Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

骨髄異形成症候群のgenome-wide analysis

We generated a high-density genetic linkage map of soybean using expressed sequence tag (EST)-derived microsatellite markers. A total of 6920 primer pairs (10.9%) were designed to amplify simple sequence repeats (SSRs) from 63 676 publicly available non-redundant soybean ESTs. The polymorphism of two parent plants, tlie Japanese cultivar 'Misuzudaizu' and the Chinese line 'Moshidou Gong 503', were examined using 10% polyacrylamide gel electrophoresis. Primer pairs showing polymorphism were then used for genotyping 94 recombinant inbred lines (RILs) derived from a cross between tlie parents. In addition to previously reported markers, 680 EST-derived microsatellite markers were selected and subjected to linkage analysis. As a result, 935 marker loci were mapped successfully onto 20 linkage groups, which totaled 2700.3 cM in length: 693 loci were detected using the 668 EST-derived microsatellite markers developed in this study, the other 242 loci were detected with 105 RFLP markers, 136 genome-derived microsatellite markers, and one phenotypic marker. We examined allelic variation among 23 soybean cultivars/lines and a wild soybean line using 668 mapped EST-derived microsatellite markers (corresponding to 686 marker loci), in order to determine the transferability of the markers among soybean germplasms. A limited degree of macrosynteny was observed at tlie segmental level between the genomes of soybean and the model legume Lotus japonicus, which suggests that considerable genome shuffling occurred after separation of the species and during establishment of the paleopolyploid soybean genome.

Characterization of the Soybean Genome Using EST-derived Microsatellite Markers. Commentary

Cadmium (Cd) is a highly toxic heavy metal in nature, which causes severe damage to plant growth. The molecular mechanisms for Cd detoxification are poorly understood. Here, we report that a G-type ATP-binding cassette transporter, OsABCG36, is involved in Cd tolerance in rice. OsABCG36 was expressed in both roots and shoots at a low level, but expression in the roots rather than the shoots was greatly up-regulated by a short exposure to Cd. A spatial expression analysis showed that Cd-induced expression of OsABCG36 was found in both the root tip and the mature root region. Transient expression of OsABCG36 in rice protoplast cells showed that it was localized to the plasma membrane. Immunostaining showed that OsABCG36 was localized in all root cells except the epidermal cells. Knockout of OsABCG36 resulted in increased Cd accumulation in root cell sap and enhanced Cd sensitivity, but did not affect tolerance to other metals including Al, Zn, Cu, and Pb. The concentration of Cd in the shoots was similar between the knockout lines and wild-type rice. Heterologous expression of OsABCG36 in yeast showed an efflux activity for Cd, but not for Zn. Taken together, our results indicate that OsABCG36 is not involved in Cd accumulation in the shoots, but is required for Cd tolerance by exporting Cd or Cd conjugates from the root cells in rice.

The ABC transporter ABCG36 is required for cadmium tolerance in rice.

インゲンマメ(Phaseolus vulgaris L.)の蛋白の分別

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant development and stress response. In the present study, GmWRKY16 encoding a WRKY transcription factor in soybean was functionally characterized in Arabidopsis. GmWRKY16 is a nuclear protein that contains a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has the characteristics of transcriptional activation ability, presenting a constitutive expression pattern with relative expression levels of over fourfold in the old leaves, flowers, seeds and roots of soybean. The results of quantitative real time polymerase chain reaction (qRT-PCR) showed that GmWRKY16 could be induced by salt, alkali, ABA, drought and PEG-6000. As compared with the control, overexpression of GmWRKY16 in Arabidopsis increased the seed germination rate and root growth of seedlings in transgenic lines under higher concentrations of mannitol, NaCl and ABA. In the meantime, GmWRKY16 transgenic lines showed over 75% survival rate after rehydration and enhanced Arabidopsis tolerance to salt and drought with higher proline and lower MDA accumulation, less water loss of the detached leaves, and accumulated more endogenous ABA than the control under stress conditions. Further studies showed that AtWRKY8, KIN1, and RD29A were induced in GmWRKY16 transgenic plants under NaCl treatment. The expressions of the ABA biosynthesis gene (NCED3), signaling genes (ABI1, ABI2, ABI4, and ABI5), responsive genes (RD29A, COR15A, COR15B, and RD22) and stress-related marker genes (KIN1, LEA14, LEA76, and CER3) were regulated in transgenic lines under drought stress. In summary, these results suggest that GmWRKY16 as a WRKY TF may promote tolerance to drought and salt stresses through an ABA-mediated pathway.

