De novo sequencing and comparative transcriptome analysis of the male and hermaphroditic flowers provide insights into the regulation of flower formation in andromonoecious taihangia rupestris

The Taihangia mitogenome provides new insights into its adaptation and organelle genome evolution in Rosaceae

MAIN CONCLUSION

We present the first Taihangia mitogenome, uncovering frequent rearrangements and significant length variation in Rosaceae, likely driven by hybridization and repeat content, alongside widespread mito-chloroplast phylogenetic conflicts. Taihangia, an ancient and endangered monotypic genus within the subfamily Rosoideae of the family Rosaceae, is endemic to cliffs and serves as an ideal material for studying the adaptations of cliff-dwelling plants and the evolutionary processes of the Rosaceae family. In this study, the mitogenome and plastome of T. rupestris var. ciliata were assembled, with lengths of 265,633 bp and 155,467 bp, both exhibiting typical circular structures. Positive selection was detected in the nad4L and sdh4 genes, likely playing a role in adaptation to harsh environments. Comparative genomic analysis indicated that repetitive sequences are likely the main contributors to genome size variation in Rosaceae and also influence horizontal gene transfer between organelle genomes. In T. rupestris var. ciliata, 20 mitochondrial plastid DNA sequences were identified, including 16 complete plastid genes. Moreover, frequent rearrangements were observed in the non-coding regions of mitogenome within the subfamily Rosoideae, potentially linked to the complex evolutionary history and the presence of repetitive sequences. In contrast, coding regions remained highly conserved (over 83% similarity) to maintain essential mitochondrial functions. Phylogenomic analysis of the two organelle genomes revealed conflicts in the phylogenetic relationships within Rosaceae, potentially due to the inconsistent mutation rates and frequent hybridization events in the evolutionary history of the family. In conclusion, the organelle genome analysis of Taihangia provides crucial genomic resources for understanding the evolution and adaptation of Rosaceae species.

Chromosome-level genome assembly of a cliff plant Taihangia rupestris var. ciliata provides insights into its adaptation and demographic history

BACKGROUND

Cliffs are recognized as one of the most challenging environments for plants, characterized by harsh conditions such as drought, infertile soil, and steep terrain. However, they surprisingly host ancient and diverse plant communities and play a crucial role in protecting biodiversity. The Taihang Mountains, which act as a natural boundary in eastern China, support a rich variety of plant species, including many unique to cliff habitats. However, it is little known how cliff plants adapt to harsh habitats and the demographic history in this region.

RESULTS

To better understand the demographic history and adaptation of cliff plants in this area, we analyzed the chromosome-level genome of a representative cliff plant, T. rupestris var. ciliata, which has a genome size of 769.5 Mb, with a scaffold N50 of 104.92 Mb. The rapid expansion of transposable elements may have contributed to the increasing genome and its ability to adapt to unique and challenging cliff habitats. Comparative analysis of the genome evolution between Taihangia and non-cliff plants in Rosaceae revealed a significant expansion of gene families associated with oxidative phosphorylation, which is likely a response to the abiotic stresses faced by cliff plants. This expansion may explain the long-term adaptation of Taihangia to harsh cliff environments. The effective population size of the two varieties has continuously decreased due to climatic fluctuations during the Quaternary period. Furthermore, significant differences in gene expression between the two varieties may explain the varied leaf phenotypes and adaptations to harsh conditions in different natural distributions.

CONCLUSION

Our study highlights the extraordinary adaptation of T. rupestris var. ciliata, shedding light on the evolution of cliff plants worldwide.

Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis

Geum japonicum (Rosaceae) has been widely used in China as a traditional herbal medicine due to its high economic and medicinal value. However, the appearance of Geum species is relatively similar, making identification difficult by conventional phenotypic methods, and the studies of genomics and species evolution are lacking. To better distinguish the medicinal varieties and fill this gap, we carried out relevant research on the chloroplast genome of G. japonicum. Results show a typical quadripartite structure of the chloroplast genome of G. japonicum with a length of 156,042 bp. There are totally 131 unique genes in the genome, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, and there were also 87 SSRs identified and mostly mononucleotide Adenine-Thymine. We next compared the plastid genomes among four Geum species and obtained 14 hypervariable regions, including ndhF, psbE, trnG-UCC, ccsA, trnQ-UUG, rps16, psbK, trnL-UAA, ycf1, ndhD, atpA, petN, rps14, and trnK-UUU. Phylogenetic analysis revealed that G. japonicum is most closely related to Geum aleppicum, and possibly has some evolutionary relatedness with an ancient relic plant Taihangia rupestris. This research enriched the genome resources and provided fundamental insights for evolutionary studies and the phylogeny of Geum.

