Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum

Structural, developmental and functional analyses of leaf salt glands of mangrove recretohalophyte Aegiceras corniculatum

Salt secretion is an important strategy used by the mangrove plant Aegiceras corniculatum to adapt to the coastal intertidal environment. However, the structural, developmental and functional analyses on the leaf salt glands, particularly the salt secretion mechanism, are not well documented. In this study, we investigated the structural, developmental and degenerative characteristics and the salt secretion mechanisms of salt glands to further elucidate the mechanisms of salt tolerance of A. corniculatum. The results showed that the salt gland cells have a large number of mitochondria and vesicles, and plenty of plasmodesmata as well, while chloroplasts were found in the collecting cells. The salt glands developed early and began to differentiate at the leaf primordium stage. We observed and defined three stages of salt gland degradation for the first time in A. corniculatum, where the secretory cells gradually twisted and wrinkled inward and collapsed downward as the salt gland degeneration increased and the intensity of salt gland autofluorescence gradually diminished. In addition, we found that the salt secretion rate of the salt glands increased when the treated concentration of NaCl increased, reaching the maximum at 400 mM NaCl. The salt-secreting capacity of the salt glands of the adaxial epidermis is significantly greater than that of the abaxial epidermis. The real-time quantitative PCR results indicate that SAD2, TTG1, GL2 and RBR1 may be involved in regulating the development of the salt glands of A. corniculatum. Moreover, Na+/H+ antiporter, H+-ATPase, K+ channel and Cl- channel may play important roles in the salt secretion of salt glands. In sum mary, this study strengthens the understanding of the structural, developmental and degenerative patterns of salt glands and salt secretion mechanisms in mangrove recretohalophyte A. corniculatum, providing an important reference for further studies at the molecular level.

Sediment nitrates reduction processes affected by non-native Sonneratia apetala plantation in South China

Numerous studies have highlighted the importance of nitrates (NOx-) reduction processes in estuarine and coastal ecosystems over the past decades. However, the biotic and abiotic factors sediment NOx- reduction processes in mangrove of varying ages are still not fully understood. Here, we investigated the dynamics of sediment NOx- reduction processes and associated gene abundances in mangroves of different ages (including 0-year unvegetated mudflats, 10 and 20-years Sonneratia apetala, as well as >40 years of mature native Kandelia obovate) on the Qi'ao Island using 15N stable-isotope pairing techniques and quantitative PCR. The denitrification (2.64-11.30 nmol g-1 h-1), anammox (0.06-0.83 nmol g-1 h-1), and dissimilatory nitrate reduction to ammonium (DNRA, 0.58-16.34 nmol g-1 h-1) rates varied spatially and seasonally, but their contributions to the total NOx- reduction (DEN%, ANA%, and DNRA%), associated gene abundance (nirS, anammox 16S rRNA, and nrfA), and organic matter only varied spatially. Organic matter and microbial abundances are the dominating factors controlling N loss and retention. Without considering confounding factors, mangroves conservation and restoration significantly increased DNRA rates, NIRI (DNRA/(denitrification + anammox)), organic matter content, and microbial abundances (p < 0.05 for all), but reduced N loss rates. Mangroves conservation and restoration are estimated to have increased sediment N retention (~931.81 t N yr-1) and reduced N loss (~481.32 t N yr-1) in coastal wetlands of China over the past 40 years (1980-2020). Overall, our results indicate that mangrove restoration and conservation can significantly increase sediment N retention due to the rapid biomass accumulation, and it can provide more nutrients for mangrove and microorganism growth, thus creating a virtuous cycle in these N-limited ecosystems.

Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa)

Brassica orphan gene BrFLM, identified by two allelic mutants, was involved in leafy head formation in Chinese cabbage. Leafy head formation is a unique agronomic trait of Chinese cabbage that determines its yield and quality. In our previous study, an EMS mutagenesis Chinese cabbage mutant library was constructed using the heading Chinese cabbage double haploid (DH) line FT as the wild-type. Here, we screened two extremely similar leafy head deficiency mutants lfm-1 and lfm-2 with geotropic growth leaves from the library to investigate the gene(s) related to leafy head formation. Reciprocal crossing results showed that these two mutants were allelic. We utilized lfm-1 to identify the mutant gene(s). Genetic analysis showed that the mutated trait was controlled by a single nuclear gene Brlfm. Mutmap analysis showed that Brlfm was located on chromosome A05, and BraA05g012440.3C or BraA05g021450.3C were the candidate gene. Kompetitive allele-specific PCR analysis eliminated BraA05g012440.3C from the candidates. Sanger sequencing identified an SNP from G to A at the 271st nucleotide on BraA05g021450.3C. The sequencing of lfm-2 detected another non-synonymous SNP (G to A) located at the 266st nucleotide on BraA05g021450.3C, which verified its function on leafy head formation. We blasted BraA05g021450.3C on database and found that it belongs to a Brassica orphan gene encoding an unknown 13.74 kDa protein, named BrLFM. Subcellular localization showed that BrLFM was located in the nucleus. These findings reveal that BrLFM is involved in leafy head formation in Chinese cabbage.

