Background: Chestnut seeds are important kinds of edible nuts rich in starch and protein. The characteristics and nutrient contents of chestnut have been found to show obvious metaxenia effects in previous studies. To improve the understanding of the effect of metaxenia on chestnut starch and sucrose metabolism, this study used three varieties of chestnut, ‘Yongfeng 1’, ‘YongRen Zao’ and ‘Yimen 1’, as male parents to pollinate the female parent, ‘Yongfeng 1’, and investigated the mechanisms of starch and sucrose metabolism in three starch accumulation stages (70 (S1), 82 (S2), and 94 (S3) days after pollination, DAP) in chestnut seed kernels.Result: Most carbohydrate metabolism genes were highly expressed in YFF (self-pollinated ‘Yongfeng 1’) in stage S2 and in YFR (‘Yongfeng 1’ × ‘Yongren Zao’) and YFM (‘Yongfeng 1’ × ‘Yimen 1’) in stage S3. In stage S3, hub genes encoding HSF_DNA-binding, ACT, Pkinase, and LIM proteins and four transcription factors were highly expressed, with YFF showing the highest expression, followed by YFR and YFM. In addition, transcriptome analysis of the kernels at 70, 82 and 94 DAP showed that the starch granule-bound starch synthase (EC 2.4.1.242) and ADP-glucose pyrophosphorylase (EC 2.7 .7.27) genes were actively expressed at 94 DAF. Chestnut seeds regulate the accumulation of soluble sugars, reducing sugars and starch by controlling glycosyl transferase and hydrolysis activity during development.Conclusion: These results and resources have important guiding significance for further research on starch and sucrose metabolism and other types of metabolism related to chestnut metaxenia.

The Chinese chestnut, Castanea mollissima Blume, a nut-bearing tree native to China and North Korea, belongs to the Fagaceae family. As an important genetic resource, C. mollissima is vital in enhancing edible chestnut varieties and offers significant insights into the origin and evolution of chestnut species. While the chloroplast genome of C. mollissima has been sequenced, its mitochondrial genome (mitogenome) remains largely uncharted. In this study, we have characterized the C. mollissima mitogenome, assembling it utilizing reads from both BGI and Nanopore sequencing platforms, and conducted a comparative analysis with the mitochondrial genomes of closely related species. The mitogenome of C. mollissima manifests a polycyclic structure consisting of two circular molecules measuring 363,232 bp and 24,806 bp, respectively. This genome encompasses 35 unique protein-coding genes, 19 tRNA genes, and three rRNA genes. A total of 139 SSRs were identified throughout the entire C. mollissima mitogenome. Furthermore, the combined length of homologous fragments between the chloroplast and mitochondrial genomes was 5766 bp, constituting 1.49% of the mitogenome. We also predicted 484 RNA editing sites in C. mollissima, demonstrating C-to-U RNA editing. Phylogenetic analysis of related species' mitogenomes showed that C. mollissima was closely related to Lithocarpus litseifolius (Hance) Chun and Quercus acutissima Carruth. Interestingly, the mitogenome sequences of C. mollissima, L. litseifolius, Q. acutissima, Fagus sylvatica L., and Juglans mandshurica Maxim did not show conservation in their alignments, indicating frequent genome reorganization. This report marks the inaugural study of the C. mollissima mitogenome, serving as a benchmark genome for economically significant plants within the Castanea genus. Moreover, it supplies invaluable information that can guide future molecular breeding efforts and contribute to the broader understanding of chestnut genomics.

Chestnuts are popular edible nuts that are rich in starch. In order to enhance the transcriptomic resources and further understand starch and sucrose metabolism in maturing chestnuts, a comparative transcriptomic study of Chinese chestnut kernels was conducted at three ripening stages (70, 82, and 94 DAF). At 82 and 94 days after flowering (DAF), starch continued to accumulate, and the amylopectin/amylose ratio increased. Transcriptomic profiling of kernels at 70 (stage I), 82 (stage II), and 94 DAF (stage III) indicated that soluble starch synthase and α-1,4-glucan branching enzyme genes are actively expressed at 82 and 94 DAF. The starch degradation enzymes amylase, phosphoglucan phosphatase DSP4, and maltose exporter did not show differential gene expression, while glycogen phosphorylase-encoding unigenes were significantly down-regulated at 94 DAF. In addition to starch and sucrose metabolism, RNA transport, RNA degradation, pyrimidine metabolism, purine metabolism, plant hormone signal transduction, plant–pathogen interactions, and glycerophospholipid metabolism were found to be significantly enriched in all comparisons included in the study. As Chinese chestnut matured, the unique enriched pathways switched from ribosomal biogenesis and RNA polymerase of eukaryotes to endocytosis and spliceosomes. These genomic resources and findings are valuable for further understanding starch and sucrose metabolism in the Chinese chestnut.