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GmWRKY16 Enhances Drought and Salt Tolerance Through an ABA-Mediated Pathway in Arabidopsis thaliana.

Sugarcane-soybean intercropping has been widely used to control disease and improve nutrition in the field. However, the response of the soil microbial community diversity and structure to intercropping is not well understood. Since microbial diversity corresponds to soil quality and plant health, a pot experiment was conducted with sugarcane intercropped with soybean. Rhizosphere soil was collected 40 days after sowing, and MiSeq sequencing was utilized to analyze the soil microbial community diversity and composition. Soil columns were used to assess the influence of intercropping on soil microbial activity (soil respiration and carbon-use efficiency: nitrogen-use efficiency ratio). PICRUSt and FUNGuild analysis were conducted to predict microbial functional profiling. Our results showed that intercropping decreased pH by approximately 8.9% and enhanced the soil organic carbon, dissolved organic carbon, and available nitrogen (N) by 5.5%, 13.4%, and 10.0%, respectively. These changes in physicochemical properties corresponded to increased microbial diversity and shifts in soil microbial communities. Microbial community correlated significantly (p < 0.05) with soil respiration rates and nutrient use efficiency. Furthermore, intercropping influenced microbial functions, such as carbon fixation pathways in prokaryotes, citrate cycle (TCA cycle) of bacteria and wood saprotrophs of fungi. These overrepresented functions might accelerate nutrient conversion and control phytopathogens in soil.

Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies.

Aluminum is a major deleterious factor for soybean productivity in acidic soils. Soil enzyme activities and bacteria play important roles in improving the stress tolerance of soybean. We assessed soil enzyme activities and bacterial structure and functions in Al-tolerant (Al-T) and Al-sensitive (Al-S) soybean genotypes subjected to different Al stress. We used a pot experiment system and determined plant biomass, urease, acid phosphatase, catalase, sucrase, and amylase activities, soil chemical properties, and the rhizosphere bacterial community diversity and structure of Al-T and Al-S soybean genotypes under different Al concentrations (0, 0.2, and 0.4 Al3+ g kg−1). Significant differences in soil enzyme activities and bacterial community structure were only observed between Al-T and Al-S soybeans under high Al stress. We identified 23 operational taxonomic units (OTUs), including OTU46 (Tumebacillus), OTU253 (Granulicella), and OTU180 (Burkholderia), which may improve soybean tolerance to Al toxicity. The results of canonical correspondence analysis (CCA) indicated that NH4+-N was an important factor that drove bacterial community structure differences between the two genotypes. Al stress simplified the network structure in the Al-T soybean, which may cause the soil bacterial community to be easily influenced by biotic and abiotic factors. High Al stress drove different soil enzyme activities and bacterial community structures between Al-T and Al-S soybean genotypes, and NH4+-N was the most important factor that drove the bacterial community structure between the two genotypes. Al-T soybeans recruited Al-tolerant microorganisms, such as Tumebacillus, Granulicella, and Burkholderia, to improve the resistance to Al stress. Nevertheless, Al stress simplified the network structure in the Al-T soybeans, which may allow for the soil bacterial community to be easily influenced by other biotic and abiotic factors.

