Development of EST-SSR markers in Bergenia ciliata using de novo transcriptome sequencing

Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in the Indian Himalayan Region. It is widely used in medicines, healthcare systems, cosmetics, fodder, and ornamental purposes. The Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers. A total of 18 226 simple sequence repeats (SSRs) were identified wherein di-nucleotides were found to be abundant (47.88%), followed by mono-nucleotide (35.03%) and tri-nucleotide (15.88%) repeats. A total of 11 839 EST-SSR primers were designed, of which 96 primer pairs were commercially synthesized. Finally, 17 primer pairs revealed clear, distinct polymorphic bands, and these primers were validated with 40 diverse B. ciliata accessions. The present study revealed moderate level of genetic diversity (Ho = 0.389, He = 0.542, and PIC = 0.513). Furthermore, the transcriptome data and EST-SSR markers generated during the present investigation could be an important genetic resource for functional genomics, population studies, and conservation genetics of the genus Bergenia.

The ESTS-AIR database-initial results of a multi-institutional database on airway surgery

OBJECTIVES

Compared to lung resections, airway procedures are relatively rare in thoracic surgery. Despite this, a growing number of dedicated airway centres have formed throughout Europe. These centres are characterized by a close interdisciplinary collaboration and they often act as supra-regional referring centres. To date, most evidence of airway surgery comes from retrospective, single-centre analysis as there is a lack of large-scale, multi-institutional databases.

METHODS

In 2018, an initiative was formed, which aimed to create an airway database within the framework of the ESTS database (ESTS-AIR). Five dedicated airway centres were asked to test the database in a pilot phase. A 1st descriptive analysis of ESTS-AIR was performed.

RESULTS

A total of 415 cases were included in the analysis. For adults, the most common indication for airway surgery was post-tracheostomy stenosis and idiopathic subglottic stenosis; in children, most resections/reconstructions had to be performed for post-intubation stenosis. Malignant indications required significantly longer resections [36.0 (21.4-50.6) mm] when compared to benign indications [26.6 (9.4-43.8) mm]. Length of hospital stay was 11.0 (4.1-17.3) days (adults) and 13.4 (7.6-19.6) days (children). Overall, the rates of complications were low with wound infections being reported as the most common morbidity.

CONCLUSIONS

This evaluation of the 1st cases in the ESTS-AIR database allowed a large-scale analysis of the practice of airway surgery in dedicated European airway centres. It provides proof for the functionality of ESTS-AIR and sets the basis for rolling out the AIR subsection to all centres participating in the ESTS database.

[Development and application of SSR markers of Saposhnikovia divaricata based on transcriptome]

Transcriptome sequencing was employed to mine the simple sequence repeat(SSR) locus information of Saposhnikovia divaricata and design specific primers, which aimed to provide a basis for the research on the genetic diversity of S. divaricata germplasm resources. The seed purity, 1 000-seed weight, germination rate, and seed vigor were determined. MISA was used to obtain the SSR locus information from 12 606 unigene longer than 1 kb in the transcriptome database. Forty-three pairs of SSR primers designed in Primer 3 were used to analyze the polymorphism of 28 S. divaricata samples of different sources. The results showed that there were differences in the seed purity, 1 000-seed weight, germination rate, vigor, and seed length and width among S. divaricata samples of different sources. Particularly, the germination rate and seed vigor had significant differences, and HB-ZJK1, NMG-CF4, NMG-BT, NMG-HLE1, and NMG-CF2 had significantly higher 1 000-seed weight, germination rate, and seed vigor than the samples of other sources. Among the 86 233 unigene, 12 606(14.62%) unigene contained 15 958 SSR loci, with one SSR locus every 5 009 bp on average. The SSR loci were mainly single nucleotide and dinucleotide repeats, which were dominated by G/C and TC/AG, respectively. All the primers were screened by using 28 S. divaricata sample from different habitats, and the primers corresponding to the amplification products with clear bands and stable polymorphism were obtained. The clustering results of the biological characteristics and genetic diversity of the 28 S. divaricata samples were basically consistent, and the samples of the same origin(HB-AG1, HB-AG2, HB-ZJK1, and HB-ZJK2) generally gathered together and had close genetic relationship. The SSRs in S. divaricata transcriptome has high frequency, rich types, and high polymorphism, which provides candidate molecular markers for the germplasm identification, genetic map construction, and molecular-assisted breeding.

Application of Integrated Computational Approaches in Prediction of Plant Virus Encoded miRNAs and Their Targeted Plant Genes

This chapter presents a comprehensive approach to predict novel miRNAs encoded by plant viruses and identify their target plant genes, through integration of various ab initio computational approaches. The predictive process begins with the analysis of plant viral sequences using the VMir Analyzer software. VMir Viewer software is then used to extract primary hairpins from these sequences. To distinguish real miRNA precursors from pseudo miRNA precursors, MiPred web-based software is employed. Verified real pre-miRNA sequences with a minimum free energy of < -20 Kcal/mol, are further analyzed using the RNAshapes software. Validation of predictions involves comparing them with available Expressed Sequence Tags (ESTs) from the relevant plant using BlastN. Short sequences with lengths ranging from 19 to 25 nucleotides and exhibiting <5 mismatches are prioritized for miRNA prediction. The precise locations of these short sequences within pre-miRNA structures generated using RNAshapes are meticulously identified, with a focus on those situated on the 5' and 3' arms of the structures, indicating potential miRNAs. Sequences within the arms of pre-miRNA structures are used to predict target sites within the ESTs of the specific plant, facilitated by psRNA Target software, revealing genes with potential regulatory roles in the plant. To confirm the outcome of target prediction, results are individually submitted to the RNAhybrid web-based software. For practical demonstration, this approach is applied to analyze African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) viruses, as well as the ESTs of Jatropha and cassava.

Transcriptome analysis reveals the peptide toxins diversity of Macrothele palpator venom

Spider venom is a large pharmacological repertoire of different bioactive peptide toxins. However, obtaining crude venom from some spiders is challenging. Thus, studying individual toxins through venom purification is a daunting task. In this study, we constructed the cDNA library and transcriptomic sequencing from the Macrothele palpator venom glands. Subsequently, 718 high-quality expressed sequence tags (ESTs) were identified, and grouped into three categories, including 449 toxin-like (62.53 %), 136 cellular component (18.94 %) and 133 non-matched (18.52 %) based on the gene function annotation. Additionally, 112 non-redundant toxin-like peptides were classified into 13 families (families A-M) based on their sequence homology and cysteine framework. Bioinformatics analysis revealed a high sequence similarity between families A-J and the toxins from Macrothele gigas in the NR database. In contrast, families K-M had a generally low sequence homology with known spider peptide toxins and unpredictable biological functions. Taken together, this study adds many new members to the spider toxin superfamily and provides a basis for identifying various potential biological tools in M. palpator venom.

What is the optimal (neo)adjuvant strategy of extremity high-risk soft tissue sarcomas (ESTS)?

