Genome survey sequencing and identification of genomic SSR markers for Rhododendron micranthum

Recent advancements in the physiological, genetic, and genomic research on Rhododendrons for trait improvement

High species diversity, hybridization potential, broad geographical dispersal range and ornamental characteristics (i.e., attractive size, shape, structure, flowers, and evergreen) have fetched a good international market for Rhododendron. However, most species are restricted to specific geographic areas due to their habitat specificity in acidic soil and cold climates, resulting many species being classified under threat categories of the IUCN. In this review, advances in research on Rhododendron for improvement to floral display quality and stress resistance have been described. The low genetic barrier among species has created opportunities for extensive hybridization and ploidy alteration for introducing quality and adaptive traits during the development of new varieties. Recent technological advances have supported investigations into the mechanism of flower development, as well as cold tolerance and pathogen resistance mechanisms in the Rhododendron. However, most of the species have limited adaptability to drought, line-tolerance, pathogen resistance, and high-temperature conditions and this resistance ability present in few species largely remains unexplored. Additionally, the available genetic diversity and genomic information on species, and possibilities for their application in molecular breeding have been summarized. Overall, genomic resource data are scarce in the majority of the members of this genus. Finally, various research gaps such as genetic mapping of quality traits, understanding the molecular mechanism of quality-related traits and genomic assortment in Rhododendron members have been discussed in the future perspective section.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04006-6.

A first insight into the genomic background of Ilex pubescens (Aquifoliaceae) by flow cytometry and genome survey sequencing

BACKGROUND

Ilex pubescens is an important traditional Chinese medicinal plant with many naturally occurring compounds and multiple pharmacological effects. However, the lack of reference genomic information has led to tardiness in molecular biology research and breeding programs of this plant.

RESULTS

To obtain knowledge on the genomic information of I. pubescens, a genome survey was performed for the first time by next generation sequencing (NGS) together with genome size estimation using flow cytometry. The whole genome survey of I. pubescens generated 46.472 Gb of sequence data with approximately 82.2 × coverage. K-mer analysis indicated that I. pubescens has a small genome of approximately 553 Mb with 1.93% heterozygosity rate and 39.1% repeat rate. Meanwhile, the genome size was estimated to be 722 Mb using flow cytometry, which was possibly more precise for assessment of genome size than k-mer analysis. A total of 45.842 Gb clean reads were assembled into 808,938 scaffolds with a relatively short N50 of 760 bp. The average guanine and cytosine (GC) content was 37.52%. In total, 197,429 microsatellite motifs were detected with a frequency of 2.8 kb, among which mononucleotide motifs were the most abundant (up to 62.47% of the total microsatellite motifs), followed by dinucleotide and trinucleotide motifs.

CONCLUSION

In summary, the genome of I. pubescens is small but complex with a high level of heterozygosity. Even though not successfully applied for estimation of genome size due to its complex genome, the survey sequences will help to design whole genome sequencing strategies and provide genetic information support for resource protection, genetic diversity analysis, genetic improvement and artificial breeding of I. pubescens.

Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing

Ilex chinensis Sims. is an evergreen arbor species with high ornamental and medicinal value that is widely distributed in China. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. To obtain the whole reference genome, we first conducted a genome survey of I. chinensis by next-generation sequencing (NGS) to perform de novo whole-genome sequencing. As a result, our estimates using k-mer and flow cytometric analysis suggested the genome size of I. chinensis to be around 618-655 Mb, with the GC content, heterozygous rate, and repeat sequence rate of 37.52%, 1.1%, and 38%, respectively. A total of 334,649 microsatellite motifs were detected from the I. chinensis genome data, which will provide basic molecular markers for germplasm characterization, genetic diversity, and QTL mapping studies for I. chinensis. In summary, the I. chinensis genome is complex with high heterozygosity and few repeated sequences. Overall, this is the first report on the genome features of I. chinensis, and the information may lay a strong groundwork for future whole-genome sequencing and molecular breeding studies of this species.

The karyotype, genome survey, and assembly of Mud artemisia (Artemisia selengensis)

BACKGROUND

Artemisia selengensis is traditional Chinese medicine and phytochemical analysis indicated that A. selengensis contains essential oils, fatty acids and phenolic acids. The lack of reference genomic information may lead to tardiness in molecular biology research of A. selengensis.

