Simple Sequence Repeat Analysis Research Articles

Clustering Analysis of Natural D-borneol Resource Plants Based on Simple Sequence Repeat (SSR) Markers, Leaf Morphology, and Chemical Composition.

D-borneol is a double-loop monoterpene with a wide use in the pharmaceutical, food, and cosmetics industries. Natural D-borneol can be extracted from branches and leaves of D-borneol resource plants. With the widespread use of natural D-borneol, the identification of D-borneol resource plants and the protection of germplasm resources have become the focus of research. In this study, plant leaf morphology, chemical composition, and simple sequence repeat (SSR) molecular marker analysis were used to analyze and cluster 5 species of D-borneol resource plants and their closely related species. It was found that all three analysis methods could distinguish and cluster these D-borneol resource plants to some degree. The result of SSR analysis using capillary electrophoresis was the best, and it could distinguish Mei Pian tree from Yin Xiang as well as Longnao Zhang from An Zhang. The correlation analysis between SSR similarity matrix and leaf morphology analysis and between SSR similarity matrix and chemical composition similarity matrix revealed that they both had significant correlations (P < 0.0001) and the correlation (r = 0.588) between SSR and leaf morphology was a little higher than that (r = 0.519) between SSR and chemical composition. This indicated that the environment had a greater impact on the chemical composition than on leaf morphology. The research findings will offer efficient techniques to cluster natural D-borneol resource plants and establish a theoretical basis for their future development and utilization.

Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper

AbstractThe Arnaucho chili pepper (ACP) is a traditional vegetable used in Peru because of its gastronomic properties. Due to its importance in the Peruvian diet and economy, this species is a resource that can be a candidate to plant breeding programs. In this study, the complete genome nucleotide sequence of this chili pepper was generated using the Illumina Hiseq 2500 sequencing technology. We sequenced the whole genome of the ACP using a paired-end 150 strategy, obtaining 330.46 GB of sequencing data. The genome size of the ACP was 2.98 Gb with a contig N50 of 237 Mb and 95.39% complete BUSCOs. Also, we identified 71.96% of repetitive DNA of the genome assembly, of which retroelements occupy 37.95% of the total genome. We downloaded genomes of the Solanoideae subfamily and conducted a comparative analysis of simple sequence repeats (SSRs) with our draft genome, and we identified lower number of SSRs in the ACP genome compared to other pepper species. This first ACP genome is expected to contribute to a better understanding of its genetics to adapt to the arid conditions of the Peruvian coastal ecosystem and evolution.

Novel loci associated with resistance to downy and powdery mildew in grapevine.

Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.

Short Communication: Analysis of simple sequence repeats variations for the assessment of genotypic diversity in Centella asiatica (L.) Urb.

Abstract. Maruzy A, Susandarini R. 2024. Short Communication: Analysis of simple sequence repeats variations for the assessment of genotypic diversity in Centella asiatica (L.) Urb. Biodiversitas 25: 734-740. Centella asiatica (L.) Urb. is a perennial plant widely known as herbal ingredient in traditional and modern medicine, as well as in the cosmetics industry. This herbaceous species grows in various types of habitat, and is known for its morphological variations among populations, indicating the existence of genotypic variation. In this study, the assessment of genotypic diversity using simple sequence repeats (SSR) was carried out on C. asiatica accessions from 32 populations collected from eight mountains in Central Java. Representative individuals from four populations grow at different altitudes were sampled in each mountain. Amplification of genomic DNA using the SSR primer mCaCIR002 produced a single amplicon of 180 bp. The results of SSR analysis showed that there is high genotypic diversity in C. asiatica which is characterized by variations in the number of microsatellite repeats of (CT)10 to (CT)19. Variations in the number of repeats are mainly caused by insertions and deletions in DNA sequences at the positions 102-145. Haplotype analysis also showed high genetic diversity within and between populations of C. asiatica, indicated by the haplotype diversity of 1.00 in all populations. The haplotype network analysis indicated that there was no gene flow between the four populations at each mountain where C. asiatica populations grow. The results of this study provide evidence for the role of SSR as a suitable molecular marker for studying genotypic diversity at the intraspecific level, and confirming the morphological variability in this species.