Currently, the standard treatment for extremity high-risk soft tissue sarcomas (ESTS) combines surgery and pre- or post-op radiation therapy (RT). In some selected cases, chemotherapy (CT) is incorporated into the therapeutic algorithm as a neoadjuvant approach to enable conservative management. Given the risk of local or metastatic relapse, this paper discusses the potential benefits of CT and RT in high-grade ESTs. The role of adjuvant chemotherapy in addition to neoadjuvant CT, the prognostic value of the pathological response to neoadjuvant treatment, and the role for an adjuvant "boost" following resection after pre-operative radiotherapy will be discussed.

Tolerance evaluation and genetic relationship analysis among some economically important chestnut cultivars in Türkiye using drought-associated SSR and EST-SSR markers

The aim of this study was to evaluate drought tolerance and genetic relationships among some important chestnut cultivars for Türkiye by using drought-related genomic simple sequence repeat (SSR) markers and genic expressed sequence tag-simple sequence repeat (EST-SSR) markers. Using five SSR markers, the average number of alleles (avNa), mean heterozygosity (Havp) and polymorphism information content (PIC) were determined to be 9.22, 0.395 and 0.375, respectively. In addition, using eight EST-SSR markers, the values of avNa, Havp and PIC were determined to be 7.75, 0.309 and 0.262, respectively. All microsatellite markers used in this study showed 100% polymorphism among chestnut cultivars. In UPGMA dendrograms obtained with both SSR and EST-SSR markers, the Erfelek and Hacıömer chestnut cultivars were determined to be the most similar cultivars. Some assessments are discussed regarding drought tolerance for specific alleles obtained from the EST-SSR markers GOT045, GOT021, GOT004, FIR094 and VIT033 in chestnut cultivars. Some preliminary results regarding drought tolerance in chestnut cultivars were obtained in our study with the help of these markers. Our study also characterized the genetic relationships among chestnut cultivars of great importance using drought-related character-specific markers.

Development and characterization of expressed sequence tag-simple sequence repeat markers for Anaphalis margaritacea var. yedoensis (Asteraceae)

RNA-sequencing was used to develop 16 microsatellite markers for the pearly everlasting, Anaphalis margaritacea var. yedoensis (Franch. et Sav.) Ohwi (Asteraceae), which inhabits gravel bars throughout the Japanese archipelago. The mean number of alleles for these 16 markers in two populations in the Hokkaido and Shizuoka Prefectures, was 3.5 and 4.0, respectively, while the mean expected heterozygosity was 0.525 and 0.560, respectively, with a significant genetic differentiation between the two populations. All markers could also be amplified in two conspecific taxa, A. margaritacea var. margaritacea and var. angustifolia, whereas 11 of the 16 markers were amplifiable in two congeneric species, A. sinica and A. alpicola. These newly developed microsatellite markers will support understanding of population genetics and mating systems in A. margaritacea var. yedoensis, and several will potentially be of use in similar studies in other Anaphalis species.

Genetic diversity, population structure, and DNA fingerprinting of Ailanthus altissima var. erythrocarpa based on EST-SSR markers

Ailanthus altissima var. erythrocarpa is an A. altissima variety with high economic, ecological and ornamental value, but there have been no reports on the development of SSR primers for it. According to the SSR primer information provided by the transcriptome of A. altissima var. erythrocarpa, 120 individuals with different redness levels were used to screen polymorphic primers. Transcriptomic analysis revealed 10,681 SSR loci, of which mononucleotide repeats were dominant (58.3%), followed by dinucleotide and trinucleotide repeats (16.6%, 15.1%) and pentanucleotide repeats (0.2%). Among 140 pairs of randomly selected primers, nineteen pairs of core primers with high polymorphism were obtained. The average number of alleles (Na), average number of effective alleles (Ne), average Shannon's diversity index (I), average observed heterozygosity (Ho), average expected heterozygosity (He), fixation index (F) and polymorphic information content (PIC) were 11.623, 4.098, 1.626, 0.516, 0.696, 0.232 and 0.671, respectively. Nineteen EST-SSR markers were used to study the genetic diversity and population structure of A. altissima var. erythrocarpa. The phylogenetic tree, PCoA, and structure analysis all divided the tested resources into two categories, clearly showing the genetic variation between individuals. The population showed high genetic diversity, mainly derived from intraspecific variation. Among nineteen pairs of primers, 4 pairs (p33, p15, p46, p92) could effectively distinguish and be used for fingerprinting of the tested materials. This study is of great significance for genetic diversity analysis and molecular-assisted breeding of A. altissima var. erythrocarpa.

ERS/ESTS/ESTRO/ESR/ESTI/EFOMP statement on management of incidental findings from low dose CT screening for lung cancer

BACKGROUND

Screening for lung cancer with low radiation dose computed tomography has a strong evidence base, is being introduced in several European countries and is recommended as a new targeted cancer screening programme. The imperative now is to ensure that implementation follows an evidence-based process that will ensure clinical and cost effectiveness. This European Respiratory Society (ERS) task force was formed to provide an expert consensus for the management of incidental findings which can be adapted and followed during implementation.

METHODS

A multi-European society collaborative group was convened. 23 topics were identified, primarily from an ERS statement on lung cancer screening, and a systematic review of the literature was conducted according to ERS standards. Initial review of abstracts was completed and full text was provided to members of the group for each topic. Sections were edited and the final document approved by all members and the ERS Science Council.

RESULTS

Nine topics considered most important and frequent were reviewed as standalone topics (interstitial lung abnormalities, emphysema, bronchiectasis, consolidation, coronary calcification, aortic valve disease, mediastinal mass, mediastinal lymph nodes and thyroid abnormalities). Other topics considered of lower importance or infrequent were grouped into generic categories, suitable for general statements.

CONCLUSIONS

This European collaborative group has produced an incidental findings statement that can be followed during lung cancer screening. It will ensure that an evidence-based approach is used for reporting and managing incidental findings, which will mean that harms are minimised and any programme is as cost-effective as possible.

ERS/ESTS/ESTRO/ESR/ESTI/EFOMP statement on management of incidental findings from low dose CT screening for lung cancer

BACKGROUND

Screening for lung cancer with low radiation dose computed tomography has a strong evidence base, is being introduced in several European countries and is recommended as a new targeted cancer screening programme. The imperative now is to ensure that implementation follows an evidence-based process that will ensure clinical and cost effectiveness. This European Respiratory Society (ERS) task force was formed to provide an expert consensus for the management of incidental findings which can be adapted and followed during implementation.

METHODS

A multi-European society collaborative group was convened. 23 topics were identified, primarily from an ERS statement on lung cancer screening, and a systematic review of the literature was conducted according to ERS standards. Initial review of abstracts was completed and full text was provided to members of the group for each topic. Sections were edited and the final document approved by all members and the ERS Science Council.

RESULTS

Nine topics considered most important and frequent were reviewed as standalone topics (interstitial lung abnormalities, emphysema, bronchiectasis, consolidation, coronary calcification, aortic valve disease, mediastinal mass, mediastinal lymph nodes and thyroid abnormalities). Other topics considered of lower importance or infrequent were grouped into generic categories, suitable for general statements.

