Gut Dysbiosis Drives Inflammatory Bowel Disease Through the CCL4L2-VSIR Axis in Glycogen Storage Disease.

Patients with glycogen storage disease type Ib (GSD-Ib) frequently have inflammatory bowel disease (IBD). however, the underlying etiology remains unclear. Herein, this study finds that digestive symptoms are commonly observed in patients with GSD-Ib, presenting as single or multiple scattered deep round ulcers, inflammatory pseudo-polyps, obstructions, and strictures, which differ substantially from those in typical IBD. Distinct microbiota profiling and single-cell clustering of colonic mucosae in patients with GSD are conducted. Heterogeneous oral pathogenic enteric outgrowth induced by GSD is a potent inducer of gut microbiota immaturity and colonic macrophage accumulation. Specifically, a unique population of macrophages with high CCL4L2 expression is identified in response to pathogenic bacteria in the intestine. Hyper-activation of the CCL4L2-VSIR axis leads to increased expression of AGR2 and ZG16 in epithelial cells, which mediates the unique progression of IBD in GSD-Ib. Collectively, the microbiota-driven pathomechanism of IBD is demonstrated in GSD-Ib and revealed the active role of the CCL4L2-VSIR axis in the interaction between the microbiota and colonic mucosal immunity. Thus, targeting gut dysbiosis and/or the CCL4L2-VISR axis may represent a potential therapy for GSD-associated IBD.

Characteristics of gut microbiota in patients with gastric cancer by surgery, chemotherapy and lymph node metastasis

Gastric cancer (GC) is a malignant gastrointestinal tumor that can result in high mortality. Surgery and chemotherapy are often used for the effective treatment of GC. In addition, lymph node metastasis is a significant factor affecting the therapy of GC. Current researches have revealed that gut microbiota has the potential as biomarkers to distinguish healthy people and GC patients. However, the relationship between surgery, chemotherapy, and lymph node metastasis is still unclear.MethodsIn this study, 16S rRNA sequencing was used to investigate 157 GC fecal samples to identify the role of surgery, chemotherapy, and lymph node metastasis. Immunohistochemical analysis was used to value the expression of Ki67, HER2 in GC patient tissues.ResultsThere exist some gut microbiotas which can distinguish surgery from non-surgery GC patients, including Enterococcus, Megasphaera, Corynebacterium, Roseburia, and Lachnospira. Differences between lymph node metastasis and chemotherapy in GC patients are not significant. Moreover, we found the abundance of Blautia, Ruminococcus, Oscillospira were related to the expression of Ki67 and the abundance of Prevotella, Lachnospira, Eubacterium, Desulfovibiro were correlated with the expression of HER2.ConclusionsThe choice of treatment has a certain impact on the intestinal flora of patients with gastric cancer. Our research shows that surgery has a great effect on the intestinal flora of patients with gastric cancer. However, there were no significant differences in the characteristics of intestinal flora in patients with gastric cancer whether they received chemotherapy or whether they had lymph node metastasis. In addition, the association of gut microbiota with Ki67 and HER2 indicators is expected to provide the possibility of gut microbiota as a tumor prognostic marker. (AU)

Characteristics of gastric cancer gut microbiome according to tumor stage and age segmentation.

With the development of 16S rRNA technology, gut microbiome evaluation has been performed in many diseases, including gastrointestinal tumors. Among these cancers, gastric cancer (GC) exhibits high morbidity and mortality and has been extensively studied in its pathogenesis and diagnosis techniques. The current researches have proved that the gut microbiome may have the potential to distinguish GC patients from healthy patients. However, the change of the gut microbiome according to tumor node metastasis classification (TNM) has not been clarified. Besides, the characteristics of gut microbiome in GC patients and their ages of onset are also ambiguous. To address the above shortcomings, we investigated 226 fecal samples and divided them according to their tumor stage and onset age. The findings revealed that surgery and tumor stage can change the characteristic of GC patients' gut microbiota. In specific, the effect of surgery on early gastric cancer (EGC) was greater than that on advanced gastric cancer (AGC), and the comparison of postoperative microflora with healthy people indicated that EGC has more differential bacteria than AGC. Besides, we found that Collinsella, Blautia, Anaerostipes, Dorea, and Lachnospiraceae_ND3007_group expressed differently between EGC and AGC. More importantly, it is the first time revealed that the composition of gut microbiota in GC is different between different onset ages. KEY POINTS: •Gut microbiota of gastric cancer (GC) patients are either highly associated with TNM stage and surgery or not. It shows surgery has more significant changes in early gastric cancer (EGC) than advanced gastric cancer (AGC). •There existed specific gut microbiota between EGC and AGC which may have potential to distinguish the early or advanced GC. •Onset age of GC may influence the gut microbiota: the composition of gut microbiota of early-onset gastric cancer (EOGC) and late-onset gastric cancer (LOGC) is significantly different.

