- and intraspecific variations across coding and non-coding regions. Pan-genomes of perennial fruit crops are being developed to identify the genetic basis of traits. This will help overcome breeding challenges, enabling faster and more targeted development of new cultivars with novel traits through breeding and biotechnology.

Telomere-to-telomere Genome Assembly of two representative Asian and European pear cultivars

As the third most important temperate fruit, Pear (Pyrus spp.) exhibits a remarkable genetic diversity and is classified into two mainly categories known as Asian pear and European pear. Although several pear genomes are available, most of the released versions are fragmented and not chromosome-level high-quality. In this study, we report two high-quality genomes for Pyrus bretschneideri Rhed. cv. 'Danshansuli' (DS) and Pyrus communis L. cv. 'Conference' (KFL), which represent the predominant Asian and European cultivars, respectively, with nearly telomere-to-telomere (T2T) gap-free level. The finally assembled genome sizes for DS and KFL were 510.98 Mb and 510.71 Mb, respectively, with Contig N50 of 29.47 Mb and 30.47 Mb, where each chromosome was represented by a single contig. The DS and KFL genomes yielded a total of 46,394 and 44,702 protein-coding genes, respectively. Among these genes, the functional annotation accounted for 96.47% and 96.46% in the DS and KFL genomes. The two novels nearly T2T genomic information offers an invaluable resource for comparative genomics, genetic diversity analysis, molecular breeding strategies, and functional exploration.

Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced (TAIL)-PCR

Whole-genome genotyping (WGG) stands as a pivotal element in genomic-assisted plant breeding. Nevertheless, sequencing-based approaches for WGG continue to be costly, primarily owing to the high expenses associated with library preparation and the laborious protocol. During prior development of foreground and background integrated genotyping by sequencing (FBI-seq), we discovered that any sequence-specific primer (SP) inherently possesses the capability to amplify a massive array of stable and reproducible non-specific PCR products across the genome. Here, we further improved FBI-seq by replacing the adapter ligated by Tn5 transposase with an arbitrary degenerate (AD) primer. The protocol for the enhanced FBI-seq unexpectedly mirrors a simplified thermal asymmetric interlaced (TAIL)-PCR, a technique that is widely used for isolation of flanking sequences. However, the improved TAIL-PCR maximizes the primer-template mismatched annealing capabilities of both SP and AD primers. In addition, leveraging of next-generation sequencing enhances the ability of this technique to assay tens of thousands of genome-wide loci for any species. This cost-effective, user-friendly, and powerful WGG tool, which we have named TAIL-PCR by sequencing (TAIL-peq), holds great potential for widespread application in breeding programs, thereby facilitating genome-assisted crop improvement.

Four glycosyltransferase genes are responsible for synthesis and accumulation of different flavonol glycosides in apple tissues

Flavonols are widely synthesized throughout the plant kingdom, playing essential roles in plant physiology and providing unique health benefits for humans. Their glycosylation plays significant role in improving their stability and solubility, thus their accumulation and function. However, the genes encoding the enzymes catalyze this glycosylation remain largely unknown in apple. This study utilized a combination of methods to identify genes encoding such enzymes. Initially, candidate genes were selected based on their potential to encode UDP-dependent glycosyltransferases (UGTs) and their expression patterns in response to light induction. Subsequently, through testing the in vitro enzyme activity of the proteins produced in Escherichia coli cells, four candidates were confirmed to encode a flavonol 3-O-galactosyltransferase (UGT78T6), flavonol 3-O-glucosyltransferase (UGT78S1), flavonol 3-O-xylosyltransferase/arabinosyltransferase (UGT78T5), and flavonol 3-O-rhamnosyltransferase (UGT76AE22), respectively. Further validation of these genes' functions was conducted by modulating their expression levels in stably transformed apple plants. As anticipated, a positive correlation was observed between the expression levels of these genes and the content of specific flavonol glycosides corresponding to each gene. Moreover, overexpression of a flavonol synthase gene, MdFLS, resulted in increased flavonol glycoside content in apple roots and leaves. These findings provide valuable insights for breeding programs aimed at enriching apple flesh with flavonols and for identifying flavonol 3-O-glycosyltransferases of other plant species.

Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex

The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits; however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aimed to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the apricot-peach-plum-mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes 251.25 and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of ~1.17 Mb in the apricot genomes compared with peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting titratable acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress tolerance, flower development, and fruit ripening, along with divergent selection shaping specific crop, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal collinearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.

Chromosome-level genome assemblies of Musa ornata and Musa velutina provide insights into pericarp dehiscence and anthocyanin biosynthesis in banana

Musa ornata and Musa velutina are members of the Musaceae family and are indigenous to the South and Southeast Asia. They are very popular in the horticultural market, but the lack of genomic sequencing data and genetic studies has hampered efforts to improve their ornamental value. In this study, we generated the first chromosome-level genome assemblies for both species by utilizing Oxford Nanopore long reads and Hi-C reads. The genomes of M. ornata and M. velutina were assembled into 11 pseudochromosomes with genome sizes of 427.85 Mb and 478.10 Mb, respectively. Repetitive sequences comprised 46.70% and 50.91% of the total genomes for M. ornata and M. velutina, respectively. Differentially expressed gene (DEG) and Gene Ontology (GO) enrichment analyses indicated that upregulated genes in the mature pericarps of M. velutina were mainly associated with the saccharide metabolic processes, particularly at the cell wall and extracellular region. Furthermore, we identified polygalacturonase (PG) genes that exhibited higher expression level in mature pericarps of M. velutina compared to other tissues, potentially being accountable for pericarp dehiscence. This study also identified genes associated with anthocyanin biosynthesis pathway. Taken together, the chromosomal-level genome assemblies of M. ornata and M. velutina provide valuable insights into the mechanism of pericarp dehiscence and anthocyanin biosynthesis in banana, which will significantly contribute to future genetic and molecular breeding efforts.

Technology-enabled great leap in deciphering plant genomes

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.