The sacred deer conflict of management after a 1000‐year history: Hunting in the name of conservation or loss of their genetic identity

AbstractHuman–wildlife conflict involves diverse stakeholders with conflicting values. Resolving such conflicts necessitates the development of management plans rooted in scientific knowledge and establishing of social consensus. In Nara City, situated within the Japanese Archipelago, wild sika deer (Cervus nippon) hold sacred significance due to religious reasons and have been protected for over a millennium, resulting in a distinct genetic identity. However, the escalating deer population has caused significant agricultural damage in the areas surrounding the sanctuary. Consequently, a debate has arisen regarding the advantages and disadvantages of implementing lethal measures to address individuals that might be considered sacred deer but are regarded as pests in the vicinity of the sanctuary. Here, we used mitochondrial DNA (mtDNA) control region and nuclear simple sequence repeat (SSR) markers to detect the origin of deer in the areas neighboring the sanctuary (management areas). As a result, two genetic populations of deer were detected in Nara City. In the sanctuary, we detected only one specific mtDNA haplotype (S4). On the other hand, seven haplotypes, including S4, were detected in the management area. SSR analysis also suggested that the sika deer in the management area may be an admixed population of multiple origins from the sanctuary and out of Nara City. Interbreeding populations may expand into the sanctuary, and unique genetic populations for more than 1000 years may disappear. This study suggests that ordinary deer could soon replace the deer revered and protected by the people of Nara. Additionally, the proximity of sanctuary deer to tourists worldwide and the interaction with wild deer in other areas pose a potential risk of spreading zoonotic diseases. Urgent decisions are required to determine whether to advocate for extermination in managed areas for ‘conservation’ purposes or risk losing the genetic identity of the sacred deer.

Study on Italian Onion Cultivars/Ecotypes towards Onion Yellow Dwarf Virus (OYDV) Infection

The onion yellow dwarf virus (OYDV) represents a limiting biotic stress in onion (Allium cepa L.); little information is available regarding resistant varieties. In Italy, onion production is limited but represented by a wide diversity of ecotypes. A two-year trial was carried out to test the OYDV-susceptibility/tolerance of different Italian onion cultivars by rating symptom severity and plant growth parameters and assessing post-harvest secondary infections. The cultivar and ecotypes included in the study were characterized by simple sequence repeats (SSR) analysis, and the expression analysis of two genes (Eukaryotic translation initiation factors, EIFs) involved in potyvirus replication was also performed. Two susceptible and one tolerant cultivar were identified based on symptom expression and virus impact on plants. Although differences in growth parameters were limited to the first-year trial, the infection was correlated to a higher incidence of secondary infections in post-harvest, with altered water balance in infected bulbs. This correlation was also demonstrated during the long-term storage of bulbs. SSR analysis identified different clusters and only one gene isoform (EIF4eiso1) showed different expression levels in the OYDV/onion pathosystem. In conclusion, this study defines the genetic profile of Italian onion cultivars and provides evidence on susceptibility/tolerance features which will be useful in the future for the identification of viral resistance traits in onion.

In vitro mutagenesis on patchouli (Pogostemon cablin Benth.) with gamma-ray irradiation on leaf explants

Abstract. Normasari R, Arumingtyas EL, Retnowati R, Widoretno W. 2023. In vitro mutagenesis on patchouli (Pogostemon cablin Benth.) with gamma-ray irradiation on leaf explants. Biodiversitas 24: 6407-6414. Patchouli oil production in Indonesia has yet to meet international market demand, one of which is the quality of the patchouli superior seeds. Patchouli is propagated vegetatively through cuttings, causing limited variability and decreasing plant quality. In vitro mutagenesis with gamma-ray irradiation can increase plant genetic variability and produce superior patchouli plants. This study aimed to produce patchouli variants through in vitro mutagenesis by gamma-ray irradiation on patchouli leaf explants. To accomplish the research objectives mentioned above, the research stages included in vitro mutagenesis through gamma-ray irradiation, shoot regeneration, plantlet growth, and molecular analysis using SSR (Simple Sequence Repeat). Gamma-ray irradiation inhibited the growth of explants and shoot formation but could increase plantlet growth ability at low doses of 15-30 Gy. The dose of gamma-ray irradiation that caused the death of explants in fifty percent of the tested population (LD50) was 69 Gy. Molecular analysis of SSR on 50 plants regenerated from gamma-irradiated explants revealed monomorphic and polymorphic fragments compared to non-irradiated and donor plants. Primers Pca1 and Pca2 showed the highest percentage of polymorphic, with 77.3 and 50%, respectively. Gamma irradiation during in vitro culture is an alternate method for increasing genetic variety in patchouli breeding.