Characteristics of gut microbiota in patients with gastric cancer by surgery, chemotherapy and lymph node metastasis.

BACKGROUND: Gastric cancer (GC) is a malignant gastrointestinal tumor that can result in high mortality. Surgery and chemotherapy are often used for the effective treatment of GC. In addition, lymph node metastasis is a significant factor affecting the therapy of GC. Current researches have revealed that gut microbiota has the potential as biomarkers to distinguish healthy people and GC patients. However, the relationship between surgery, chemotherapy, and lymph node metastasis is still unclear. METHODS: In this study, 16S rRNA sequencing was used to investigate 157 GC fecal samples to identify the role of surgery, chemotherapy, and lymph node metastasis. Immunohistochemical analysis was used to value the expression of Ki67, HER2 in GC patient tissues. RESULTS: There exist some gut microbiotas which can distinguish surgery from non-surgery GC patients, including Enterococcus, Megasphaera, Corynebacterium, Roseburia, and Lachnospira. Differences between lymph node metastasis and chemotherapy in GC patients are not significant. Moreover, we found the abundance of Blautia, Ruminococcus, Oscillospira were related to the expression of Ki67 and the abundance of Prevotella, Lachnospira, Eubacterium, Desulfovibiro were correlated with the expression of HER2. CONCLUSIONS: The choice of treatment has a certain impact on the intestinal flora of patients with gastric cancer. Our research shows that surgery has a great effect on the intestinal flora of patients with gastric cancer. However, there were no significant differences in the characteristics of intestinal flora in patients with gastric cancer whether they received chemotherapy or whether they had lymph node metastasis. In addition, the association of gut microbiota with Ki67 and HER2 indicators is expected to provide the possibility of gut microbiota as a tumor prognostic marker.

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders.

Gut microbiota is a primary driver of inflammation in the colon and is linked to early colorectal cancer (CRC) development. Thus, a novel and noninvasive microbiome-based model could promote screening in patients at average risk for CRC. Nevertheless, the relevance and effectiveness of microbial biomarkers for noninvasive CRC screening remains unclear, and researchers lack the data to distinguish CRC-related gut microbiome biomarkers from those of other common gastrointestinal (GI) diseases. Microbiome-based classification distinguishes patients with CRC from normal participants and excludes other CRC-relevant diseases (e.g., GI bleed, adenoma, bowel diseases, and postoperative). The area under the receiver operator characteristic curve (AUC) was 92.2%. Known associations with oral pathogenic features, benefits-generated features, and functional features of CRC were confirmed using the model. Our optimised prediction model was established using large-scale experimental population-based data and other sequence-based faecal microbial community data. This model can be used to identify the high-risk groups and has the potential to become a novel screening method for CRC biomarkers because of its low false-positive rate (FPR) and good stability. KEY POINTS: • A total of 5744 CRC and non-CRC large-scale faecal samples were sequenced, and a model was constructed for CRC discrimination on the basis of the relative abundance of taxonomic and functional features. • This model could identify high-risk groups and become a novel screening method for CRC biomarkers because of its low FPR and good stability. • The association relationship of oral pathogenic features, benefits-generated features, and functional features in CRC was confirmed by the study.

Deviated and early unsustainable stunted development of gut microbiota in children with autism spectrum disorder.

OBJECTIVE: Recent studies have provided insights into the gut microbiota in autism spectrum disorder (ASD); however, these studies were restricted owing to limited sampling at the unitary stage of childhood. Herein, we aimed to reveal developmental characteristics of gut microbiota in a large cohort of subjects with ASD combined with interindividual factors impacting gut microbiota. DESIGN: A large cohort of 773 subjects with ASD (aged 16 months to 19 years), 429 neurotypical (NT) development subjects (aged 11 months to 15 years) were emolyed to determine the dynamics change of gut microbiota across different ages using 16S rRNA sequencing. RESULT: In subjects with ASD, we observed a distinct but progressive deviation in the development of gut microbiota characterised by persistently decreased alpha diversity, early unsustainable immature microbiota, altered aboudance of 20 operational taxonomic units (OTUs), decreased taxon detection rate and 325 deregulated microbial metabolic functions with age-dependent patterns. We further revealed microbial relationships that have changed extensively in ASD before 3 years of age, which were associated with the severity of behaviour, sleep and GI symptoms in the ASD group. This analysis demonstrated that a signature of the combination of 2 OTUs, Veillonella and Enterobacteriaceae, and 17 microbial metabolic functions efficiently discriminated ASD from NT subjects in both the discovery (area under the curve (AUC)=0.86), and validation 1 (AUC=0.78), 2 (AUC=0.82) and 3 (AUC=0.67) sets. CONCLUSION: Our large cohort combined with clinical symptom analysis highlights the key regulator of gut microbiota in the pathogenesis of ASD and emphasises the importance of monitoring and targeting the gut microbiome in future clinical applications of ASD.