Reproductive Biology and Breeding Systems of Two Opisthopappus Endemic and Endangered Species on the Taihang Mountains

Opisthopappus is a perennial, endemic herb of the Taihang Mountains in China. Two species of this genus (O. longilobus and O. taihangensis) are important wild genetic resources for Asteraceae; however, their reproductive biology has been lacking until now. This study is the first detailed report on the reproductive biology and breeding systems of two Opisthopappus species. Through field observations, the floral syndromes of O. longilobus and O. taihangensis were found to possess a similar pattern, although O. taihangensis has a relatively larger capitulum, more ray ligules, and disc florets. The flowers of both O. longilobus and O. taihangensis are protandrous, a character that can prevent autogamy at the single-flower level, and insects are required for pollination. Further, brightly ligules, brightly bisexual florets, unique fragrance, and amount of nectar suggest that these species propagate via an entomophilous pollination system. Hymenopteran and Diptera species were observed as the effective pollinators for these two species. The outcrossing index, pollen/ovule ratio and the results of hand pollination indicated that these Opisthopappus species might have a mixed mating system that combines cross-fertilization and partial self-fertilization for O. longilobus and O. taihangensis, outcrossing predominated in the breeding system, while self-pollination played an important role in seed production when insect pollination was unavailable, particularly in a harsh environment, such as the Taihang Mountains cliffs. Meanwhile, O. taihangensis might better adapt to severe surroundings with relatively complex floral syndromes, specifically through the attraction of visiting insects and a high seed set rate. The above results not only provide reference information toward a better understanding of the survival strategies of O. longilobus and O. taihangensis in the Taihang Mountains but also lay a solid foundation for further exploring the molecular mechanisms that underly their adaptation under cliff environments.

Reproductive biology of an endangered lithophytic shrub and implications for its conservation

BACKGROUND

Plants in cliff habitats may evolve specific reproductive strategies to cope with harsh environments, and unraveling these reproductive characteristics can improve our understanding of survival strategies and lithophyte evolution. This understanding is especially important for efforts to protect rare and endemic plants. Here, we investigated the reproductive biology of Lonicera oblata, an endangered lithophytic shrub that is scattered in highly fragmented and isolated cliff habitats of the Taihang and Yan mountains in North China.

RESULTS

Flowers of L. oblata are herkogamous and protandrous, characteristics that can prevent autogamy at the single-flower level, and insects are necessary for pollination. The outcrossing index, pollen/ovule ratio, and the results of hand pollination were measured and all revealed a mixed mating system for L. oblata, that combines cross-fertilization and partial self-fertilization. The floral traits of L. oblata of zygomorphic and brightly yellowish corolla, heavy fragrance, and rich nectar, suggest an entomophilous pollination system. Sweat bees were observed as the most effective pollinators but their visiting frequencies were not high. Pollen limitation may limit the reproductive success of L. oblata.

CONCLUSIONS

We determined the reproductive characteristics of L. oblata, a critically endangered species endemic to cliffs in North China, providing insight into its endangerment and suggesting conservation strategies. L. oblata has highly pollinator-dependent self-fertilization as part of a mixed mating system. Floral features such as low-flowering synchrony, asynchronous anthers dehiscence, and high duration of stigma receptivity, improve pollination efficiency in the case of low pollinator service. Our work provides reference information to understand the survival strategies and conservation of L. oblata and other lithophytes.