CONCLUSIONS

This European collaborative group has produced an incidental findings statement that can be followed during lung cancer screening. It will ensure that an evidence-based approach is used for reporting and managing incidental findings, which will mean that harms are minimised and any programme is as cost-effective as possible.

Identification and validation of the first EST-SSR markers based on transcriptome of Anopheles darlingi, the primary transmitter of malaria in Brazil

BACKGROUND

Anopheles darlingi is a monotypic species in terms of its morphological, genetic, and behavioral aspects and is the primary transmitter of human malaria (99%) in Brazil, especially in the Brazilian Amazon. In this pioneering study, 15 expressed sequence tag (EST)-simple sequence repeat (SSR) markers were obtained and characterized in samples from the municipality of São Gabriel da Cachoeira, Amazonas state, Brazil, with polymorphisms that can be used for further genetic research.

METHODS AND RESULTS

The specimens (from egg to larval stage) collected were bred in the insectary at INPA (National Institute for Amazonian Research). The SSR repeats within the contigs of the A. darlingi EST banks were confirmed on the Vector Base site. DNA was extracted and amplified using polymerase chain reaction and then genotyped. Fifteen polymorphic SSR loci were identified and characterized. The number of alleles totaled 76 and ranged from 2 to 9. The observed heterozygosity varied between 0.026 and 0.769, the expected heterozygosity between 0.025 and 0.776, and the mean polymorphism information content was 0.468. Eight loci showed Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (P: (5%) ≤ 0.0033). No linkage disequilibrium was found among the loci.

CONCLUSIONS

The polymorphic SSRs of the loci have been shown to be efficient for investigation of the variability and genetic population structure of A. darlingi.

Development of EST-SSRs based on the transcriptome of Castanopsis carlesii and cross-species transferability in other Castanopsis species

Castanopsis carlesii (Hemsl.) Hay. is a widely distributed and dominant tree species native to subtropical China with significant ecological and economic value. Due to serious human-related disturbance, its wild resources have been increasingly reduced, and whether may result in the loss of genetic diversity. However, no population genetics studies of natural C. carlesii have been reported to date. Microsatellite markers have been a useful tool in population genetics. Therefore, we developed EST-SSR markers based on the transcriptome sequencing of C. carlesii leaves. A total of 149,380,224 clean reads were obtained, and 63,012 nonredundant unigenes with a mean length of 1,034 bp were assembled and annotated based on sequence similarity searches in the Nr, Nt, KO, SwissProt, PFAM, KOG, and GO databases. The results showed that only 5,559 (8.82%) unigenes were annotated in all seven databases, but 46,338 (73.53%) could be annotated in at least one database. A total of 31,459 potential EST-SSRs were identified in 18,690 unigenes, with an average frequency of one SSR approximately 2 kb. Among the 100 EST-SSR primer pairs designed, 49 primer pairs successfully produced the expected product by amplification, with a success rate of 49%, but only 20 primer pairs showed abundant polymorphisms. Polymorphisms were verified using 25 samples from C. carlesii in Qimen, Anhui. A total of 119 alleles were detected, with a mean number of alleles (Na) of 5.95 per locus and a mean polymorphism information content (PIC) of 0.6125. All the 20 newly developed EST-SSR markers were verified in other Castanopsis species (C. sclerophylla, C. lamontii, C. fargesii, C. eyrei and C. jucunda). Sixteen primer pairs showed successful amplification in all five Castanopsis species (80%), and the transferability ratios ranged from 90% to 100%. These developed EST-SSR markers can be applied to population genetic and germplasm evaluations of C. carlesii and related species.

ERS/ESTS statement on the management of pleural infection in adults

Pleural infection is a common condition encountered by respiratory physicians and thoracic surgeons alike. The European Respiratory Society (ERS) and European Society of Thoracic Surgeons (ESTS) established a multidisciplinary collaboration of clinicians with expertise in managing pleural infection with the aim of producing a comprehensive review of the scientific literature. Six areas of interest were identified: 1) epidemiology of pleural infection, 2) optimal antibiotic strategy, 3) diagnostic parameters for chest tube drainage, 4) status of intrapleural therapies, 5) role of surgery and 6) current place of outcome prediction in management. The literature revealed that recently updated epidemiological data continue to show an overall upwards trend in incidence, but there is an urgent need for a more comprehensive characterisation of the burden of pleural infection in specific populations such as immunocompromised hosts. There is a sparsity of regular analyses and documentation of microbiological patterns at a local level to inform geographical variation, and ongoing research efforts are needed to improve antibiotic stewardship. The evidence remains in favour of a small-bore chest tube optimally placed under image guidance as an appropriate initial intervention for most cases of pleural infection. With a growing body of data suggesting delays to treatment are key contributors to poor outcomes, this suggests that earlier consideration of combination intrapleural enzyme therapy (IET) with concurrent surgical consultation should remain a priority. Since publication of the MIST-2 study, there has been considerable data supporting safety and efficacy of IET, but further studies are needed to optimise dosing using individualised biomarkers of treatment failure. Pending further prospective evaluation, the MIST-2 regimen remains the most evidence based. Several studies have externally validated the RAPID score, but it requires incorporating into prospective intervention studies prior to adopting into clinical practice.

Development of EST-SSR markers based on transcriptome sequencing for germplasm evaluation of 65 lilies (Lilium)

BACKGROUND

Lilium genus consists of approximately 100 species and numerous varieties, many of which are interspecific hybrids, which result in a complicated genetic background. The germplasm identification, genetic relationship analysis, and breeding of Lilium rely on exploiting genetic information among different accessions. Hence, an attempt was made to develop new EST-SSR markers and study the molecular divergence among 65 genotypes of Lilium.

METHODS AND RESULTS

A total of 5509 EST-SSRs were identified from the high-throughput sequencing database of L. 'Elodie'. After primer screening, six primer pairs with the most abundant polymorphic bands were selected from 100 primer pairs. Combined with the other 10 reported SSR primers, a total of 16 pairs detected genetic information with an average PIC value of 0.7583. The number of alleles per locus varied from four to 33, the expected heterozygosity varied from 0.3289 to 0.9231, and the observed heterozygosity varied from 0.2857 to 0.5122. Based on the phylogenic results, 22 Asiatic hybrids (A), seven Longiflorum × Asiatic hybrids (LA), as well as two native species were grouped. Eighteen Oriental hybrids (O) and nine Oriental × Trumpet (OT) hybrids, four native species, one LO, and one LL (L. pardalinum × L. longiflorum) variety were grouped.

CONCLUSIONS

Two major clusters were reported and a large number of genotypes were grouped based on UPGMA and STRUCTURE analysis methods. The PIC value as well as other parameters revealed that the EST-SSR markers selected were informative. In addition, the clustering pattern displayed better agreement with the cultivar's pedigree. The newly identified SSRs in this study provides molecular markers for germplasm characterization and genetic diversity for Lilium.