Draft genome sequencing of Tilletia caries inciting common bunt of wheat provides pathogenicity-related genes.

Common bunt of wheat caused by Tilletia caries is an important disease worldwide. The T. caries TC1_MSG genome was sequenced using the Illumina HiSeq 2500 and Nanopore ONT platforms. The Nanopore library was prepared using the ligation sequencing kit SQK-LSK110 to generate approximately 24 GB for sequencing. The assembly size of 38.18 Mb was generated with a GC content of 56.10%. The whole genome shotgun project was deposited at DDBJ/ENA/GenBank under the accession number JALUTQ000000000. Forty-six contigs were obtained with N50 of 1,798,756 bp. In total, 10,698 genes were predicted in the assembled genome. Out of 10,698 genes, 10,255 genes were predicted significantly in the genome. The repeat sequences made up approximately 1.57% of the genome. Molecular function, cellular components, and biological processes for predicted genes were mapped into the genome. In addition, repeat elements in the genome were assessed. In all, 0.89% of retroelements were observed, followed by long terminal repeat elements (0.86%) in the genome. In simple sequence repeat (SSR) analysis, 8,582 SSRs were found in the genome assembly. The trinucleotide SSR type (3,703) was the most abundant. Few putative secretory signal peptides and pathogenicity-related genes were predicted. The genomic information of T. caries will be valuable in understanding the pathogenesis mechanism as well as developing new methods for the management of the common bunt disease of wheat.

Plant Regeneration via Organogenesis in Jerusalem Artichokes and Comparative Analysis of Endogenous Hormones and Antioxidant Enzymes in Typical and Atypical Shoots.

The Jerusalem artichoke (Helianthus tuberosus) is a tuberous plant with considerable nutrient and bioactive compounds. The optimization of the in vitro clonal propagation protocol is critical for large-scale reproduction and biotechnological applications of Jerusalem artichoke production. In this work, in vitro plant regeneration from the stem nodes of the Jerusalem artichoke via direct organogenesis is presented. In the shoot induction stage, the stem segments produced more shoots with vigorous growth on MS medium containing 0.5 mg/L 6-benzylaminopurine (6-BA). The concentrations of 6-BA and gibberellic acid (GA3) were both optimized at 0.5 mg/L for shoot multiplication, and the combination of 0.05 mg/L indole-3-butyric acid (IBA) and 0.05 mg/L 1-naphthylacetic acid (NAA) was the most responsive for root induction, yielding the largest number of roots. The regenerated plantlets were successfully hardened at a 96% survival rate and vigorously grew in the field. The genetic stability of the regenerated plants was confirmed by flow cytometry and simple sequence repeat (SSR) analysis. However, 17.3% of shoots on the optimum shoot induction medium had withered leaves and excessive callus (atypical shoots), which greatly reduced the induction efficiency. Enzyme activity in the typical and atypical shoots was compared. The atypical shoots had significantly higher levels of endogenous indole-3-acetic acid (IAA) and abscisic acid (ABA), as well as increased activity of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), whereas the content of 6-BA, zeatin (ZT), and GA3 was significantly reduced. The activity of the three enzymes was positively correlated with the content of IAA and ABA, while being negatively correlated with that of 6-BA, ZT, and GA3. The results suggest that the poor growth of the atypical shoots might be closely related to the significant accumulation of endogenous IAA and ABA, thus significantly increasing antioxidant enzyme activity.

Changes in Allele Frequencies and Genetic Diversity in Red Clover after Selection for Cold Tolerance Using SSR Markers

The selection of red clover (Trifolium pratense L.) populations adapted to extreme environmental conditions is of great importance due to continuing climate change. The plant material analyzed with simple sequence repeat (SSR) markers included two parent populations, P1 (cultivar ‘Reichersberger’) and P3 (cultivar ‘Croatia’) and their reselections, which were created after one cycle of selection under cold temperature conditions. The reselections PS1 and PS3 were produced by intercrossing 38 surviving plants of parent populations P1 and P3, respectively. A total of 48 plants from each cultivar and each reselection were randomly selected for SSR analysis. Sixteen SSR primer pairs were selected, taking into account the presence of loci on all seven pairs of red clover chromosomes. An increase in the average frequency of alleles from the initial populations to the populations after one cycle of selection was observed, followed by a decrease in the number of alleles. Out of a total of 16 loci, the Waples neutrality test revealed significant frequency changes at 12 loci from P1 to PS1 and 9 loci from P3 to PS3 populations. The genetic diversity in the studied populations did not change significantly after selection, leaving enough genetic variability as a prerequisite for the success of future selection.

