Impacts of parental genomic divergence in non-syntenic regions on cotton heterosis.

INTRODUCTION: Heterosis has revolutionized crop breeding, enhancing global agricultural production. However, the mechanisms underlying heterosis remain obscure. Xiangzamian 2# (XZM2), a super hybrid upland cotton (Gossypium hirsutum L.) characterized by high-yield heterosis, has been developed and extensively planted in China. OBJECTIVES: We conducted a systematic analysis of CRI12 and J8891, two parents of XZM2. We aimed to reveal the precise genetic information and the role of non-syntenic divergence in shaping heterosis, laying a foundation for advancing understanding of heterosis. METHODS: We de novo assembled high-quality genomes of CRI12 and J8891, and further uncovered abundant genetic variations and non-syntenic regions between the parents. Whole-genome comparison, association analysis, transcriptomic analysis and relative identity-by-descent (rIBD) estimation were conducted to identify structural variations (SVs) and introgressions within non-syntenic blocks and to analyze their impacts on promoting heterosis. RESULTS: Parental genetic divergence increased in non-syntenic regions. Furthermore, these regions, accounting for only 16.71% of the total genome, contained more loci with significantly higher heterotic effects, far exceeding the syntenic background. SVs covered 97.26% of non-syntenic sequences and caused widespread gene expression differences in these regions, driving dynamic complementation of gene expression in the hybrid. A set of SVs were responsible for trait improvement and had positive effects on heterosis, contributing larger heritability than short variations. We characterized numerous parental-specific introgressions from G. barbadense. Specifically, a functional introgression segment within non-syntenic blocks introduced an elite haplotype, which significantly increased lint yield and enhanced heterosis. CONCLUSION: Our study clarified non-syntenic regions to harbor more loci with higher heterotic effects, revealed their importance in promoting heterosis and supported the crucial role of genetic complementation in heterosis. SVs and introgressions were identified as key factors responsible for non-syntenic divergence between the parents. They had important effects on gene expression and trait improvement, positively contributing to heterosis.

Robust non-syntenic gene expression patterns in diverse maize hybrids during root development.

Distantly related maize (Zea mays L.) inbred lines exhibit an exceptional degree of structural genomic diversity, which is probably unique among plants. This study systematically investigated the developmental and genotype-dependent regulation of the primary root transcriptomes of a genetically diverse panel of maize F1-hybrids and their parental inbred lines. While we observed substantial transcriptomic changes during primary root development, we demonstrated that hybrid-associated gene expression patterns, including differential, non-additive, and allele-specific transcriptome profiles, are particularly robust to these developmental fluctuations. For instance, differentially expressed genes with preferential expression in hybrids were highly conserved during development in comparison to their parental counterparts. Similarly, in hybrids a major proportion of non-additively expressed genes with expression levels between the parental values were particularly conserved during development. Importantly, in these expression patterns non-syntenic genes that evolved after the separation of the maize and sorghum lineages were systemically enriched. Furthermore, non-syntenic genes were substantially linked to the conservation of all surveyed gene expression patterns during primary root development. Among all F1-hybrids, between ~40% of the non-syntenic genes with unexpected allelic expression ratios and ~60% of the non-syntenic differentially and non-additively expressed genes were conserved and therefore robust to developmental changes. Hence, the enrichment of non-syntenic genes during primary root development might be involved in the developmental adaptation of maize roots and thus the superior performance of hybrids.

Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids.

Maize (Zea mays L.) displays an exceptional degree of structural genomic diversity [1, 2]. In addition, variation in gene expression further contributes to the extraordinary phenotypic diversity and plasticity of maize. This study provides a systematic investigation on how distantly related homozygous maize inbred lines affect the transcriptomic plasticity of their highly heterozygous F1 hybrids. The classical dominance model of heterosis explains the superiority of hybrid plants by the complementation of deleterious parental alleles by superior alleles of the second parent at many loci [3]. Genes active in one inbred line but inactive in another represent an extreme instance of allelic diversity defined as single-parent expression [4]. We observed on average ∼1,000 such genes in all inbred line combinations during primary root development. These genes consistently displayed expression complementation (i.e., activity) in their hybrid progeny. Consequently, extreme expression complementation is a general mechanism that results on average in ∼600 additionally active genes and their encoded biological functions in hybrids. The modern maize genome is complemented by a set of non-syntenic genes, which emerged after the separation of the maize and sorghum lineages and lack syntenic orthologs in any other grass species [5]. We demonstrated that non-syntenic genes are the driving force of gene expression complementation in hybrids. Among those, the highly diversified families of bZIP and bHLH transcription factors [6] are systematically overrepresented. In summary, extreme gene expression complementation extensively shapes the transcriptomic plasticity of maize hybrids and might therefore be one factor controlling the developmental plasticity of hybrids.

Motif-independent de novo detection of secondary metabolite gene clusters-toward identification from filamentous fungi.

Secondary metabolites are produced mostly by clustered genes that are essential to their biosynthesis. The transcriptional expression of these genes is often cooperatively regulated by a transcription factor located inside or close to a cluster. Most of the secondary metabolism biosynthesis (SMB) gene clusters identified to date contain so-called core genes with distinctive sequence features, such as polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS). Recent efforts in sequencing fungal genomes have revealed far more SMB gene clusters than expected based on the number of core genes in the genomes. Several bioinformatics tools have been developed to survey SMB gene clusters using the sequence motif information of the core genes, including SMURF and antiSMASH. More recently, accompanied by the development of sequencing techniques allowing to obtain large-scale genomic and transcriptomic data, motif-independent prediction methods of SMB gene clusters, including MIDDAS-M, have been developed. Most these methods detect the clusters in which the genes are cooperatively regulated at transcriptional levels, thus allowing the identification of novel SMB gene clusters regardless of the presence of the core genes. Another type of the method, MIPS-CG, uses the characteristics of SMB genes, which are highly enriched in non-syntenic blocks (NSBs), enabling the prediction even without transcriptome data although the results have not been evaluated in detail. Considering that large portion of SMB gene clusters might be sufficiently expressed only in limited uncommon conditions, it seems that prediction of SMB gene clusters by bioinformatics and successive experimental validation is an only way to efficiently uncover hidden SMB gene clusters. Here, we describe and discuss possible novel approaches for the determination of SMB gene clusters that have not been identified using conventional methods.

Genomic analysis of the aconidial and high-performance protein producer, industrially relevant Aspergillus niger SH2 strain.

Aspergillus niger is usually regarded as a beneficial species widely used in biotechnological industry. Obtaining the genome sequence of the widely used aconidial A. niger SH2 strain is of great importance to understand its unusual production capability. In this study we assembled a high-quality genome sequence of A. niger SH2 with approximately 11,517 ORFs. Relatively high proportion of genes enriched for protein expression related FunCat items verify its efficient capacity in protein production. Furthermore, genome-wide comparative analysis between A. niger SH2 and CBS513.88 reveals insights into unique properties of A. niger SH2. A. niger SH2 lacks the gene related with the initiation of asexual sporulation (PrpA), leading to its distinct aconidial phenotype. Frame shift mutations and non-synonymous SNPs in genes of cell wall integrity signaling, ß-1,3-glucan synthesis and chitin synthesis influence its cell wall development which is important for its hyphal fragmentation during industrial high-efficiency protein production.