BackgroundThe utilization of soybean heterosis is probably one of the potential approaches in future yield breakthrough as was the situation in rice breeding in China. Cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds. However, the molecular mechanism of CMS in soybean remains unclear.ResultsThe comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its near-isogenic maintainer NJCMS1B in soybean was conducted using Illumina sequencing technology. A total of 88,643 transcripts were produced in Illumina sequencing. Then 56,044 genes were obtained matching soybean reference genome. Three hundred and sixty five differentially expressed genes (DEGs) between NJCMS1A and NJCMS1B were screened by threshold, among which, 339 down-regulated and 26 up-regulated in NJCMS1A compared to in NJCMS1B. Gene Ontology (GO) annotation showed that 242 DEGs were annotated to 19 functional categories. Clusters of Orthologous Groups of proteins (COG) annotation showed that 265 DEGs were classified into 19 categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 46 DEGs were assigned to 33 metabolic pathways. According to functional and metabolic pathway analysis combined with reported literatures, the relations between some key DEGs and the male sterility of NJCMS1A were discussed. qRT-PCR analysis validated that the gene expression pattern in RNA-Seq was reliable. Finally, enzyme activity assay showed that energy supply was decreased in NJCMS1A compared to in NJCMS1B.ConclusionsWe concluded that the male sterility of NJCMS1A might be related to the disturbed functions and metabolism pathways of some key DEGs, such as DEGs involved in carbohydrate and energy metabolism, transcription factors, regulation of pollen development, elimination of reactive oxygen species (ROS), cellular signal transduction, and programmed cell death (PCD) etc. Future research will focus on cloning and transgenic function validation of possible candidate genes associated with soybean CMS.

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There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitogenome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species that distribute across different climates. We sequenced 26 complete mitogenomes of Tetranychus truncates, which occurs in both warm and cold regions, and nine complete mitogenomes of Tetranychus pueraricola, which is restricted to warm regions. Patterns of evolution in the two species' mitogenomes were compared through a series of d /d methods and physicochemical profiles of amino acid replacements. We found that: (1) the mitogenomes of both species were under widespread purifying selection; (2) elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus; and (3) the strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation.

Background: Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular breeding of R. solani-resistant rice cultivars, the changes of transcriptome profiles in response to R. solani infection were compared between a moderate resistant cultivar (Yanhui-888, YH) and a susceptible cultivar (Jingang-30, JG). Results: In the present study, 3085 differentially express genes (DEGs) were detected between the infected leaves and the control in JG, with 2853 DEGs in YH. A total of 4091 unigenes were significantly upregulated in YH than in JG before infection, while 3192 were significantly upregulated after infection. Further analysis revealed that YH and JG showed similar molecular responses to R. solani infection, but the responses were earlier in JG than in YH. Expression levels of trans-cinnamate 4-monooxygenase (C4H), ethylene-insensitive protein 2 (EIN2), transcriptome factor WRKY33 and the KEGG pathway plant-pathogen interaction were significantly affected by R. solani infection. More importantly, these components were all over-represented in YH cultivar than in JG cultivar before and/or after infection. Conclusions: These genes possibly contribute to the higher resistance of YH to R. solani than JG and were potential target genes to molecularly breed R. solani-resistant rice cultivar.

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BackgroundUse of a risk of bias (ROB) tool has been encouraged and advocated to reviewers writing systematic reviews (SRs) and meta-analyses (MAs). Selective outcome reporting and other sources of bias are included in the Cochrane ROB tool. It is important to know how this specific tool for assessing ROB has been applied since its release. Our objectives were to evaluate whether and to what extent the new Cochrane ROB tool has been used in Chinese journal papers of acupuncture.MethodsWe searched CBM, TCM database, CJFD, CSJD, and the Wanfang Database from inception to March 2011. Two reviewers independently selected SRs that primarily focused on acupuncture and moxibustion, from which the data was extracted and analyzed.ResultsA total of 836 SRs were identified from the search, of which, 105 were included and four are awaiting assessment. Thirty-six of the 105 SRs were published before release of the Cochrane ROB tool (up to 2009). Most used the Cochrane Handbook 4.2 or Jadad's scale for risk or quality assessment. From 2009 to March 2011 69 SRs were identified. While “risk of bias” was reported for approximately two-thirds of SRs, only two SRs mentioned use of a “risk of bias tool” in their assessment. Only 5.8% (4/69) of reviews reported information on all six domains which are involved in the ROB tool. A risk of bias graph/summary figure was provided in 2.9% (2/69) of reviews. Most SRs gave information about sequence generation, allocation concealment, blindness, and incomplete outcome data, however, few reviews (5.8%; 4/69) described selective reporting or other potential sources of bias.ConclusionsThe Cochrane “risk of bias” tool has not been used in all SRs/MAs of acupuncture published in Chinese Journals after 2008. When the ROB tool was used, reporting of relevant information was often incomplete.