Brassica rapa orphan gene BR1 delays flowering time in Arabidopsis

Orphan genes are essential to the emergence of species-specific traits and the process of evolution, lacking sequence similarity to any other identified genes. As they lack recognizable domains or functional motifs, however, efforts to characterize these orphan genes are often difficult. Flowering is a key trait in Brassica rapa, as premature bolting can have a pronounced adverse impact on plant quality and yield. Bolting resistance-related orphan genes, however, have yet to be characterized. In this study, an orphan gene designated BOLTING RESISTANCE 1 (BR1) was identified and found through gene structural variation analyses to be more highly conserved in Chinese cabbage than in other available accessions. The expression of BR1 was increased in bolting resistant Chinese cabbage and decreased in bolting non-resistant type, and the expression of some mark genes were consist with bolting resistance phenotype. BR1 is primarily expressed in leaves at the vegetative growth stage, and the highest BR1 expression levels during the flowering stage were observed in the flower buds and silique as compared to other tissue types. The overexpression of BR1 in Arabidopsis was associated with enhanced bolting resistance under long day (LD) conditions, with these transgenic plants exhibiting significant decreases in stem height, rosette radius, and chlorophyll content. Transcriptomic sequencing of WT and BR1OE plants showed the association of BR1 with other bolting resistance genes. Transcriptomic sequencing and qPCR revealed that six flowering integrator genes and one chlorophyll biosynthesis-related gene were downregulated following BR1 overexpression. Six key genes in photoperiodic flowering pathway exhibited downward expression trends in BR1OE plants, while the expression of floral repressor AtFLC gene was upregulated. The transcripts of these key genes were consistent with observed phenotypes in BR1OE plants, and the results indicated that BR1 may function through vernalization and photoperiodic pathway. Instead, the protein encoded by BR1 gene was subsequently found to localize to the nucleus. Taken together, we first propose that orphan gene BR1 functions as a novel regulator of flowering time, and these results suggested that BR1 may represent a promising candidate gene to support the selective breeding of Chinese cabbage cultivars with enhanced bolting resistance.

Diversity in Expression Biases of Lineage-Specific Genes During Development and Anhydrobiosis Among Tardigrade Species

Lineage-specific genes can contribute to the emergence and evolution of novel traits and adaptations. Tardigrades are animals that have adapted to tolerate extreme conditions by undergoing a form of cryptobiosis called anhydrobiosis, a physical transformation to an inactive desiccated state. While studies to understand the genetics underlying the interspecies diversity in anhydrobiotic transitions have identified tardigrade-specific genes and family expansions involved in this process, the contributions of species-specific genes to the variation in tardigrade development and cryptobiosis are less clear. We used previously published transcriptomes throughout development and anhydrobiosis (5 embryonic stages, 7 juvenile stages, active adults, and tun adults) to assess the transcriptional biases of different classes of genes between 2 tardigrade species, Hypsibius exemplaris and Ramazzottius varieornatus. We also used the transcriptomes of 2 other tardigrades, Echiniscoides sigismundi and Richtersius coronifer, and data from 3 non-tardigrade species (Adenita vaga, Drosophila melanogaster, and Caenorhabditis elegans) to help identify lineage-specific genes. We found that lineage-specific genes have generally low and narrow expression but are enriched among biased genes in different stages of development depending on the species. Biased genes tend to be specific to early and late development, but there is little overlap in functional enrichment of biased genes between species. Gene expansions in the 2 tardigrades also involve families with different functions despite homologous genes being expressed during anhydrobiosis in both species. Our results demonstrate the interspecific variation in transcriptional contributions and biases of lineage-specific genes during development and anhydrobiosis in 2 tardigrades.

Research Advances and Prospects of Orphan Genes in Plants

Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.

A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model

Background

Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cultural value. Studies have shown that the growth of moso bamboo is influenced by various stresses. Several traditional methods are time-consuming and inefficient. Hence, the development of efficient and high-accuracy computational methods for predicting orphan genes is of great significance.

Results

In this paper, we propose a novel deep learning model (CNN + Transformer) for identifying orphan genes in moso bamboo. It uses a convolutional neural network in combination with a transformer neural network to capture k-mer amino acids and features between k-mer amino acids in protein sequences. The experimental results show that the average balance accuracy value of CNN + Transformer on moso bamboo dataset can reach 0.875, and the average Matthews Correlation Coefficient (MCC) value can reach 0.471. For the same testing set, the Balance Accuracy (BA), Geometric Mean (GM), Bookmaker Informedness (BM), and MCC values of the recurrent neural network, long short-term memory, gated recurrent unit, and transformer models are all lower than those of CNN + Transformer, which indicated that the model has the extensive ability for OG identification in moso bamboo.

Conclusions

CNN + Transformer model is feasible and obtains the credible predictive results. It may also provide valuable references for other related research. As our knowledge, this is the first model to adopt the deep learning techniques for identifying orphan genes in plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04702-1.

Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes

Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.

Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.