Comparative Transcriptome Reveals the Genes' Adaption to Herkogamy of Lumnitzera littorea (Jack) Voigt

Lumnitzera littorea (Jack) Voigt is among the most endangered mangrove species in China. The morphology and evolution of L. littorea flowers have received substantial attention for their crucial reproductive functions. However, little is known about the genomic regulation of flower development in L. littorea. In this study, we characterized the morphology of two kinds of L. littorea flowers and performed comparative analyses of transcriptome profiles of the two different flowers. Morphological observation showed that some flowers have a column embedded in the petals while others produce a stretched flower style during petal unfolding in flowering. By using RNA-seq, we obtained 138,857 transcripts that were assembled into 82,833 unigenes with a mean length of 1055.48 bp. 82,834 and 34,997 unigenes were assigned to 52 gene ontology (GO) functional groups and 364 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 4,267 differentially expressed genes (DEGs), including 1,794 transcription factors (TFs), were identified between two types of flowers. These TFs are mainly involved in bHLH, B3, bZIP, MYB-related, and NAC family members. We further validated that 12 MADS-box genes, including 4 MIKC-type and 8 M-type TFs, were associated with the pollinate of L. littorea by herkogamy. Our current results provide valuable information for genetic analysis of L. littorea flowering and may be useful for illuminating its adaptive evolutionary mechanisms.

Comparative Transcriptomic Analysis of Two Bottle Gourd Accessions Differing in Fruit Size

The bottle gourd (Lagenaria siceraria) is an important horticultural and medicinal crop with high nutritional value. This study aimed at examining the molecular regulation of fruit size in bottle gourd. We performed transcriptome sequencing of two bottle gourd cultivars differing in their fruit size. The average fruit length and weight of the cultivar Hang (39.48 cm/624.4 g) were higher than those of the cultivar USA (10.34 cm/152.8 g) at maturity. Transcriptome sequencing and assembly resulted in 89,347 unigenes. A total of 1250 differentially expressed genes (DEG) were found between the two cultivars, including 422 upregulated genes and 828 downregulated genes in Hang as compared to USA. Genes related to cell wall metabolism, phytohormones, cell cycle, and cell division showed significant differential expression between the two cultivars. DEGs encoding transcription factors (TF) from nine TF families were also identified. The ethylene response factor family was the most enriched among these families. Our study provides a basis for further investigations of the molecular regulation of fruit size in bottle gourd.

Selection and Validation of Appropriate Reference Genes for Quantitative Real-Time PCR Normalization in Staminate and Perfect Flowers of Andromonoecious Taihangia rupestris

Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is the most commonly used and powerful method for gene expression analysis due to its high sensitivity, specificity, and high throughput, and the accuracy of this approach depends on the stability of reference genes used for normalization. Taihangia rupestris Yu and Li (Rosaceae), an andromonoecious plant, produces both bisexual flowers and unisexual male flowers within the same individual. Using qRT-PCR technique, investigation of the gene expression profiling in staminate and perfect flowers would improve our understanding of the molecular mechanism in regulation of flower formation and sex differentiation in andromonoecious T. rupestris. To accurate normalize the gene expression level in Taihangia flower, 16 candidate reference genes, including 10 traditional housekeeping genes, and 6 newly stable genes, were selected based on transcriptome sequence data and previous studies. The expressions of these genes were assessed by qRT-PCR analysis in 51 samples, including 30 staminate and perfect flower samples across developmental stages and 21 different floral tissue samples from mature flowers. By using geNorm, NormFinder, BestKeeper, and comprehensive RefFinder algorithms, ADF3 combined with UFD1 were identified as the optimal reference genes for staminate flowers, while the combination of HIS3/ADF3 was the most accurate reference genes for perfect floral samples. For floral tissues, HIS3, UFD1, and TMP50 were the most suitable reference genes. Furthermore, two target genes, TruPI, and TruFBP24, involved in floral organ identity were selected to validate the most and least stable reference genes in staminate flowers, perfect flowers, and different floral tissues, indicating that the use of inappropriate reference genes for normalization will lead to the adverse results. The reference genes identified in this study will improve the accuracy of qRT-PCR quantification of target gene expression in andromonoecious T. rupestris flowers, and will facilitate the functional genomics studies on flower development and sex differentiation in the future.