[Construction and Evaluation of a Prognostic Risk Prediction Model of Pancreatic Ductal Adenocarcinoma Based on Immune-Related Genes].

Objective To construct a risk prediction model by integrating the molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) and immune-related genes.Methods With GSE71729 data set (n=145) as the training set,the differentially expressed genes and differential immune-related genes between the squamous and non-squamous subtypes of PDAC were integrated to construct a regulatory network,on the basis of which five immune marker genes regulating the squamous subtype were screened out.An integrated immune score (IIS) model was constructed based on patient survival information and immune marker genes to predict the clinical prognosis of PDAC patients,and its predictive performance was tested with 5 validation sets (n=758).Results PDAC patients were assigned into high risk and low risk groups according to the IIS.In both training and validation sets,the overall survival of patients in the high risk group was shorter than that in the low risk group (both P<0.001).The multivariable Cox regression showed that IIS was an independent prognostic factor for PDAC (HR=2.16,95%CI=1.50-3.10,P<0.001).Conclusion IIS can be used for risk stratification of PDAC patients and may become a potential prognostic marker for PDAC.

Taxonomy and phylogeny of Panus (Polyporales, Panaceae) in China and its relationship with allies.

Panus is a typical wood-rotting fungi, which plays considerable roles in ecosystems and has significant economic value. The genus Panus currently consists of more than 100 species; however, only eight species have been reported from China. This study aims to distinguish and describe two novel species from the Panussimilis complex, namely Panusminisporus and Panusbaishanzuensis, one new record species from Zhejiang Province, Panussimilis and three common species, Panusconchatus, Panusneostrigosus and Panusrudis, based on detailed morphological and phylogenetic studies, relying on Chinese specimens. Panusminisporus is characterised by its reddish-brown pileus, decurrent lamellae with cross-veins, slender stipe, smaller basidiospores, wider generative hyphae and absence of sclerocystidia. Panusbaishanzuensis is featured by its pileus with concentric and darker ring zone, decurrent lamellae with cross-veins, shorter stipe, longer basidiospores, diverse and shorter cheilocystidia and smaller sclerocystidia. Internal transcribed spacer (ITS) regions, large subunit nuclear ribosomal RNA gene (nLSU) and translation elongation factor 1-α gene (tef-1α) were employed to perform a thorough phylogenetic analysis for genus Panus and related genera, using Bayesian Inference and Maximum Likelihood analysis. The results indicate that Panusminisporus and Panusbaishanzuensis form two independent clades within the Panussimilis complex themselves. Detailed descriptions, taxonomic notes, illustrations etc. were provided. In addition, a key to the reported species of Panus from China is also provided.

New insights into the stipitate hydnoid fungi Sarcodon, Hydnellum, and the formerly informally defined Neosarcodon, with emphasis on the edible species marketed in Southwest China.

Sarcodon and Hydnellum are two ectomycorrhizal genera of important ecological and economic value in Southwest China, and they are common in the free markets in this region. It was estimated that more than 1,500 tonnes of them were sold as edible per year, but there was little information about the taxonomic placements of these edible mushrooms sold in the markets. Traditional concepts of the two genera have also been challenged recently, and circumscription of Sarcodon and the informally defined clade "Neosarcodon" remained unresolved. In the present study, specimens collected in the field and purchased from the markets in Southwest China were analyzed based on morphological characters and DNA sequences. Phylogeny of the traditional Sarcodon s. lat. and Hydnellum s. lat. was reconstructed from the combined internal transcribed spacer (ITS), nuclear large ribosomal subunit (nLSU) and RNA polymerase II second largest subunit (RPB2) dataset based on expanded samples to reevaluate the taxonomic placements of the two genera. In the present molecular analyses, four distinct clades were recovered and strongly supported: Hydnellum, Neosarcodon, Phellodon and Sarcodon. Neosarcodon is formally introduced as a generic name to include nine species previously placed in Sarcodon, and the delimitation of Sarcodon is revised based on phylogenetic and morphological studies. Phylogenetic analyses also revealed an unexpected species diversity (17 phylogenetic species) of Sarcodon and Hydnellum in the markets; nine phylogenetic species of Sarcodon and eight of Hydnellum were uncovered from the samples collected in the markets. Eight species were resolved in the traditional S. imbricatus complex, with S. imbricatus s.str. being the most common edible stipitate hydnoid fungal species. Three of the edible Hydnellum species (H. edulium, H. subalpinum, and H. subscabrosellum), and five separated from the S. imbricatus complex (Sarcodon flavidus, S. giganteus, S. neosquamosus, S. nigrosquamosus, and S. pseudoimbricatus), are described as new. Three new Chinese records (H. illudens, H. martioflavum, and H. versipelle), and the notable S. imbricatus and S. leucopus are also reported.