Gut microbiome analysis as a predictive marker for the gastric cancer patients.

Gut microbiota have been implicated in the development of cancer. Colorectal and gastric cancers, the major gastrointestinal tract cancers, are closely connected with the gut microbiome. Nevertheless, the characteristics of gut microbiota composition that correlate with gastric cancer are unclear. In this study, we investigated gut microbiota alterations during the progression of gastric cancer to identify the most relevant taxa associated with gastric cancer and evaluated the potential of the microbiome as an indicator for the diagnosis of gastric cancer. Compared with the healthy group, gut microbiota composition and diversity shifted in patients with gastric cancer. Different bacteria were used to design a random forest model, which provided an area under the curve value of 0.91. Verification samples achieved a true positive rate of 0.83 in gastric cancer. Principal component analysis showed that gastritis shares some microbiome characteristics of gastric cancer. Chemotherapy reduced the elevated bacteria levels in gastric cancer by more than half. More importantly, we found that the genera Lactobacillus and Megasphaera were associated with gastric cancer.Key Points• Gut microbiota has high sensitivity and specificity in distinguishing patients with gastric cancer from healthy individuals, indicating that gut microbiota is a potential noninvasive tool for the diagnosis of gastric cancer.• Gastritis shares some microbiota features with gastric cancer, and chemotherapy reduces the microbial abundance and diversity in gastric cancer patients.• Two bacterial taxa, namely, Lactobacillus and Megasphaera, are predictive markers for gastric cancer.

Analysis of Gut Microbiota in Patients with Coronary Artery Disease and Hypertension.

Cardiovascular and cerebrovascular diseases are characterized by high rates of morbidity and mortality. Microbiota is closely associated with cardiovascular disease. We aimed to comprehensively analyze the microbiotas of 300 healthy controls, 300 patients with high blood pressure (HBP), and 300 patients with coronary heart disease (CHD). The results indicated no significant difference in microbiota diversity among the three groups (P > 0.05). However, differences in microbiota richness among the three groups were significant (P < 0.05). Bacteroidetes and Bacteroidia were the dominant bacteria in the CHD group, Enterobacteriales and Escherichia-shigella in the HBP group, and Acidaminococcaceae and Phascolarctobacterium in the healthy control group. The prediction results of the random forest model indicated that the population with CHD displayed prominent features with high sensitivity, indicating that microbiota detection might become a novel clinical indicator to predict and monitor the risk of cardiovascular events. The prediction of microbiota function suggested differences in oxygen supply and chronic inflammation between populations with HBP/CHD and healthy populations. Although there is no difference in gut microbiota diversity among the three groups, each group has its dominant microbiota in terms of richness.

Natural variation among Arabidopsis thaliana accessions in tolerance to high magnesium supply.

High magnesium (Mg2+) in some extreme serpentine soils or semi-arid regions is an important factor affecting crop growth and development. Specific loci that form the genetic framework underlying high Mg2+ homeostasis, however, are not well understood. By using GWA mapping on 388 accessions of Arabidopsis thaliana selected from a worldwide collection and genotyped at approximately 250,00 SNPs, we successfully identified 109 and 74 putative genetic regions associated in nutrient traits under normal (1,000 µM) and high Mg2+ (10,000 µM), respectively. Above 90% SNPs associated with nutrients including Mg2+ and only two SNPs shared between normal and high Mg2+. A single strong peak of SNPs associated with Ca concentration corresponding to candidate gene At1g60420 ARABIDOPSIS NUCLEOREDOXIN (AtNRX1) under high Mg2+ was further determined. Compared with wildtype, mutants of Atnrx1-1 and Atnrx1-2 supplied with high Mg2+ had higher Ca concentrations in the plant, and higher cytosolic Ca2+ concentrations during root elongation, as well as higher fresh weight and lateral-root number. This suggests that AtNRX1 was a critical gene negatively regulating Ca uptake under high Mg2+ conditions. The discovery could help to breed/select crops that can adapt to high-Mg2+ soils such as serpentine soils (high ratio of Mg2+: Ca2+) or Mars soil with high levels of magnesium sulfate.