METHOD AND RESULTS

Karyotype analysis, genome survey, and genome assembly was employed to acquire information on the genome structure of A. selengensis. The chromosome number is 2n = 2x = 36, karyotype formula is 28 m + 8Sm, karyotype asymmetry coefficient is 58.8%, and karyotypes were symmetric to Stebbins' type 2A. Besides, the flow cytometry findings reported that the mean peak value of fluorescent intensity is 1,170,677, 2C DNA content is 12 pg and the genome size was estimated to be approximately 5.87 Gb. Furthermore, the genome survey generates 341,478,078 clean reads, unfortunately, after K-mer analysis, no significant peak can be observed, the heterozygosity, repetitive rate and genome size was unable to estimated. It is speculated that this phenomenon might be due to the complexity of genome structure. 37,266 contigs are preliminary assembled with Oxford Nanopore Technology (ONT) sequencing, totaling 804 Mb and GC content was 34.08%. The total length is 804,475,881 bp, N50 is 29,624 bp, and the largest contig length is 239,792 bp.

CONCLUSION

This study reveals the preliminary information of genome size of A. selengensis. These findings may provide supportive information for sequencing and assembly of whole-genome sequencing and encourage the progress of functional gene discovery, genetic improvement, evolutionary study, and structural studies of A. selengensis.

Genome Survey Sequencing of In Vivo Mother Plant and In Vitro Plantlets of Mikania cordata

Mikania cordata, the only native congener of the invasive weed Mikania micrantha in China, is an ideal species for comparative study to reveal the invasion mechanism. However, its genome resources are lagging far behind its congener, which limits the comparative genomic analysis. Our goal is to characterize the genome of M. cordata by next-generation sequencing and propose a scheme for long-read genome sequencing. Previous studies have shown that the genomic resources of the host plant would be affected by the endophytic microbial DNA. An aseptic sample of M. cordata will ensure the proper genome in downstream analysis. Because endophytes are ubiquitous in the greenhouse-grown M. cordata, the in vitro culture with cefotaxime or timentin treatment was undertaken to obtain the aseptic plantlets. The in vivo mother plant and in vitro plantlets were used to survey the genome. The microbial contamination in M. cordata was recognized by blast search and eliminated from the raw reads. The decontaminated sequencing reads were used to predict the genome size, heterozygosity, and repetitive rate. The in vivo plant was so contaminated that microbes occupied substantial sequencing resources and misled the scaffold assembly. Compared with cefotaxime, treatment with timentin performed better in cultivating robust in vitro plantlets. The survey result from the in vitro plantlets was more accurate due to low levels of contamination. The genome size was estimated to be 1.80 Gb with 0.50% heterozygosity and 78.35% repetitive rate. Additionally, 289,831 SSRs were identified in the genome. The genome is heavily contaminated and repetitive; therefore, the in vitro culture technique and long-read sequencing technology are recommended to generate a high-quality and highly contiguous genome.

Novel microsatellite markers for evaluation of genetic diversity in the tetraploid flame azalea, Rhododendron calendulaceum (Ericaceae)

Microsatellite markers have become a popular and useful tool for investigating evolutionary processes at shallow taxonomic scales such as within a species or between extremely closely related species. Rhododendron sect. Pentanthera is a closely related group of deciduous azaleas that demonstrate both naturally occurring and horticulturally derived hybridization. Two species, flame azalea and Cumberland azalea, represent a particularly recalcitrant evolutionary problem, which will benefit from the development of rapidly evolving molecular markers. Microsatellite markers were specifically developed for Rhododendron calendulaceum, the flame azalea, for use in studies of genetic structure and potential hybridization with its close relative Rhododendron cumberlandense, the Cumberland azalea. Forty-eight primer pairs designed from paired-end Illumina MiSeq data were screened for robust amplification. Sixteen of these pairs were PCR-amplified in the presence of fluorescently labeled primers and genotyped in 66 flame azalea individuals from three geographically dispersed populations. Fifteen primer pairs were both reliable and polymorphic and exhibit ample variability for use in downstream population-level investigations. Cross-amplification in all other members of Rhododendron sect. Pentanthera was highly successful, suggesting broad utility across the entire clade. The novel microsatellite markers presented here functioned well within the target species and amplified with high success in the remaining members of the clade. They represent a significant improvement to the genetic toolkit available for Rhododendron sect. Pentanthera, and particularly for the flame/Cumberland azalea evolutionary problem.