De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum

Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.

Combined physiological responses and differential expression of drought-responsive genes preliminarily explain the drought resistance mechanism of Lotus corniculatus

Lotus corniculatus L. is a perennial high-quality legume forage species but is vulnerable to drought, and water deficit reduces productivity. To understand the drought response mechanism of L. corniculatus , we investigated physiological responses under drought stress and constructed suppression subtractive hybridisation (SSH) cDNA libraries to isolate drought-inducible genes and quantitatively study the expression levels of candidate drought- responsive genes. Genes encoding calmodulin-like protein, mitogen-activated protein kinase, indole-3-acetic acid-induced protein, ser/thr-protein phosphatase homolog-related proteins, and β -galactosidase-related protein with hydrolysis activity were isolated and considered the main factors that explained the resistance of L. corniculatus to drought. Approximately 632 expressed sequence tags (ESTs) were identified and confirmed in the constructed SSH library. The Gene Ontology (GO) analysis revealed that these genes were involved mainly in transcription processes, protein synthesis, material metabolism, catalytic reactions, sugar metabolism, and photosynthesis. The interaction between the functions of these drought-related genes and the physiological responses preliminarily explains the drought resistance mechanisms of L. corniculatus .

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

BACKGROUND

Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers.

RESULTS

A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species.

CONCLUSIONS

Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.

Common and novel metabolic pathways related ESTs were upregulated in three date palm cultivars to ameliorate drought stress

Date palm is an important staple crop in Saudi Arabia, and about 400 different date palm cultivars grown here, only 50-60 of them are used commercially. The most popular and commercially consumed cultivars of these are Khalas, Reziz, and Sheshi, which are also widely cultivated across the country. Date palm is high water-demanding crop in oasis agriculture, with an inherent ability to tolerate drought stress. However, the mechanisms by which it tolerates drought stress, especially at the transcriptomic level, are still elusive. This study appraised the physiological and molecular response of three commercial date palm cultivars Khalas, Reziz, and Sheshi at two different field capacities (FC; 100% and 25%) levels. At 25% FC (drought stress), leaf relative water content, chlorophyll, photosynthesis, stomatal conductance, and transpiration were significantly reduced. However, leaf intercellular CO2 concentration and water use efficiency increased under drought stress. In comparison to cvs. Khalas and Reziz, date palm cv. Sheshi showed less tolerance to drought stress. A total of 1118 drought-responsive expressed sequence tags (ESTs) were sequenced, 345 from Khalas, 391 from Reziz, and 382 from Sheshi and subjected to functional characterization, gene ontology classification, KEGG pathways elucidation, and enzyme codes dissemination. Three date palm cultivars deployed a multivariate approach to ameliorate drought stress by leveraging common and indigenous molecular, cellular, biological, structural, transcriptional and reproductive mechanisms. Approximately 50% of the annotated ESTs were related to photosynthesis regulation, photosynthetic structure, signal transduction, auxin biosynthesis, osmoregulation, stomatal conductance, protein synthesis/turnover, active transport of solutes, and cell structure modulation. Along with the annotated ESTs, ca. 45% of ESTs were novel. Conclusively, the study provides novel clues and opens the myriads of genetic resources to understand the fine-tuned drought amelioration mechanisms in date palm.

Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.

Expression Profiles of Microsatellites in Fruit Tissues of Akebia trifoliata and Development of Efficient EST-SSR Markers

Akebia trifoliata, a member of the family Lardizabalaceae, has high exploitation potential for multiple economic purposes, so genetic improvements to meet requirements for commercial demand are needed. However, this progress is largely impeded by a lack of effective selection markers. In this study, we obtained 271.49 Gb of clean transcriptomic data from 12 samples (three tissues at four developmental stages) of A. trifoliata fruit. We identified 175,604, 194,370, and 207,906 SSRs from the de novo assembled 416,363, 463,756, and 491,680 unigene sequences obtained from the flesh, seed, and rind tissues, respectively. The profile and proportion of SSR motifs expressed in each fruit tissue and developmental stage were remarkably similar, but many trinucleotide repeats had differential expression levels among different tissues or at different developmental stages. In addition, we successfully designed 16,869 functional EST-SSR primers according to the annotated unigenes. Finally, 94 and 72 primer pairs out of 100 randomly selected primer pairs produced clear bands and polymorphic bands, respectively. These results were also used to elucidate the expression profiles of different tissues at various stages. Additionally, we provided a set of effective, polymorphic, and reliable EST-SSR markers sufficient for accelerating the discovery of metabolic and pathway-specific functional genes for genetic improvement and increased commercial productivity.

Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer

Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.

LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement

Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform in silico validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that legumeSSRdb would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.

Transcriptome-derived microsatellite markers for population diversity analysis in Archidendron clypearia (Jack) I.C. Nielsen

BACKGROUND

The medicinal woody leguminous genus Archidendron F. Mueller serves as important herbal resources for curing upper respiratory tract infection, acute pharyngitis, tonsillitis, and gastroenteritis. However, genomic resources including transcriptomic sequences and molecular markers remain scarce in the genus.

METHODS AND RESULTS

Transcriptome sequencing, genic microsatellite marker development, and population diversity analysis were conducted in Archidendron clypearia (Jack) I.C. Nielsen. Flower and flower bud transcriptomes were de novo assembled into 173,172 transcripts, with an average transcript length of 1597.3 bp and an N50 length of 2427 bp. A total of 34,701 microsatellite loci were identified from 26,716 (15.4 %) transcripts. Primer pairs were designed for 718 microsatellite loci, of which 456 (63.5 %) were polymorphic. Of the 456 polymorphic markers, 391 (85.7 %) and 402 (88.1 %) were transferable to A. lucidum (Benth.) I.C. Nielsen and A. multifoliolatum (H.Q. Wen) T.L. Wu, respectively. Using a subset of 15 microsatellite markers, relatively high genetic diversity was detected over two A. clypearia populations, with overall mean expected heterozygosity (H_e) being 0.707 and demonstrating the necessity of conservation. Relatively low differentiation between the two populations was revealed despite the distant separation (about 700 km), with overall inbreeding coefficient of sub-population to the total population (F_st) being 8.7 %.

CONCLUSIONS

This study represents the first attempt to conduct transcriptome sequencing, SSR marker development, and population genetics analysis in the medicinally important genus Archidendron. Our results will offer valuable resources and information for further genetic studies and practical applications in Archidendron and the related taxa.

FDG-PET/CT for pretherapeutic lymph node staging in non-small cell lung cancer: A tailored approach to the ESTS/ESMO guideline workflow

OBJECTIVES

In patients with NSCLC, current ESTS and ESMO guidelines recommend invasive lymph node (LN) staging with EBUS-TBNA even if FDG-PET/CT is negative for mediastinal LNs if at least one of three risk factors is present (cN1, non-peripheral primary or primary >3 cm). Modified workflows to avoid unnecessary invasive procedures were evaluated.