Genomic adaptation to drought in wild barley is driven by edaphic natural selection at the Tabigha Evolution Slope.

Ecological divergence at a microsite suggests adaptive evolution, and this study examined two abutting wild barley populations, each 100 m across, differentially adapted to drought tolerance on two contrasting soil types, Terra Rossa and basalt at the Tabigha Evolution Slope, Israel. We resequenced the genomes of seven and six wild barley genotypes inhabiting the Terra Rossa and basalt soils, respectively, and identified a total of 69,192,653 single-nucleotide variants (SNVs) and insertions/deletions in comparison with a reference barley genome. Comparative genomic analysis between these abutting wild barley populations involved 19,615,087 high-quality SNVs. The results revealed dramatically different selection sweep regions relevant to drought tolerance driven by edaphic natural selection within 2,577 selected genes in these regions, including key drought-responsive genes associated with ABA synthesis and degradation (such as Cytochrome P450 protein) and ABA receptor complex (such as PYL2, SNF1-related kinase). The genetic diversity of the wild barley population inhabiting Terra Rossa soil is much higher than that from the basalt soil. Additionally, we identified different sets of genes for drought adaptation in the wild barley populations from Terra Rossa soil and from wild barley populations from Evolution Canyon I at Mount Carmel. These genes are associated with abscisic acid signaling, signaling and metabolism of reactive oxygen species, detoxification and antioxidative systems, rapid osmotic adjustment, and deep root morphology. The unique mechanisms for drought adaptation of the wild barley from the Tabigha Evolution Slope may be useful for crop improvement, particularly for breeding of barley cultivars with high drought tolerance.

Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley.

Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third-generation sequencer (PacBio), we de novo assembled a 4.84-Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59-Gb sequence to seven chromosomes. Of the 46,787 annotated 'high-confidence' genes, 31 564 were validated by RNA-sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low-diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.

Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed.

Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.

Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome.

Ustilago esculenta, infects Zizania latifolia, and induced host stem swollen to be a popular vegetable called Jiaobai in China. It is the long-standing artificial selection that maximizes the occurrence of favourable Jiaobai, and thus maintaining the plant-fungi interaction and modulating the fungus evolving from plant pathogen to entophyte. In this study, whole genome of U. esculenta was sequenced and transcriptomes of the fungi and its host were analysed. The 20.2 Mb U. esculenta draft genome of 6,654 predicted genes including mating, primary metabolism, secreted proteins, shared a high similarity to related Smut fungi. But U. esculenta prefers RNA silencing not repeat-induced point in defence and has more introns per gene, indicating relatively slow evolution rate. The fungus also lacks some genes in amino acid biosynthesis pathway which were filled by up-regulated host genes and developed distinct amino acid response mechanism to balance the infection-resistance interaction. Besides, U. esculenta lost some surface sensors, important virulence factors and host range-related effectors to maintain the economic endophytic life. The elucidation of the U. esculenta genomic information as well as expression profiles can not only contribute to more comprehensive insights into the molecular mechanism underlying artificial selection but also into smut fungi-host interactions.

Genome-wide profiling of genetic variation in Agrobacterium-transformed rice plants.

Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate "transgene-clean" targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed. To reveal the genome-wide variation in transformed plants, we sequenced the genomes of five independent T0 rice plants using next-generation sequencing (NGS) techniques. Bioinformatics analyses followed by experimental validation revealed the following: (1) in addition to transfer-DNA (T-DNA) insertions, three transformed plants carried heritable plasmid backbone DNA of variable sizes (855-5216 bp) and in different configurations with the T-DNA insertions (linked or apart); (2) each transgenic plant contained an estimated 338-1774 independent genetic variations (single nucleotide variations (SNVs) or small insertion/deletions); and (3) 2-6 new Tos17 insertions were detected in each transformed plant, but no other transposable elements or bacterial genomic DNA.

Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum.

Epipremnum aureum is an extremely popular houseplant belonging to the Araceae family of angiosperms, but it does not flower either in the wild or under cultivation. We uncovered the potential causes of its shy-flowering nature by building the transcriptome using next-generation sequencing and identifying floral-related genes that are differentially expressed between vertical growth (VG, adult) and horizontal growth (HG, juvenile) plants. Transcripts of the gibberellin (GA) biosynthetic gene EaGA3ox1 and GA-responsive floral meristem identity gene EaLFY were absent in both VG and HG plants, suggesting that a deficiency of bioactive GAs may be responsible for its shy-flowering nature. This hypothesis is supported by undetectable or low levels of three bioactive GAs, and exogenous GA3 triggered flowering in both plants. Our study resolves the mystery why E. aureum fails to flower, and reveals the positive role of GAs in floral transition in perennials.