Characterization of Bacillus thuringiensis bacteriophages: morphogenesis, lytic potentials and inter simple sequence repeat analysis

Characterization of Bacillus thuringiensis bacteriophages: morphogenesis, lytic potentials and inter simple sequence repeat analysis

Population structure and genetic diversity of Moroccan cannabis (Cannabis sativa L.) germplasm through simple sequence repeat (SSR) analysis

Population structure and genetic diversity of Moroccan cannabis (Cannabis sativa L.) germplasm through simple sequence repeat (SSR) analysis

Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing Rosa rugosa via High-Resolution Melting (HRM) Analysis.

Oil-bearing Rosa rugosa are popular in the essential oil and perfume markets. The similar botanical characteristics between high-oil-yield or low-oil-yield cultivars are confusing and it is hard for farmers or breeders to identify the high-oil-yield cultivar by phenotype difference. High-resolution melting (HRM) analysis of simple sequence repeats (SSRs) can construct accurate DNA fingerprints quickly, which was shown to be effective for identification of closely related cultivars of R. rugosa. Optimization of HRM-SSR indicated that the 10 µL HRM reaction mixture containing 20 ng of genomic DNA of R. rugosa and 0.75 µL of 10 µmol/L of each primer with an annealing temperature of 64 °C was a robust SSR genotyping protocol. Using this protocol, 9 polymorphic SSR markers with 3-9 genotypes among the 19 R. rugosa cultivars were identified. The top three polymorphic makers SSR9, SSR12 and SSR19 constructed a fingerprint of all cultivars, and the rare insertion in the flanking sequences of the repeat motif of SSR19 generated three characteristic genotypes of three high-oil-yield cultivars. These results may be economical and practical for the identification of high-oil-yield R. rugosa and be helpful for the selection and breeding of oil-bearing roses.

Optimization of Plant Growth Regulators for In Vitro Mass Propagation of a Disease-Free 'Shine Muscat' Grapevine Cultivar.

This study addresses the propagation challenges faced by 'Shine Muscat', a newly introduced premium grapevine cultivar in South Korea, where multiple viral infections pose considerable economic loss. The primary objective was to establish a robust in vitro propagation method for producing disease-free grapes and to identify effective plant growth regulators to facilitate large-scale mass cultivation. After experimentation, 2.0 µM 6-benzyladenine (BA) exhibited superior shoot formation in the Murashige and Skoog medium compared with kinetin and thidiazuron. Conversely, α-naphthaleneacetic acid (NAA) hindered shoot growth and induced callus formation, while indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) demonstrated favorable root formation, with IBA showing better results overall. Furthermore, inter simple sequence repeat analysis confirmed the genetic stability of in vitro-cultivated seedlings using 2.0 μM BA and 1.0 μM IBA, validating the suitability of the developed propagation method for generating disease-free 'Shine Muscat' grapes. These findings offer promising prospects for commercial grape cultivation, ensuring a consistent supply of healthy grapes in the market.

Assembly and phylogenetic analysis of the mitochondrial genome of endangered medicinal plant Huperzia crispata.