MATERIALS AND METHODS

Monocentric retrospective analysis of pretherapeutic FDG-PET/CT in 247 patients with NSCLC (62 % male; age, 68 [43-88] years) using an analog or digital PET/CT scanner. PET windowing was standardized. LNs were positive if 'LN uptake > mediastinal blood pool' or short axis >10 mm. Surgery or EBUS-TBNA served as reference for diagnostic accuracy per LN station. In all patients with negative mediastinal LNs by PET/CT, LN histology from surgery was available.

RESULTS

Among 700 L N stations analyzed, 180 were malignant. Sensitivity and specificity of PET/CT per LN station were 93 % and 71 %. Following current guidelines, 76 patients with mediastinal negative PET/CT required confirmatory invasive staging. Only 5/76 patients had unexpected pN2 (all had adenocarcinoma). In a modified approach, confirmatory invasive staging was confined to patients with mediastinal negative PET/CT who showed all three risk factors. Using this modification, EBUS-TBNA could have been omitted in 62 (82 %) of the 76 patients who required EBUS-TBNA based on current recommendation. Among these 62 patients, only one patient had unsuspected pN2 (single-level) while the remaining 61 of 62 omitted EBUS-TBNA were deemed unnecessary because mediastinal LNs were confirmed to be negative. No multi-level pN2 would have been missed.

CONCLUSION

In the current analysis, 82 % of EBUS-TBNA procedures in patients with mediastinal negative PET/CT could have been omitted by modifying the current guideline workflow as proposed (i.e., restricting EBUS-TBNA in patients with cN0/1 to those with all three risk factors). This was consistent with different PET/CT scanners. Prospective confirmation is required.

Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

BACKGROUND

Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus.

RESULTS

Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding.

CONCLUSION

A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.

Genome-Wide Analysis of nsLTP Gene Family and Identification of SiLTPs Contributing to High Oil Accumulation in Sesame (Sesamum indicum L.)

The biosynthesis and storage of lipids in oil crop seeds involve many gene families, such as nonspecific lipid-transfer proteins (nsLTPs). nsLTPs are cysteine-rich small basic proteins essential for plant development and survival. However, in sesame, information related to nsLTPs was limited. Thus, the objectives of this study were to identify the Sesamum indicum nsLTPs (SiLTPs) and reveal their potential role in oil accumulation in sesame seeds. Genome-wide analysis revealed 52 SiLTPs, nonrandomly distributed on 10 chromosomes in the sesame variety Zhongzhi 13. Following recent classification methods, the SiLTPs were divided into nine types, among which types I and XI were the dominants. We found that the SiLTPs could interact with several transcription factors, including APETALA2 (AP2), DNA binding with one finger (Dof), etc. Transcriptome analysis showed a tissue-specific expression of some SiLTP genes. By integrating the SiLTPs expression profiles and the weighted gene co-expression network analysis (WGCNA) results of two contrasting oil content sesame varieties, we identified SiLTPI.23 and SiLTPI.28 as the candidate genes for high oil content in sesame seeds. The presumed functions of the candidate gene were validated through overexpression of SiLTPI.23 in Arabidopsis thaliana. These findings expand our knowledge on nsLTPs in sesame and provide resources for functional studies and genetic improvement of oil content in sesame seeds.

A functional molecular marker for detecting blister blight disease resistance in tea (Camellia sinensis L.)

Identification of an EST-SSR molecular marker associated with Blister blight, a common fungal disease of tea, facilitating marker-assisted selection, marking a milestone in tea molecular breeding. lister blight (BB) leaf disease of tea, caused by the fungus Exobasidium vexans, results in 25-30% crop loss annually. BB is presently controlled by Cu based fungicides, but genetic resistance is the most viable option in disease management. Tea is a naturally out-crossing, woody perennial necessitating a long time for completion of a breeding programme. Marker-assisted selection (MAS) is vital to expedite breeding programmes and also for better accuracy in gene identification. The aim of the current research was to derive marker-trait associations using an F₁ population segregating for BB. The population was genotyped at 11 expressed sequence tag simple sequence repeat loci followed by detecting the alleles by fragment analysis. The genotypic and phenotypic data were subjected to single-marker analysis resulting in the identification of EST-SSR073 as a diagnostic marker amplifying three alleles of the sizes, 168, 170 and 190 bp in F₁. Of them, alleles 190 and 168 bp were confirmed to concur BB resistance and susceptibility, respectively. The alleles were validated in a panel of 64 tea cultivars, resulting in the amplification of 12 alleles at EST-SSR073. The EST-SSR073 allele sequences matched with Camellia sinensis photosystem-I reaction center subunit-II. The marker EST-SSR073 can be effectively used in breeding tea against BB, recording a milestone in MAS in tea.

Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L

BACKGROUND

Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process.

RESULTS

In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness.

CONCLUSIONS

This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.

Discovery of SNPs in important legumes through comparative genome analysis and conversion of SNPs into PCR-based markers

Compared to cereal crops several legumes are less characterized at the genomic level and rightly referred as orphan crops. Transfer of knowledge between model and crop legumes allows development of orthologous pan-taxon genomic tools to benefit research on resource poor taxa. Here, we developed 278 intron flanking gene-specific markers by BLAST aligning pigeonpea (Cajanus cajan (L.) Millsp.) expressed sequence tags (ESTs) with complete genome sequence of barrel medic (Medicago truncatula). A random 192 PCR primer pairs representing loci across the haploid genome (n = 8) of barrel medic were tested on a few important members of legume family. The single copy amplification rates of 31.8% (peanut, Arachis hypogaea) to 77.6% (barrel medic) signifies the success of cross taxon primers and suggested their potential use in comparative legume genomics. Genetic diversity was assessed in 48 pigeonpea genotypes using 143 intron flanking markers which revealed 71 polymorphic markers with PIC values ranging from 0.04 to 0.45 with an average of 0.23 per marker. The PCR products of different varieties of pigeonpea, cowpea and chickpea were sequenced and aligned to find putative SNPs. Integration of these newly developed markers into genetic maps in resource poor legumes will not only aid in the map saturation but also in designing successful marker-assisted selection programmes.

In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)

RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which are involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families and their regulatory elements. However, these RNAi gene families and their sub-cellular locations, functional pathways and regulatory components were not extensively investigated in the case of economically and nutritionally important fruit plant sweet orange (Citrus sinensis L.). Therefore, in silico characterization, gene diversity and regulatory factor analysis of RNA silencing genes in C. sinensis were conducted by using the integrated bioinformatics approaches. Genome-wide comparison analysis based on phylogenetic tree approach detected 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi candidate genes in C. sinensis corresponding to the RNAi genes of model plant Arabidopsis thaliana. The domain and motif composition and gene structure analyses for all three gene families exhibited almost homogeneity within the same group members. The Gene Ontology enrichment analysis clearly indicated that the predicted genes have direct involvement into the gene-silencing and other important pathways. The key regulatory transcription factors (TFs) MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP were identified by their interaction network analysis with the predicted genes. The cis-acting regulatory elements associated with the predicted genes were detected as responsive to light, stress and hormone functions. Furthermore, the expressed sequence tag (EST) analysis showed that these RNAi candidate genes were highly expressed in fruit and leaves indicating their organ specific functions. Our genome-wide comparison and integrated bioinformatics analyses provided some necessary information about sweet orange RNA silencing components that would pave a ground for further investigation of functional mechanism of the predicted genes and their regulatory factors.