Establishment of a prediction model for severe acute radiation enteritis associated with cervical cancer radiotherapy.

BACKGROUND: Cervical cancer is one of the most common gynecological malignant tumors. Radiation enteritis (RE) leads to radiotherapy intolerance or termination of radiotherapy, which negatively impacts the therapeutic effect and seriously affects the quality of life of patients. If the incidence of RE in patients can be predicted in advance, and targeted clinical preventive treatment can be carried out, the side effects of radiotherapy in cervical cancer patients can be significantly reduced. Furthermore, accurate prediction of RE is essential for the selection of individualized radiation dose and the optimization of the radiotherapy plan. AIM: To analyze the relationships between severe acute RE (SARE) of cervical cancer radiotherapy and clinical factors and dose-volume parameters retrospectively. METHODS: We included 50 cervical cancer patients who received volumetric modulated arc therapy (VMAT) from September 2017 to June 2018 in the Department of Radiotherapy at The First Affiliated Hospital Soochow University. Clinical and dose-volume histogram factors of patients were collected. Logistic regression analysis was used to evaluate the predictive value of each factor for SARE. A nomogram to predict SARE was developed (SARE scoring system ≥ 3 points) based on the multiple regression coefficients; validity was verified by an internal verification method. RESULTS: Gastrointestinal and hematological toxicity of cervical cancer VMAT gradually increased with radiotherapy and reached the peak at the end of radiotherapy. The main adverse reactions were diarrhea, abdominal pain, colitis, anal swelling, and blood in the stool. There was no significant difference in the incidence of gastrointestinal toxicity between the radical and postoperative adjuvant radiotherapy groups (P > 0.05). There were significant differences in the small intestine V20, V30, V40, and rectal V40 between adjuvant radiotherapy and radical radiotherapy after surgery (P < 0.05). Univariate and multivariate analyses revealed anal bulge rating (OR: 14.779, 95%CI: 1.281-170.547, P = 0.031) and disease activity index (DAI) score (OR: 53.928, 95%CI: 3.822-760.948, P = 0.003) as independent predictors of SARE. CONCLUSION: Anal bulge rating (> 0.500 grade) and DAI score (> 2.165 points) can predict SARE. The nomogram shows potential value in clinical practice.

[Effect of Notch1 on extracellular matrix deposition in the renal tubulointerstitium of diabetes].

The aim of the present study was to observe the effects of Notch1 and autophagy on extracellular matrix deposition in renal tubulointerstitium of diabetes and to explore the mechanism. The mice were randomly divided into normal control group (db/m mice) and diabetes group (db/db mice). After 12 weeks of feeding, the mice were sacrificed and the corresponding biochemical indexes were measured. Rat renal tubular epithelial cells NRK52E were cultured under normal glucose (NG) and high glucose (HG) respectively, and the expression of Notch1 and LC3 proteins were detected by Western blotting. Autophagosomes in NRK52E cells with overexpressed and knockdown Notch1 under NG and HG conditions were observed by confocal microscope, and the expression changes of Notch1, Collagen-I and III protein were detected by immunofluorescence. The results showed that the Notch1 and Collagen-III expressions were increased (P < 0.01) and the LC3 expression was decreased (P < 0.05) in db/db mice compared with db/m mice. In vitro, the Notch1 was increased (P < 0.01) and the LC3 expression was decreased significantly (P < 0.01) in NRK52E cells of HG group compared with NG group. There was no significant change of Notch1 and LC3 expression between the mannitol (MA) group and the NG group. Autophagy was decreased and extracellular matrix deposition was aggravated when Notch1 was overexpressed. In contrast, autophagy was increased and extracellular matrix deposition was relieved by knockdown of Notch1 under HG conditions. In conclusion, Notch1 protein expression was increased and autophagy was reduced in renal tissue of diabetes and renal tubular epithelial cells under HG. The extracellular matrix deposition in the renal tubulointerstitium was relieved by regulating autophagy after the knockdown of Notch1.