Identification of Mild Freezing Shock Response Pathways in Barley Based on Transcriptome Profiling.

Low temperature is a major abiotic stress affecting crop growth and productivity. A better understanding of low temperature tolerance mechanisms is imperative for developing the crop cultivars with improved tolerance. We herein performed an Illumina RNA-sequencing experiment using two barley genotypes differing in freezing tolerance (Nure, tolerant and Tremois, sensitive), to determine the transcriptome profiling and genotypic difference under mild freezing shock treatment after a very short acclimation for gene induction. A total of 6474 differentially expressed genes, almost evenly distributed on the seven chromosomes, were identified. The key DEGs could be classified into six signaling pathways, i.e., Ca(2+) signaling, PtdOH signaling, CBFs pathway, ABA pathway, jasmonate pathway, and amylohydrolysis pathway. Expression values of DEGs in multiple signaling pathways were analyzed and a hypothetical model of mild freezing shock tolerance mechanism was proposed. Expression and sequence profile of HvCBFs cluster within Frost resistance-H2, a major quantitative trait locus on 5H being closely related to low temperature tolerance in barley, were further illustrated, considering the crucial role of HvCBFs on freezing tolerance. It may be concluded that multiple signaling pathways are activated in concert when barley is exposed to mild freezing shock. The pathway network we presented may provide a platform for further exploring the functions of genes involved in low temperature tolerance in barley.

Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria.

Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in four Burkholderia seminalis strains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose and d-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria.

Phosphorus and magnesium interactively modulate the elongation and directional growth of primary roots in Arabidopsis thaliana (L.) Heynh.

A balanced supply of essential nutrients is an important factor influencing root architecture in many plants, yet data related to the interactive effects of two nutrients on root growth are limited. Here, we investigated the interactive effect between phosphorus (P) and magnesium (Mg) on root growth of Arabidopsis grown in pH-buffered agar medium at different P and Mg levels. The results showed that elongation and deviation of primary roots were directly correlated with the amount of P added to the medium but could be modified by the Mg level, which was related to the root meristem activity and stem-cell division. High P enhanced while low P decreased the tip-focused fluorescence signal of auxin biosynthesis, transport, and redistribution during elongation of primary roots; these effects were greater under low Mg than under high Mg. The altered root growth in response to P and Mg supply was correlated with AUX1, PIN2, and PIN3 mRNA abundance and expression and the accumulation of the protein. Application of either auxin influx inhibitor or efflux inhibitor inhibited the elongation and increased the deviation angle of primary roots, and decreased auxin level in root tips. Furthermore, the auxin-transport mutants aux1-22 and eir1-1 displayed reduced root growth and increased the deviation angle. Our data suggest a profound effect of the combined supply of P and Mg on the development of root morphology in Arabidopsis through auxin signals that modulate the elongation and directional growth of primary root and the expression of root differentiation and development genes.

FastGCN: a GPU accelerated tool for fast gene co-expression networks.

Gene co-expression networks comprise one type of valuable biological networks. Many methods and tools have been published to construct gene co-expression networks; however, most of these tools and methods are inconvenient and time consuming for large datasets. We have developed a user-friendly, accelerated and optimized tool for constructing gene co-expression networks that can fully harness the parallel nature of GPU (Graphic Processing Unit) architectures. Genetic entropies were exploited to filter out genes with no or small expression changes in the raw data preprocessing step. Pearson correlation coefficients were then calculated. After that, we normalized these coefficients and employed the False Discovery Rate to control the multiple tests. At last, modules identification was conducted to construct the co-expression networks. All of these calculations were implemented on a GPU. We also compressed the coefficient matrix to save space. We compared the performance of the GPU implementation with those of multi-core CPU implementations with 16 CPU threads, single-thread C/C++ implementation and single-thread R implementation. Our results show that GPU implementation largely outperforms single-thread C/C++ implementation and single-thread R implementation, and GPU implementation outperforms multi-core CPU implementation when the number of genes increases. With the test dataset containing 16,000 genes and 590 individuals, we can achieve greater than 63 times the speed using a GPU implementation compared with a single-thread R implementation when 50 percent of genes were filtered out and about 80 times the speed when no genes were filtered out.

Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species.

The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species (Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data from their fresh green leaves. The two Echinochloa chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus Echinochloa and Panicum occurred about 21.6 million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about 3.3 million years ago. The two reported Echinochloa chloroplast genome sequences contribute to better understanding of the diversification of this genus.