Genetic structure of coast redwood (Sequoia sempervirens [D. Don] Endl.) populations in and outside of the natural distribution range based on nuclear and chloroplast microsatellite markers

Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively. These data sets were also used as reference to infer the origin of 147 coast redwood trees growing in Germany (data set G). Coast redwood was introduced to Europe, including Germany as an ornamental species, decades ago. Due to its fast growth and high timber quality, it could be considered as a potential commercial timber species, especially in perspective to climate warming that makes more regions in Germany suitable for its growing. The well performing trees in colder Germany could be potential frost resistant genotypes, but their genetic properties and origin are mostly unknown. Within the natural range in southern Oregon and northern California, only two relatively weak clusters were identified, one northern and one southern, separated by the San Francisco Bay. High genetic diversity, but low differentiation was found based on the 12 nuclear SSR markers for all three data sets F, C and G. We found that investigated 147 German trees represented only 37 different genotypes. They showed genetic diversity at the level less than diversity observed within the natural range in the northern or southern cluster, but more similar to the diversity observed in the southern cluster. It was difficult to assign German trees to the original single native populations using the six cpSSR markers, but rather to either the northern or southern cluster. The high number of haplotypes found in the data sets based on six cpSSR markers and low genetic differentiation based on 12 nuclear SSRs found in this study helps us study and better understand population genetic structure of this complex polyploid tree and supports the selection of potential genotypes for German forestry.

Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species

BACKGROUND

The Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus.

RESULTS

In this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility.

CONCLUSIONS

This study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.

Early nodulin 93 protein gene: essential for induction of somatic embryogenesis in oil palm

Transcript profiling during the early induction phase of oil palm tissue culture and RNAi studies in a model somatic embryogenesis system showed that EgENOD93 expression is essential for somatic embryogenesis. Micropropagation of oil palm through tissue culture is vital for the generation of superior and uniform elite planting materials. Studies were carried out to identify genes to distinguish between leaf explants with the potential to develop into embryogenic or non-embryogenic callus. Oil palm cDNA microarrays were co-hybridized with cDNA probes of reference tissue, separately with embryo forming (media T527) and non-embryo (media T694) forming leaf explants sampled at Day 7, Day 14 and Day 21. Analysis of the normalized datasets has identified 77, 115 and 127 significantly differentially expressed genes at Day 7, Day 14, and Day 21, respectively. An early nodulin 93 protein gene (ENOD93), was highly expressed at Day 7, Day 14, and Day 21 and in callus (media T527), as assessed by RT-qPCR. Validation of EgENOD93 across tissue culture lines of different genetic background and media composition showed the potential of this gene as an embryogenic marker. In situ RNA hybridization and functional characterization in Medicago truncatula provided additional evidence that ENOD93 is essential for somatic embryogenesis. This study supports the suitability of EgENOD93 as a marker to predict the potential of leaf explants to produce embryogenic callus. Crosstalk among stresses, auxin, and Nod-factor like signalling molecules likely induces the expression of EgENOD93 for embryogenic callus formation.

Population genetic structure and marker-trait associations in East and West African Striga hermonthica with varying phenotypic response to Fusarium oxysporum f. sp. strigae isolates Foxy-2 and FK3

To examine the genetic basis for the variable susceptibility of Striga hermonthica from differing zones of sub-Saharan Africa to Fusarium oxysporum f. sp. strigae (Fos) isolates Foxy-2 and FK3, 10 S. hermonthica populations from Eastern and Western Africa were phenotyped for their susceptibility response to Foxy-2 and FK3, and then genotyped with 22 simple sequence repeat (SSR) markers. There is low genetic differentiation between East African and West African S. hermonthica populations (i.e. the proportion of the total genetic variance contained in the subpopulation relative to the total genetic variance, F_ST  = 0.012, P < 0.05), but intermediate genetic differentiation (F_ST  = 0.143, P < 0.01) underlies the S. hermonthica groups that are differentiated by their phenotypic responses to Fos isolates. An expressed sequence tag SSR (EST-SSR) marker Y53 (P < 0.01) and a genomic SSR marker E1009 (P < 0.05) were associated with the S. hermonthica class susceptible to Foxy-2 and FK3 (group A). A divergent S. hermonthica class, consisting of groups with intermediate susceptibility to Foxy-2 (group B) and susceptibility to either FK3 (group C) or Foxy-2 (group D), showed no marker-trait association, instead demonstrated linkage disequilibrium decay. Owing to point substitutions and insertion-deletion mutations, the unique, protein-coding nucleotide sequence at the E1009 locus in group A was partly dissimilar to group B, but was totally distinct from groups C and D. These findings implied that the inconsistent effectiveness of a Fos isolate is better explained by genomic variation in S. hermonthica, rather than by S. hermonthica sampling zones.

Development of EST-SSR markers and association mapping with floral traits in Syringa oblata

BACKGROUND

Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata.

RESULTS

In this study, a total of 10,988 SSRs were obtained from 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. Two hundred thirty-four alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait.

CONCLUSION

The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of floral traits for lilac.

De novo transcriptome assembly and population genetic analyses of an important coastal shrub, Apocynum venetum L

BACKGROUND

Apocynum venetum L. is an important medicinal plant that is mainly distributed in the coastal areas and northwest of China. In addition to its high medical and economic value, its adaptation to saline-alkali and coastal saline lands makes A. venetum an ideal candidate for use in vegetation restoration. To date, the study of A. venetum has been limited in the northwest region of China, little attention has been paid to the genetic diversity and population structure of A. venetum populations in the coastal region. Here, we performed transcriptome sequencing of total RNA from A. venetum leaves and developed efficient expressed sequence tag-simple sequence repeat (EST-SSR) markers for analyzing the genetic diversity and population structure of A. venetum in the coastal region.

RESULTS

A total of 86,890 unigenes were generated after de novo assembly, and 68,751 of which were successfully annotated by searching against seven protein databases. Furthermore, 14,072 EST-SSR loci were detected and 10,243 primer pairs were successfully designed from these loci. One hundred primer pairs were randomly selected and synthesized, twelve primer pairs were identified as highly polymorphic and further used for population genetic analysis. Population genetic analyses showed that A. venetum exhibited low level of genetic diversity (mean alleles per locus, N_A = 3.3; mean expected heterozygosity, H_E = 0.342) and moderate level of genetic differentiation among the populations (genetic differentiation index, F_ST = 0.032-0.220) in the coastal region. Although the contemporary (mean m_c = 0.056) and historical (mean m_h = 0.106) migration rates among the six A. venetum populations were moderate, a decreasing trend over the last few generations was detected. Bayesian structure analysis clustered six populations into two major groups, and genetic bottlenecks were found to have occurred in two populations (QG, BH).