A Phylogenetic and Taxonomic Study on Phellodon (Bankeraceae, Thelephorales) from China.

In this study, phylogenetic analyses of Phellodon from China were carried out based on sequences from the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nLSU), the small subunit of nuclear ribosomal RNA gene (nSSU), the largest subunit of RNA polymerase II (RPB1), and the second largest subunit of RNA polymerase II (RPB2), combined with morphological characters of the collected specimens in China. The fruiting bodies of the specimens were used to observe their characteristics, and three new species of Phellodon are discovered. Phellodon crassipileatus is characterized by its pale brown to dark brown pileal surface, tomentose pileal margin, white spines, and the presence of clamp connections in generative hyphae of pileal surface, context, and stipe. Phellodon griseofuscus is characterized by its dark brown to black pileal surface, white to pale brown pileal margin, the presence of both simple septa and clamp connections in generative hyphae of spines, and moderately long basidia. Phellodon perchocolatus is characterized by its woody and broad pileus, brown to greyish brown pileal surface when fresh, tomentose pileal margin when young, which becomes glabrous with age, and the presence of both simple septa and clamp connections in the generative hyphae of the spines. This is the first time both single and multi-genes analysis is used in such a phylogenetic and taxonomic study on Phellodon, which can provide the basis for the phylogenetic study of the genus.

Hygrophorus annulatus, a new edible member of H. olivaceoalbus-complex from southwestern China.

Members of Hygrophorus olivaceoalbus-complex or olive waxcaps have both ecological and economic significance. European and North American species diversity of this fungal group has been presented in recent molecular phylogenetic studies, but no Chinese materials were included. In this study, a phylogenetic overview of the H. olivaceoalbus-complex based on internal transcribed spacer (ITS) sequences was made, and a local popular edible species from southwestern China was described as a new species H. annulatus. This new species is characterized by grayish brown, olive brown to dark brown pileus disc, inflexed to deflexed pileus margin, obvious and dark brown annulus, basidiospores measuring (8.0-)8.5-11.0(-12.0) × 5.0-7.5(-8.0) µm, and the distribution in subalpine forests dominated by Abies and/or Picea in southwestern China.

Hygrophorus subsection Hygrophorus (Hygrophoraceae, Agaricales) in China.

Hygrophorus subsect. Hygrophorus has been relatively well-studied in Europe and North America, but studies on the taxa in Asia, particularly in China, are still limited. In this study, phylogenetic overviews of genus Hygrophorus, based on the nuclear large subunit (LSU) ribosomal RNA gene and of subsect. Hygrophorus, based on the nuclear ribosomal internal transcribed spacer (ITS) regions were generated. Four new species, i.e. H. brunneodiscus, H. fuscopapillatus, H. glutiniceps and H. griseodiscus are described from southern China; and a rarely reported edible species H. hedrychii is described in detail, based upon the materials from north-eastern China. The main characteristics of the species under subsect. Hygrophorus worldwide are summarised in a table.

Corrigendum: He XL, Horak E, Wang D, Li TH, Peng WH, Gan BC (2019) Descriptions of five new species in Entoloma subgenus Claudopus from China, with molecular phylogeny of Entoloma s.l. MycoKeys 61: 1-26. https://doi.org/10.3897/mycokeys.61.46446.

[This corrects the article DOI: 10.3897/mycokeys.61.46446.].

Author Correction: Genome-wide identification of Major Intrinsic Proteins in Glycine soja and characterization of GmTIP2;1 function under salt and water stress.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Descriptions of five new species in Entoloma subgenus Claudopus from China, with molecular phylogeny of Entoloma s.l.