Huperzia crispata is a traditional Chinese herb plant and has attracted special attention in recent years for its products Hup A can serve as an acetylcholinesterase inhibitor (AChEI). Although the chloroplast (cp) genome of H. crispata has been studied, there are no reports regarding the Huperzia mitochondrial (mt) genome since the previously reported H. squarrosa has been revised as Phlegmariurus squarrosus. The mt genome of H. crispata was sequenced using a combination of long-read nanopore and Illumina sequencing platforms. The entire H. crispata mt genome was assembled in a circular with a length of 412,594 bp and a total of 91 genes, including 45 tRNAs, 6 rRNAs, 37 protein-coding genes (PCGs), and 3 pseudogenes. Notably, the rps8 gene was present in P. squarrosus and a pseudogene rps8 was presented in H. crispata, which was lacking in most of Pteridophyta and Gymnospermae. Intron-encoded maturase (mat-atp9i85 and mat-cobi787) genes were present in H. crispata and P. squarrosus, but lost in other examined lycophytes, ferns, and Gymnospermae plants. Collinearity analysis showed that the mt genome of H. crispata and P. squarrossus is highly conservative compared to other ferns. Relative synonymous codon usage (RSCU) analysis showed that the amino acids most frequently found were phenylalanine (Phe) (4.77%), isoleucine (Ile) (4.71%), lysine (Lys) (4.26%), while arginine (Arg) (0.32%), and histidine (His) (0.42%) were rarely found. Simple sequence repeats (SSR) analysis revealed that a total of 114 SSRs were identified in the mt genome of H. crispata and account for 0.35% of the whole mt genome. Monomer repeats were the majority types of SSRs and represent 91.89% of the total SSRs. In addition, a total of 1948 interspersed repeats (158 forward, 147 palindromic, and 5 reverse repeats) with a length ranging from 30 bp to 14,945 bp were identified in the H. crispata mt genome and the 30-39-bp repeats were the most abundant type. Gene transfer analysis indicated that a total of 12 homologous fragments were discovered between the cp and mt genomes of H. crispata, accounting for 0.93% and 2.48% of the total cp and mt genomes, respectively. The phylogenetic trees revealed that H. crispata was the sister of P. squarrosus. The Ka/Ks analysis results suggested that most PCGs, except atp6 gene, were subject to purification selection during evolution. Our study provides extensive information on the features of the H. crispata mt genome and will help unravel evolutionary relationships, and molecular identification within lycophytes.

Characterization of gill transcriptome, SSR/SNP markers and expression analysis of lysozyme LysC gene from Carassius auratus upon Aeromonas hydrophila infection

The gills are large mucosal surfaces and play primary roles in respiration and immune defences. However, the molecular mechanism for gills of fish needs still to be explored. In the present study, transcriptomic analysis and identification of SSR and SNP markers were performed in the gills of crucian carp Carassius auratus. The results showed a total of 84,259 unigenes were annotated to NCBI NR, KEGG and GO databases for 55,283, 39,303, 33,388, respectively. Enriched KEGG pathway analyses for the identified genes showed the mainly functional modules such as metabolism, cellular processes, environmental adaptation, genetic processing, organismal and immune systems. Moreover, 22,102 SSRs (simple sequence repeats) were potentially identified and 9776 (44.2%) were accounted for the most dinucleotides. Transition and transversion sites of SNPs (single nucleotide polymorphisms) were also observed. Tissue distribution showed that the expression level of lysozyme LysC gene was relatively high in intestine, liver, spleen and kidney tissues and up-regulated in gills, skin and brain after the A. hydrophila infection. We discovered the immune-related pathways through the transcriptome analysis in the gills of crucian carp, some potential SSR/SNP markers were identified, and lysozyme gene predominantly expressed in mucosal immune organs (eg., gills, skin, intestine) responded to A. hydrophila infection. To the best of our knowledge, this was the detailed report on the molecular characteristics in crucian carp gills with transcriptome analysis, which will not only provide a scientific reference for further understanding the local defense mechanism, but also lay a foundation for molecular marker-assisted breeding in fish.

Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

Cordiaceae is a family comprising more than 400 species in the order Boraginales. The classification of this family has undergone changes over time, transitioning between family and subfamily status. In the present study, the complete chloroplast (cp) genomes of Cordia monoica and Cordia sinensis were sequenced, and their cp genomes were then characterized, analyzed, and compared to those of closely related taxa. The lengths of the cp genomes of C. monoica and C. sinensis were 151,813 bp and 152,050 bp, respectively. Both genomes consisted of 114 genes, divided into 4 ribosomal RNA genes, 30 transfer RNA genes, and 80 protein-coding genes. We observed a unique gene inversion in the trnM-rbcL region of both Cordia species. The long repeats analysis revealed that both species’ chloroplast genomes contained forward and palindromic repeats. The simple sequence repeats (SSRs) analysis detected 155 microsatellites in each genome, with the majority being mononucleotide repeats (A/T). Phylogenetic analysis based on maximum likelihood and Bayesian analyses confirmed two major clades in the order Boraginales: clade I comprised Boraginaceae, while clade II included Cordiaceae, Ehretiaceae, and Heliotropiaceae. This study expands our knowledge of the evolutionary relationships across the order Boraginales and offers useful genetic resources.