The chestnut tree exhibits self-incompatibility, where the selection of the male parent (pollen xenia) significantly affects seed starch metabolism, as well as fruit yield and quality. Despite its importance, the molecular mechanisms underlying pollen xenia remains largely unknown. In this study, we utilized the ‘Lan You’ variety of C. mollissima to construct a high-quality reference genome. As a result, a first Telomere-to-telomere (T2T) gap-free genome for this species was successfully assembled. A total of 560 transcription factors and 22 structural genes were identified as consistent across the TO-GCNs, indicating a consistent regulation pattern in the co-expression of genes involved in starch accumulation. These networks were further divided into three sub-networks: T1, T2, and T3. Among these, the T1 and T2 sub-networks exhibited a higher number of structural genes with consistent regulation patterns and were closely associated with sugar biosynthesis. The gene SBE (Camol08G0254600) was identified as the hub gene with the highest degree of connectivity, encoding a key rate-limiting enzyme in the amylopectin biosynthesis pathway. This study provides a foundation for further research on C. mollissima population genetics, genetic improvement, and strategies aimed at enhancing yield and quality.

Introduction: The basic helix-loop-helix (bHLH) transcription factor family plays crucial roles in plant growth, development, and responses to environmental stresses. However, a systematic characterization of bHLH genes in Castanea mollissima has been lacking.Methods: We performed a genome-wide identification of bHLH genes in C. mollissima, followed by phylogenetic, structural, motif, chromosomal distribution, and cis-element analyses. Co-expression network analysis and transcriptomic profiling under Dryocosmus kuriphilus infestation were conducted, and representative genes were validated using qRT-PCR across seed developmental stages.Results: A total of 124 non-redundant bHLH genes (CmbHLHs) were identified and classified into eight subfamilies, consistent with conserved gene structures and motif compositions, particularly motif-1 and motif-2 of the canonical bHLH domain. Chromosomal mapping revealed non-random distribution and tandem duplication events. Promoter analysis indicated enrichment of cis-elements responsive to stress, hormone signaling, and developmental regulation. Co-expression analysis highlighted hub genes, including CmbHLH82 and CmbHLH57, with potential regulatory functions. Transcriptomic data showed that most CmbHLHs were downregulated under D. kuriphilus infestation, notably CmbHLH63 and CmbHLH51. qRT-PCR confirmed the dynamic expression of five selected genes during seed development.Discussion: These findings provide the first comprehensive overview of the bHLH gene family in Chinese chestnut. The results highlight candidate genes potentially involved in development and insect resistance, thereby laying a foundation for future functional and breeding studies.

Background: Chestnut is an important kind of edible nut rich in starch and protein. The characteristics and nutrient contents of chestnut have been found to show obvious metaxenia effects in previous studies. To improve the understanding of the metaxenia effect on chestnut starch and sucrose metabolism, this study used three varieties of chestnut, ‘Yongfeng 1’, ‘Yong Renzao’ and ‘Yimeng 1’, as male parents to pollinate ‘Yongfeng 1’, as the female parent, and studied the mechanisms of starch and sucrose metabolism in three starch accumulation stages (70 (S1), 82 (S2), and 94 (S3) days after pollination , DAP) in the chestnut seed kernel.Result: Most carbohydrate metabolism genes were highly expressed in YFF in stage S2 and in YFR and YFM in stage S3. In stage S3, hub genes encoding HSF_DNA-binding, ACT, Pkinase, and LIM proteins and four transcription factors were highly expressed, with YFF showing the higest expression, followed by YFR and, finally, YFM. In addition, transcriptome analysis of the kernels at 70, 82 and 94 DAP showed that the starch granule-bound starch synthase (EC 2.4.1.242) and ADP-glucose pyrophosphorylase (EC 2.7 .7.27) genes were actively expressed at 94 DAF. Chestnut seeds regulate the accumulation of soluble sugars, reducing sugars and starch by controlling glycosyl transferase and hydrolysis activity during development.Conclusion: These studies and resources have important guiding significance for further research on starch and sucrose metabolism and other types of metabolism related to chestnut metaxenia.