Entoloma subgenus Claudopus is widely distributed, yet the taxonomy and systematics of its species are still poorly documented. In the present study, more than forty collections of Claudopus were gathered in China and subsequently analysed, based on morphological and molecular data. The results revealed first a high level of species diversity of Claudopus in China and second, there is a wide ecological range regarding the substrates and the habitats ranging from temperate, tropical to subalpine locations. Based on morphological and molecular evidence, five novel species from China are proposed, viz. E. conchatum, E. flabellatum, E. gregarium, E. pleurotoides and E. reductum. Molecular phylogeny of Entoloma s.l. was also reconstructed, based on 187 representatives of Entoloma s.l. by employing the combined ITS, LSU, mtSSU and RPB2 sequences. Ten monophyletic clades (Claudopus, Leptonia, Nolanea, Cuboid-spored Inocephalus, "Alboleptonia", Cyanula, Pouzarella, Rhodopolia, Prunuloides and Rusticoides) were recovered, while 13 taxa could not be placed in any defined clades. The results confirmed that Claudopus in a traditional morphological sense is not monophyletic and the Rusticoides-group, previously considered within Claudopus, formed a separate clade; but section Claudopus and relatives of E. undatum belong to a distinctive monophyletic group. Despite some monophyletic groups in Entoloma s.l. being distinctive in both morphology and molecular phylogeny, they were still treated as subgenera of Entoloma s.l. temporarily, because accepting them as genera will make Entoloma s.l. paraphyletic.

Three new species of EntolomasubgenusPouzarella from China based on morphological and molecular data.

In the present paper, three additional species of EntolomasubgenusPouzarella viz. E.erectoides, E.griseocarpum and E.rubropilosum are described from China. E.rubropilosum is a typical species in section Pouzarella; E.griseocarpum and E.erectoides are members of sect. Dysthales. The taxa are further confirmed by ITS, RPB2, LSU and mtSSU analyses and phylogenetic relationships with other Entolomasubgen.Pouzarella species are also discussed. ITS sequence analysis showed that the sizes of the entire ITS region and ITS1 are remarkably divergent, while the ITS2 is conserved in length within Entolomasubgen.Pouzarella. Molecular analyses, based on the combined dataset, demonstrated that species diversity of subgen.Pouzarella in China is much higher than previously thought, in the present study twenty phylogenetic species from China are taken into consideration. On the other hand, morphological and molecular analyses suggested that classification of Entolomasubgen.Pouzarella probably has to be fundamentally re-adjusted based on additional data.

Genome-wide identification of Major Intrinsic Proteins in Glycine soja and characterization of GmTIP2;1 function under salt and water stress.

In different plant species, aquaporins (AQPs) facilitate water movement by regulating root hydraulic conductivity under diverse stress conditions such as salt and water stresses. To improve survival and yield of crop plants, a detailed understanding of stress responses is imperative and required. We used Glycine soja genome as a tool to study AQPs, considering it shows abundant genetic diversity and higher salt environment tolerance features and identified 62 Gs AQP genes. Additionally, this study identifies major aquaporins responsive to salt and drought stresses in soybean and elucidates their mode of action through yeast two-hybrid assay and BiFC. Under stress condition, the expression analysis of AQPs in roots and leaves of two contrasting ecotypes of soybean revealed diverse expression patterns suggesting complex regulation at transcriptional level. Based on expression analysis, we identify GmTIP2;1 as a potential candidate involved in salinity and drought responses. The overexpression of GmTIP2;1 in Saccharomyces cerevisiae as well as in-planta enhanced salt and drought tolerance. We identified that GmTIP2;1 forms homodimers as well as interacts with GmTIP1;7 and GmTIP1;8. This study augments our knowledge of stress responsive pathways and also establishes GmTIP2;1 as a new stress responsive gene in imparting salt stress tolerance in soybean.

Intra- and inter-isolate variation of ribosomal and protein-coding genes in Pleurotus: implications for molecular identification and phylogeny on fungal groups.