Morphological and molecular diversity in mid-late and late maturity genotypes of cauliflower.

Genetic diversity is the prerequisite for the success of crop improvement programmes. Keeping in view, the current investigation was undertaken to assess the agro-morphological and molecular diversity involving 36 diverse mid-late and late cauliflower genotypes following α-RBD design during winter season 2021-22. Six morphological descriptors predicted as polymorphic using Shannon diversity index with maximum for leaf margin (0.94). The genotypes grouped into nine clusters based on D2 analysis with four as monogenotypic and gross plant weight (32.38%) revealed maximum contribution towards the genetic diversity. Molecular diversity analysis revealed 2-7 alleles among 36 polymorphic simple sequence repeats (SSR) with average of 4.22. Primer BoESSR492 (0.77) showed maximum polymorphic information content (PIC) with mean of 0.58. SSR analysis revealed two clusters each with two subclusters with a composite pattern of genotype distribution. STRUCTURE analysis showed homogenous mixture with least amount of gene pool introgression within the genotypes. Thus, based on morphological and molecular studies, the diverse genotypes namely, DPCaCMS-1, DPCaf-W4, DPCaf-US, DPCaf-W131W, DPCaf-S121, DPCaf-18, DPCaf-13, DPCaf-29 and DPCaf-CMS5 can be utilized in hybridization to isolate potential transgressive segregants to broaden the genetic base of cauliflower or involve them to exploit heterosis.

Complete Chloroplast Genome Sequences of Two Ehretia Trees (Ehretia cymosa and Ehretia obtusifolia): Genome Structures and Phylogenetic Analysis

Ehretiaceae is a family in the order Boraginales. It contains more than 150 species. The Ehretiaceae classification has remained elusive and changed over time from subfamily to family, or vice versa. In this paper, we sequenced, characterized, and analyzed the complete chloroplast (cp) genomes of Ehretia cymosa and Ehretia obtusifolia, and their cp genomes were compared to those of related species. The length of the chloroplast genomes of E. cymosa was 156,328 bp, whereas that of E. obtusifolia was 155,961 bp. Each genome contained 114 genes, including 80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Repeat analysis revealed that complement, forward, palindromic, and reverse repeats were present in the chloroplast genomes of both species. Simple sequence repeat analysis showed that the chloroplast genomes of E. cymosa and E. obtusifolia comprise 141 and 139 microsatellites, respectively. Phylogenetic analysis based on Bayesian and maximum likelihood analyses divided the order Boraginales into two well-supported clades. The first clade includes a single family (Boraginaceae), and the second clade includes three families (Ehretiaceae, Cordiaceae, and Heliotropiaceae). This study provides valuable genomic resources and insights into the evolutionary relationships within Boraginales.

SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features.

Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae) is an important forest pest in China that mainly infests timber and economic forests. This pest primarily causes plant tissue to necrotize, rot, and eventually die by feeding on the woody parts of tree trunks. To gain a deeper understanding of the genetic mechanism of B. horsfieldi, this study employed single-molecule real-time sequencing (SMRT) and Illumina RNA-seq technologies to conduct full-length transcriptome sequencing of the insect. Total RNA extracted from male and female adults was mixed and subjected to SMRT sequencing, generating a complete transcriptome. Transcriptome analysis, prediction of long non-coding RNA (lncRNA), coding sequences (CDs), analysis of simple sequence repeats (SSR), prediction of transcription factors, and functional annotation of transcripts were performed in this study. The collective 20,356,793 subreads (38.26 G, clean reads) were generated, including 432,091 circular consensus sequences and 395,851 full-length non-chimera reads. The full-length non-chimera reads (FLNC) were clustered and redundancies were removed, resulting in 39,912 consensus reads. SSR and ANGEL software v3.0 were used for predicting SSR and CDs. In addition, four tools were used for annotating 6058 lncRNAs, identifying 636 transcription factors. Furthermore, a total of 84,650 transcripts were functionally annotated in seven different databases. This is the first time that the full-length transcriptome of B. horsfieldi has been obtained using SMRT sequencing. This provides an important foundation for investigating the gene regulation underlying the interaction between B. horsfieldi and its host plants through gene editing in the future and provides a scientific basis for the prevention and control of B. horsfieldi.