CONCLUSIONS

Using novel EST-SSR markers, we evaluated the genetic variation of A. venetum in the coastal region and determined conservation priorities based on these findings. The large dataset of unigenes and SSRs identified in our study, combining samples from a broader range, will support further research on the conservation and evolution of this important coastal plant and its related species.

De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing

Mugil incilis (lisa) is an important commercial fish species in many countries, living along the coasts of the western Atlantic Ocean. It has been used as a model organism for environmental monitoring and ecotoxicological investigations. Nevertheless, available genomic and transcriptomic information for this organism is extremely deficient. The aim of this study was to characterize M. incilis hepatic transcriptome using Illumina paired-end sequencing. A total of 32,082,124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93,912 contigs (N50 = 2,019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (13.4%). Using a sequence similarity search against the public databases GO and KEGG, a total of 7,301 and 16,967 contigs were annotated, respectively. KEGG database showed genes related to environmental information, metabolism and organismal system pathways were highly annotated. Complete or partial coding DNA sequences for several candidate genes associated with stress responses/detoxification of xenobiotics, as well as housekeeping genes, were employed to design primers that were successfully tested and validated by RT-qPCR. This study presents the first transcriptome resources for Mugil incilis and provides basic information for the development of genomic tools, such as the identification of RNA markers, useful to analyze environmental impacts on this fish Caribbean species.

EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

BACKGROUND

The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers.

METHODS

In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms.

RESULTS

Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported.

CONCLUSION

This deep EST-SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

BACKGROUND

Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers.

RESULTS

In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances.

CONCLUSION

Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

BACKGROUND

Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS).

RESULTS

The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%).

CONCLUSIONS

Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.

Development and Transferability of EST-SSR Markers for Pinus koraiensis from Cold-Stressed Transcriptome through Illumina Sequencing

Pinus koraiensis has significant economic and ecological value in Northeast China. However, due to the lack of suitable molecular markers, only a few available microsatellite markers were developed for further population genetics studies. In this study, for the first time we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers from the cold-stressed transcriptome of P. koraiensis using Illumina Sequencing. We identified a total of 7,235 EST-SSRs from 97,376 sequences, and we tested their transferability among seven related Pinus species. The results showed that trinucleotides were the most abundant type of repeat (1287, 18.74%) excluding mononucleotides, followed by dinucleotides (1284, 18.7%) and tetranucleotides (72, 1.05%). The most dominant dinucleotides and trinucleotide repeat motifs were AT/AT (535, 7.79%) and AAT/ATT (103, 1.5%). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.002 to 0.986 and 0.017 to 0.743, respectively, and the polymorphism information content (PIC) values and number of alleles (Na) varied from 0.029 to 0.794 and 2 to 23, respectively. A total of 8 natural P. koraiensis populations were divided into two main genetic clusters. Furthermore, nine of twenty polymorphic primer pairs were successfully amplified in seven Pinus species, and at least 80% of the successful P. koraiensis EST-SSR primers could be amplified in more than four species (16, 80%). Combined results for the development of EST-SSR markers in P. koraiensis and transferability among related species would contribute to improved studies on the genetic diversity and population structure in P. koraiensis and phylogenetic relationships among Pinus species. They would also provide a significant source for quantitative trait locus analysis.

Molecular cytogenetic characterization of a novel wheat-Psathyrostachys huashanica Keng T3DS-5NsL•5NsS and T5DL-3DS•3DL dual translocation line with powdery mildew resistance

BACKGROUND

Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) carries many outstanding agronomic traits, therefore is a valuable resource for wheat genetic improvement. Wheat-P. huashanica translocation lines are important intermediate materials for wheat breeding and studying the functions of alien chromosomes. However, powdery mildew resistance in these translocation lines has not been reported previously.

RESULTS

This study developed a novel wheat-P. huashanica translocation line TR77 by selecting a F₇ progeny from the cross between heptaploid hybrid H8911 (2n = 7x = 49, AABBDDNs) and durum wheat line Trs-372. Chromosome karyotype of 2n = 42 = 21II was observed in both mitotic and meiotic stages of TR77. Genomic in situ hybridization analysis identified two translocated chromosomes that paired normally at meiosis stage in TR77. Molecular marker analysis showed that part of chromosome 5D was replaced by part of alien chromosome fragment 5Ns. It meant replacement made part 5DL and part 5NsL·5NsS existed in wheat background, and then translocation happened between these chromosomes and wheat 3D chromosome. Fluorescence in situ hybridization demonstrated that TR77 carries dual translocations: T3DS-5NsL·5NsS and T5DL-3DS·3DL. Analysis using a 15 K-wheat-SNP chip confirmed that SNP genotypes on the 5D chromosome of TR77 matched well with these of P. huashanica, but poorly with common wheat line 7182. The translocation was physically located between 202.3 and 213.1 Mb in 5D. TR77 showed longer spikes, more kernels per spike, and much better powdery mildew resistance than its wheat parents: common wheat line 7182 and durum wheat line Trs-372.

CONCLUSIONS

TR77 is a novel stable wheat-P. huashanica T3DS-5NsL·5NsS and T5DL-3DS·3DL dual translocation line and showed significant improved spike traits and resistance to powdery mildew compared to its parents, thus, it can be an useful germplasm for breeding disease resistance and studying the genetic mechanism of dual translocations.

17β-Hydroxysteroid dehydrogenase type 12a responsible for testicular 11-ketotestosterone synthesis in the Japanese eel, Anguilla japonica

The production of 11-ketotestosterone (11KT), an important steroid hormone in piscine spermatogenesis, is regulated by the pituitary gonadotropins [Gths: follicle-stimulating hormone (Fsh) and luteinizing hormone (Lh)] and it is synthesized by catalytic reactions involving several steroidogenic enzymes. Among these enzymes, the role of 17β-hydroxysteroid dehydrogenases (Hsd17bs) that exhibited 17-ketosteroid reducing activity (17KSR activity) responsible for 11KT synthesis is still poorly understood. In the present study, for the deeper understanding of testicular 11KT biosynthesis, we first investigated the steroidogenic pathway to produce 11KT in Japanese eel testis. In vitro incubation of the testis with androstenedione (A4) and the subsequent analysis of the metabolites by thin-layer chromatography indicated that 11KT was synthesized from A4 via 11β-hydroxyandrostenedione (11OHA4) and 11-ketoandrostenedione (11KA4), which indicated that the steroidogenic enzyme exhibiting the 17KSR activity responsible for converting 11KA4 to 11KT is crucial for 11KT production. Subsequently, cDNAs encoding three candidate enzymes, Hsd17b type3 (Hsd17b3), Hsd17b type12a (Hsd17b12a), and 20β-hydroxysteroid dehydrogenase type2 (Hsd20b2), potentially with the 17KSR activity were isolated and characterized in the Japanese eel. The isolated hsd17b3, hsd17b12a, and hsd20b2 cDNAs putatively encoded 308, 314, and 327 amino acid residues with high homology to those of other vertebrate counterparts, respectively. The Hsd17b3, Hsd17b12a, and Hsd20b2 expressed either in HEK293T or in Hepa-E1 converted 11KA4 to 11KT. Tissue-distribution analysis by quantitative real time PCR revealed that hsd17b12a and hsd20b2 mRNAs were detected in the testis, while hsd17b3 mRNA was not detectable. Furthermore, we examined the effects of Gths on the 17KSR activity and the expression of the candidate genes in the immature testis. The 17KSR activity was upregulated by administration of Gths. Furthermore, only expression of hsd17b12a among three candidates was upregulated by Gths as well as the 17KSR activity. These findings strongly suggested that Hsd17b12a is one of the enzymes with 17KSR activity responsible for 11KT synthesis in the testis of Japanese eel.