BACKGROUND: The internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), and elongation factor 1-alpha (EF1α) are often used in fungal taxonomy and phylogenetic analysis. As we know, an ideal molecular marker used in molecular identification and phylogenetic studies is homogeneous within species, and interspecific variation exceeds intraspecific variation. However, during our process of performing ITS, RPB2, and EF1α sequencing on the Pleurotus spp., we found that intra-isolate sequence polymorphism might be present in these genes because direct sequencing of PCR products failed in some isolates. Therefore, we detected intra- and inter-isolate variation of the three genes in Pleurotus by polymerase chain reaction amplification and cloning in this study. RESULTS: Results showed that intra-isolate variation of ITS was not uncommon but the polymorphic level in each isolate was relatively low in Pleurotus; intra-isolate variations of EF1α and RPB2 sequences were present in an unexpectedly high amount. The polymorphism level differed significantly between ITS, RPB2, and EF1α in the same individual, and the intra-isolate heterogeneity level of each gene varied between isolates within the same species. Intra-isolate and intraspecific variation of ITS in the tested isolates was less than interspecific variation, and intra-isolate and intraspecific variation of RPB2 was probably equal with interspecific divergence. Meanwhile, intra-isolate and intraspecific variation of EF1α could exceed interspecific divergence. These findings suggested that RPB2 and EF1α are not desirable barcoding candidates for Pleurotus. We also discussed the reason why rDNA and protein-coding genes showed variants within a single isolate in Pleurotus, but must be addressed in further research. CONCLUSIONS: Our study demonstrated that intra-isolate variation of ribosomal and protein-coding genes are likely widespread in fungi. This has implications for studies on fungal evolution, taxonomy, phylogenetics, and population genetics. More extensive sampling of these genes and other candidates will be required to ensure reliability as phylogenetic markers and DNA barcodes.

White mold on cultivated morels caused by Paecilomyces penicillatus.

Morchella (morel) includes prized edible and medical mushrooms in the world. Since 2012, commercial cultivation of morels in the field has developed rapidly in China. However, coupled with the rapid expansion of morel cultivation, diseases have been become serious threats to morel production. White mold is one of the most serious diseases on cultivated morels. This study aimed to confirm this pathogen by following Koch's postulates, and to identify it using molecular evidence. Our results indicated that healthy Morchella fruiting bodies inoculated with Paecilomyces sp. isolates produced typical white mold symptoms, and the internal transcribed spacer sequences of the Paecilomyces sp. were 99% similar to that recovered from an epitype of Paecilomyces penicillatus. Therefore, P. penicillatus was considered to be the causative agent of white mold. White mold occurred from the initial harvest to the storage and preservation process, and it produced white mold-like symptoms on the caps and stripes of Morchella. This is the first time that white mold has been reported on cultivated Morchella.

The Enrichment of Microbial Community for Accumulating Polyhydroxyalkanoates Using Propionate-Rich Waste.

Polyhydroxyalkanoates (PHAs) are promising alternatives to plastics since they have similar properties to polyolefin but are biodegradable and biocompatible. Recently, the conversion of propionate wastewater to PHAs by undefined mixed microbial cultures becomes attractive. However, how microbial community changes remains unclear during the enrichment step, which is critical for a robust PHA-producing system. In this study, PHA-accumulating cultures were enriched under feast/famine condition using propionate-rich substrates. Our results showed that during the first 2 h of the enrichment, dissolved oxygen of cultures increased remarkably until saturation, and amounts of C, N, and chemical oxygen demand of cultures decreased significantly to a very low level. High-throughput sequencing revealed that bacterial populations affiliated with Alphaproteobacteria and Bacteroidetes dominated the cultures enriched. Most of these dominant populations contributed to the conversion of short-chain fatty acids to PHAs. Being fed with the substrate rich in propionate but without nitrogen, the cultures enriched could accumulate nearly 27% PHAs at 72 h with higher content of hydroxyvalerate. Our work reveals the process in which environmental microbes responded to propionate-rich condition and shifted to populations for accumulating PHAs; it also will be helpful to develop an efficient PHA-producing system using propionate-rich waste.

Adaption of microbial community during the start-up stage of a thermophilic anaerobic digester treating food waste.

A successful start-up enables acceleration of anaerobic digestion (AD) into steady state. The microbial community influences the AD performance during the start-up. To investigate how microbial communities changed during the start-up, microbial dynamics was analyzed via high-throughput sequencing in this study. The results confirmed that the AD was started up within 25 d. Thermophilic methanogens and bacterial members functioning in hydrolysis, acidogenesis, and syntrophic oxidation became predominant during the start-up stage, reflecting a quick adaption of microorganisms to operating conditions. Such predominance also indicated the great contribution of these members to the fast start-up of AD. Redundancy analysis confirmed that the bacterial abundance significantly correlated with AD conditions. The stable ratio of hydrogenotrophic methanogens to aceticlastic methanogens is also important to maintain the stability of the AD process. This work will be helpful to understand the contribution of microbial community to the start-up of AD.