High aluminum stress drives different rhizosphere soil enzyme activities and bacterial community structure between aluminum-tolerant and aluminum-sensitive soybean genotypes

Multidrug and toxic compound extrusion (MATE) transporters, which exist widely in plants, function as crucial regulators in plant resistance to aluminum (Al) toxicity by inducing citrate efflux. However, the functions of most MATE family members in soybean (Glycine soja) remain to be elucidated. Expression pattern analysis showed that GsMATE was constitutively expressed in different soybean organs, with the highest level in root compared with those in stem, leaf and cotyledon. In addition, Al stress induced expression of GsMATE in soybean. Temporal analysis indicated that GsMATE expression was greatly enhanced by increasing concentrations of aluminum [Al3+] after short exposure, reaching the high levels detected in the BW69 (Al-resistant) and the JW81 (Al-sensitive) lines of Glycine soja of wild soybean at 6 h and 8 h, respectively. Furthermore, transient GsMATE expression in Arabidopsis protoplasts showed that GsMATE protein localized to the plasma membrane. Overexpression of GsMATE on an Arabidopsis columbia-0 (Col-0) background resulted in increased Al tolerance in transgenic plants. Analysis of hematoxylin staining showed that the roots of GsMATE transgenic lines were stained less intensely than those of the wild-type exposured to the same AlCl3 concentrations. Therefore, GsMATE enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots. In summary, our results indicate that GsMATE is responsive to aluminum stress and may participate in the regulation of sensitivity to Al toxicity in Arabidopsis. In addition, the GsMATE protein is an Al-induced citrate transporter of the MATE family and exerts an essential role in Al tolerance in Glycine soja.

/pdf/gsmate-encoding-a-multidrug-and-toxic-compound-extrusion-48m2ubtinz.pdf

GsMATE encoding a multidrug and toxic compound extrusion transporter enhances aluminum tolerance in Arabidopsis thaliana

Cadmium (Cd) is a widespread pollutant that is toxic to living organisms. Previous studies have identified certain WRKY transcription factors, which confer Cd tolerance in different plant species. In the present study, we have identified 29 Cd-responsive WRKY genes in Soybean [Glycine max (L.) Merr.], and confirmed that 26 of those GmWRKY genes were up-regulated, while 3 were down-regulated. We have also cloned the novel, positively regulated GmWRKY142 gene from soybean and investigated its regulatory mechanism in Cd tolerance. GmWRKY142 was highly expressed in the root, drastically up-regulated by Cd, localized in the nucleus, and displayed transcriptional activity. The overexpression of GmWRKY142 in Arabidopsis thaliana and soybean hairy roots significantly enhanced Cd tolerance and lead to extensive transcriptional reprogramming of stress-responsive genes. ATCDT1, GmCDT1-1, and GmCDT1-2 encoding cadmium tolerance 1 were induced in overexpression lines. Further analysis showed that GmWRKY142 activated the transcription of ATCDT1, GmCDT1-1, and GmCDT1-2 by directly binding to the W-box element in their promoters. In addition, the functions of GmCDT1-1 and GmCDT1-2, responsible for decreasing Cd uptake, were validated by heterologous expression in A. thaliana. Our combined results have determined GmWRKYs to be newly discovered participants in response to Cd stress, and have confirmed that GmWRKY142 directly targets ATCDT1, GmCDT1-1, and GmCDT1-2 to decrease Cd uptake and positively regulate Cd tolerance. The GmWRKY142-GmCDT1-1/2 cascade module provides a potential strategy to lower Cd accumulation in soybean.

/pdf/transcription-factor-gmwrky142-confers-cadmium-resistance-by-x44sl3he81.pdf

Zhandong Cai

Papers

GmWRKY16 Enhances Drought and Salt Tolerance Through an ABA-Mediated Pathway in Arabidopsis thaliana.

Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies.

High aluminum stress drives different rhizosphere soil enzyme activities and bacterial community structure between aluminum-tolerant and aluminum-sensitive soybean genotypes

GsMATE encoding a multidrug and toxic compound extrusion transporter enhances aluminum tolerance in Arabidopsis thaliana

Transcription Factor GmWRKY142 Confers Cadmium Resistance by Up-Regulating the Cadmium Tolerance 1-Like Genes.