De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba

Gloriosa superba is an economical source of pharmaceutical colchicine, which is a mitotic poison used to treat gout, cancer and inflammatory diseases. It is important to study the genetic variations in this plant, but the progress is impeded due to limited number of molecular markers. In this study, we developed the expressed sequence tag-derived simple sequence repeat (EST-SSR) markers from the transcriptome sequence of the leaf samples of three different ecotypes of G. superba. De novo assembly was performed on these sequencing data to generate a total of 65,579 unigenes and 38,200 coding sequences (CDSs). These CDSs were annotated using NCBI Nr protein database, gene ontology terms and KEGG pathways. Differential gene expression was studied to yield differences in these ecotypes at the molecular level. Finally, a total of 14,672 potential EST-SSRs were identified from these unigenes, among which the dinucleotide (5754, 39.22%) and trinucleotide (5421, 36.95%) repeats were most abundant types followed by mononucleotides (3213, 21.83%). The most frequent motifs were CT/GA (1392, 9.48%), AG/TC (1219, 8.31%), and GA/CT (1146, 7.82%) among the dinucleotide repeats and CCG/ CGG (1487, 10.13%), AGG/CCT (1421, 9.68%), AGC/CTG (697, 4.75%) and AAG/CTT (621, 4.23%) among the trinucleotide repeats. Polymorphism study using a random set of 20 newly developed EST-SSRs revealed polymorphic information content value ranging from 0 to 0.5926 with an average of 0.4021. The large-scale ESTs developed in the current study will be useful as a genomic resource for further investigation of the genetic variations in this species.

Genetic structure and diversity analysis of tall fescue populations by EST-SSR and ISSR markers

Tall fescue is a perennial cool-season grass with economic importance especially in temperate regions of the northern hemisphere. This study was done to assess the genetic diversity and population structure of 90 tall fescue populations and cultivars using ISSR and EST-SSR markers in order to categorize valuable populations for breeding programs and to construct the core collection of tall fescue collection in Iran. The 10 EST-SSR primer pairs amplified 92 alleles. The allele numbers varied from 4 to 13 alleles per locus with an average of 9.2 alleles, of which 84 (90.6%) were polymorphic with an average of 8.4 polymorphic bands per primer. The 39 ISSR primers totally produced 387 scorable bands, of which 335 (86.6%) were polymorphic with an average of 8.6 polymorphic bands per primer. The amplified markers by ISSR primers varied from 6 to 14 markers per primer with an average of 9.92 markers per primer. The 90 tall fescue populations using both EST-SSR and ISSR data were classified into two clusters by UPGMA method that was coincide with PCA and structure analysis results. The turf-type and forage-type populations were clearly separated. Based on the results, the Iranian populations provide a valuable and novel germplasm to employ in tall fescue varietal improvement programs for both forage and turf-type applications. This progression is an important step to introduce this collection for development of a core collection of tall fescue germplasm in Iran.

Development of EST-SSR markers in Cenchrus ciliaris and their applicability in studying the genetic diversity and cross-species transferability

Most of the grasses of the genus Cenchrus (20-25 species) and Pennisetum (80-140 species) are distributed throughout the tropical and subtropical regions of the world and reproduce both by sexual and apomictic modes. However, the relationships among the Cenchrus-Pennisetum species are not very clear yet. Molecular markers like expressed sequence tag-simple sequence repeats (EST-SSRs) have been reported to be a better choice for resolving the phylogenetic relationships and to estimate the genetic diversity. The present study describes the identification of EST-SSR markers based on the transcriptome data of Cenchrus ciliaris inflorescence and illustrates the genetic diversity and phylogenetic relationships among these species. Of the 378 primer pairs used across 33 accessions of 21 Cenchrus, Pennisetum, and related grass (Bothriochloa, Dichanthium and Panicum) species, 116 EST-SSR markers were found to be polymorphic with an average polymorphism information content (PIC) of 0.49. Fifty-one EST-SSR loci and 520 alleles showed that where the PIC value is >0.5 there the GAG repeat motif was highly polymorphic. Two EST-SSR markers, CcSSR_80 and CcSSR_102, are polymorphic among the Cenchrus species, while they are absent in Pennisetum and the allied species. Five SSR markers (CcSSR_75, CcSSR_85, CcSSR_87, CcSSR_88 and CcSSR_114) showed 100% cross-transferability among the 21 Cenchrus-Pennisetum species. Species-specific alleles could also be detected for seven species of Cenchrus, Pennisetum and Panicum across 10 SSR markers. Assay of polymorphism across these agamic complexes showed that the three SSR markers (CcSSR_26, CcSSR_97 and CcSSR_109) were associated with Cenchrus-Pennisetum complex, and one (CcSSR_47) with Bothriochloa-Dichanthium complex. Markers with high discriminating power, namely CcSSR_4, CcSSR_38, CcSSR_48, CcSSR_66, CcSSR_67 and CcSSR_70, can be used to estimate the allelic sequence divergence across the sexual and apomictic lineages. Genetic diversity analysis using neighbour-joining (NJ) and principal co-ordinate analysis (PCoA) based approaches showed six and five clusters for the 33 accessions, respectively, having congruence in the pattern of clustering. These accessions were grouped according to their mode of reproduction. Cenchrus and Pennisetum species were grouped separately within the same clade, implying monophyletic group within a 'bristle clade'. Thus, this study showed high discrimination power of microsatellite (EST-SSR) markers to resolve the phylogenetic relationships.

Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa

Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using RNA-seq data we have analyzed the expression patterns of certain TF families, predicted protein-protein interactions, and analyzed evolutionary trajectories to elucidate their possible roles in salt tolerance. We have detected the top differentially expressed (DE) transcription factor families (MYB, CAMTA, MADS-box and bZIP) that show the most pronounced response to salinity. The majority of DE genes in the four aforementioned TF families cluster together on TF phylogenetic trees, which suggests common evolutionary origins and trajectories. This research represents the first comprehensive TF study of a leaf succulent halophyte including their evolutionary relationships with TFs in other halophyte and salt-senstive plants. These findings provide a foundation for understanding the function of salt-responsive transcription factors in salt tolerance and associated gene regulation in plants.