Phylogenetic relationship of two popular edible Pleurotus in China, Bailinggu (P. eryngii var. tuoliensis) and Xingbaogu (P. eryngii), determined by ITS, RPB2 and EF1α sequences.

The aims of this study are to assess the utility of the internal transcribed spacer (ITS) region, and partial translation elongation factor (EF1α) and RNA polymerase II (RPB2) genes, for differentiation of Bailinggu, P. eryngii, and P. nebrodensis; to reconstruct phylogenetic relationships between the three species; and to confirm the taxonomic status of Bailinggu based on ribosomal and protein-coding genes. Pairwise genetic distances between Bailinggu, P. eryngii, and related Pleurotus strains were calculated by using the p-distance model, and molecular phylogeny of these isolates was estimated based on ITS, RPB2, and EF1α using maximum parsimony and Bayesian methods. Differences in ITS, RPB2, and EF1α sequences show that Bailinggu, P. eryngii, and P. nebrodensis are distinct at the species level. Phylogenetic analyses reveal that P. eryngii is closer to P. nebrodensis than to Bailinggu. Sequence analyses of ribosomal and protein-coding genes confirm that P. eryngii var. tuoliensis is identical to Bailinggu. P. eryngii var. tuoliensis should be raised to species level or a new name should be introduced for Bailinggu after a thorough investigation into Pleurotus isolates from Ferula in Xinjiang Province. This study helps to resolve uncertainty regarding Bailinggu, P. eryngii and P. nebrodensis, improving the resource management of these strains. ITS, EF1α, and RPB2 sequences can be used to distinguish Bailinggu, P. eryngii and P. nebrodensis as three different species, and P. eryngii var. tuoliensis should be the scientific name for Bailinggu at present.

Genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (Glycine max L.).

Water is essential for all living organisms. Aquaporin proteins are the major facilitator of water transport activity through cell membranes of plants including soybean. These proteins are diverse in plants and belong to a large major intrinsic (MIP) protein family. In higher plants, MIPs are classified into five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). This paper reports genome wide assembly of soybean MIPs, their functional prediction and expression analysis. Using a bioinformatic homology search, 66 GmMIPs were identified in the soybean genome. Phylogenetic analysis of amino acid sequences of GmMIPs divided the large and highly similar multi-gene family into 5 subfamilies: GmPIPs, GmTIPs, GmNIPs, GmSIPs and GmXIPs. GmPIPs consisted of 22 genes and GmTIPs 23, which showed high sequence similarity within subfamilies. GmNIPs contained 13 and GmSIPs 6 members which were diverse. In addition, we also identified a two member GmXIP, a distinct 5(th) subfamily. GmMIPs were further classified into twelve subgroups based on substrate selectivity filter analysis. Expression analyses were performed for a selected set of GmMIPs using semi-quantitative reverse transcription (semi-RT-qPCR) and qPCR. Our results suggested that many GmMIPs have high sequence similarity but diverse roles as evidenced by analysis of sequences and their expression. It can be speculated that GmMIPs contains true aquaporins, glyceroporins, aquaglyceroporins and mixed transport facilitators.

Uncovering the salt response of soybean by unraveling its wild and cultivated functional genomes using tag sequencing.

Soil salinity has very adverse effects on growth and yield of crop plants. Several salt tolerant wild accessions and cultivars are reported in soybean. Functional genomes of salt tolerant Glycine soja and a salt sensitive genotype of Glycine max were investigated to understand the mechanism of salt tolerance in soybean. For this purpose, four libraries were constructed for Tag sequencing on Illumina platform. We identify around 490 salt responsive genes which included a number of transcription factors, signaling proteins, translation factors and structural genes like transporters, multidrug resistance proteins, antiporters, chaperons, aquaporins etc. The gene expression levels and ratio of up/down-regulated genes was greater in tolerant plants. Translation related genes remained stable or showed slightly higher expression in tolerant plants under salinity stress. Further analyses of sequenced data and the annotations for gene ontology and pathways indicated that soybean adapts to salt stress through ABA biosynthesis and regulation of translation and signal transduction of structural genes. Manipulation of these pathways may mitigate the effect of salt stress thus enhancing salt tolerance.