Transcriptome analysis and development of simple sequence repeat (SSR) markers in Zingiber striolatum Diels

Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer

Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders the efficiency and accuracy of genetic breeding efforts for A. heimuer. High-throughput transcriptome sequencing data are essential for gene discovery and molecular markers development. This study aimed to clarify the distribution of SSR loci across the A. heimuer transcriptome and to develop highly informative EST-SSR markers. These tools can be used for phylogenetic analysis, functional gene mining, and molecular marker-assisted breeding of A. heimuer. This study used Illumina high-throughput sequencing technology to obtain A. heimuer transcriptome data. The results revealed 37,538 unigenes in the A. heimuer transcriptome. Of these unigenes, 24,777 (66.01%) were annotated via comparison with the COG, Pfam, and NR databases. Overall, 2510 SSRs were identified from the unigenes, including 6 types of SSRs. The most abundant type of repeats were trinucleotides (1425, 56.77%), followed by mononucleotides (391, 15.58%) and dinucleotides (456, 18.17%). Primer pairs for 102 SSR loci were randomly designed for validity confirmation and polymorphism identification; this process yielded 53 polymorphic EST-SSR markers. Finally, 13 pairs of highly polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 52 wild A. heimuer germplasms, revealing that the 52 germplasms could be divided into three categories. These results indicated that SSR loci were abundant in types, numbers, and frequencies, providing a potential basis for germplasm resource identification, genetic diversity analysis, and molecular marker-assisted breeding of A. heimuer.

The complete chloroplast genome of Zingiber striolatum Diels (Zingiberaceae)

The chloroplast genome of Zingiber striolatum Diels was sequenced using the MGI paired-end sequencing method and assembled. The chloroplast genome was 163,711 bp in length, containing a large single-copy (LSC) region of 88,205 bp, a small single-copy (SSC) region of 15,750 bp, and two inverted repeat (IR) regions of 29,752 bp. The overall GC content was 36.1%, whereas the corresponding value in the IR regions was 41.1%, which was higher than that in the LSC region (33.8%) and SSC region (29.6%). A total of 136 complete genes were annotated in the chloroplast genome of Z. striolatum, including 87 protein-coding genes (79 protein-coding gene species), 40 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). A phylogenetic tree was constructed using the maximum likelihood (ML) method, and the results showed that the phylogeny of Zingiber was well resolved with high support values, and Z. striolatum was sister to Z. mioga. The assembly and sequence analysis of the chloroplast genome can provide a basis for developing high-resolution genetic makers.

Dynamic Changes in Ascorbic Acid Content during Fruit Development and Ripening of Actinidia latifolia (an Ascorbate-Rich Fruit Crop) and the Associated Molecular Mechanisms

Actinidia latifolia is one of the very few kiwifruit genotypes with extremely high ascorbic acid (AsA) content. However, a transcriptome atlas of this species is lacking. The accumulation of AsA during fruit development and ripening and the associated molecular mechanisms are still poorly understood. Herein, dynamic changes in AsA content at six different stages of A. latifolia fruit development and ripening were determined. AsA content of A. latifolia fruit reached 1108.76 ± 35.26 mg 100 g−1 FW at full maturity. A high-quality, full-length (FL) transcriptome of A. latifolia was successfully constructed for the first time using third-generation sequencing technology. The transcriptome comprises 326,926 FL non-chimeric reads, 15,505 coding sequences, 2882 transcription factors, 18,797 simple sequence repeats, 3328 long noncoding RNAs, and 231 alternative splicing events. The genes involved in AsA biosynthesis and recycling pathways were identified and compared with those in different kiwifruit genotypes. The correlation between the AsA content and expression levels of key genes in AsA biosynthesis and recycling pathways was revealed. LncRNAs that participate in AsA-related gene expression regulation were also identified. Gene expression patterns in AsA biosynthesis and metabolism exhibited a trend similar to that of AsA accumulation. Overall, this study paves the way for genetic engineering to develop kiwifruits with super-high AsA content.

Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae)

Ailanthus altissima Swingle, is a tree species native to East Asia and has a great potential in decorative, bioenergy and industrial applications in many countries. To date, despite its commercial importance, the genomic and genetic resources available for this species are still insufficient. In this study, we characterized the transcriptome of A. altissima and developed thirteen EST-SSRs (expressed sequence tag-simple sequence repeats) based on Illumina paired-end RNA sequencing (RNA-seq). Besides, we developed ten polymorphic chloroplast microsatellite (cpSSR) markers using the available chloroplast genome of A. altissima. The transcriptome data produced 87,797 unigenes, of which 64,891 (73.91%) unigenes were successfully annotated in at least one protein database. For cpSSR markers the number of detected alleles (N) per marker varied from three at cpSSR12 to twelve at cpSSR8, the unbiased haploid diversity indices (uh) varied from 0.111 to 0.485, and haploid diversity indices (h) ranged from 0.101 to 0.444 with an average unbiased haploid diversity index (uh) of 0.274. Overall, a total of 65 different cpSSR alleles were identified at the ten loci among 165 individuals of A. altissima. The allele number per locus for EST-SSRs varied from 2.143 to 9.357, and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826, respectively. The molecular markers developed in this study will facilitate future genetic diversity, population structure, long distance-gene transfer and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China focusing on planted and natural forest stands.

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, ~ 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) > 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri- (14.9%), tetra- (4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM ≤ 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.

Development of SSR markers via de novo transcriptome assembly in Akebia trifoliata (Thunb.) Koidz

Owing to its high nutritive, economic, and medicinal values, Akebia trifoliata has received increased attention, making worthy of being used as a new fruit crop for further domestication and commercialization in China. However, molecular research of A. trifoliata has lagged as investigations of its genomic resources and molecular markers are rare. In this study, a cDNA library of A. trifoliata leaves was sequenced using the Illumina NovaSeq. 6000 sequencing system. In total, 101 417 transcripts, 63 757 unigenes, and 9494 simple sequence repeats were assembled and identified from the transcriptome datasets. The majority of the SSRs were di- and trinucleotide repeats. Length and number of SSR motifs ranged from 15 to 66, and 5 to 48 bp, respectively. Of which, the A/T mononucleotide motif and AG/TC and CT/GA dinucleotide motifs were the most abundant. Furthermore, 100 SSR primers were randomly selected to validate amplification and polymorphism, and 88 A. trifoliata accessions were definitively distinguished by 49 primers. With the Qinling mountains and Huaihe River line as the boundaries, the northern and southern accessions were clustered into different groups, but no clear geographical patterns (city or origin) were observed in the southern accessions. These newly identified molecular markers may provide a foundation for the genetic identification and diversity analysis and marker-assisted selection breeding in species of Akebia.

Chemical composition, antioxidant, antimicrobial and anticancer activities of the essential oil from the rhizomes of Zingiber striolatum Diels

The chemical composition and biological activities of the essential oil (EO) from the rhizomes of Zingiber striolatum Diels were reported for the first time. Forty-five compounds were identified, and represented 95.7% of the total composition of the EO. The predominant components of the EO were β-phellandrene (24.0%), sabinene (17.3%), β-pinene (11.4%), geranyl linalool (8.6%), terpinen-4-ol (8.3%), α-pinene (5.6%) and crypton (4.5%). The EO revealed a weak DPPH and ABTS radical-scavenging activity. The EO exhibited significant antimicrobial activity with the inhibition zones (12.86-24.62 mm) and MIC (0.78-3.12 mg/mL) against Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Candida albicans. The EO showed significant cytotoxicity against human leukemic (K562), lung cancer (A549) and prostatic carcinoma (PC-3) cell lines with the IC₅₀ values of 29.67, 48.87 and 86.05 μg/mL, respectively. Thus, the EO could be regarded as a bioactive natural product with potential for utilization in the cosmetic and pharmaceutical industry.