A New Alphasatellite Molecule Associated with Ageratum yellow vein China virus in the Philippines

From Synedrella nodiflora plants with leaf curling, vein swelling and enation symptoms on Samal Island, the Philippines, a begomoviral DNA‐A and its associated alphasatellite molecule were cloned and sequenced. The begomovirus was identified as an isolate of Ageratum yellow vein China virus (AYVCNV) with 91% nucleotide sequence identity to AYVCNV‐[P157] (EU487045), while the alphasatellite molecule was most closely related to tobacco curly shoot alphasatellite‐Y99 (TbCSA‐Y99, AJ579347) with 74.5% nucleotide sequence identity. The satellite molecule has the typical features of alphasatellites, with a single gene in the virion sense, an A‐rich region and a 33‐bp predicted stem‐loop structure. According to the proposed species demarcation threshold of alphasatellites (83% nucleotide sequence identity), the alphasatellite molecule represents a new species, herein named ‘Ageratum yellow vein China alphasatellite’ ( KF785752 ).     

Completion of the Nucleotide Sequence of a Brazilian Isolate of Southern bean mosaic virus

The sequence of the central part (ORF2) of a Brazilian isolate of Southern bean mosaic virus (SBMV^SP) is described. This ORF is 2888 nt long and together with the previously-sequenced 5' and 3' ends provides the complete nucleotide sequence of this virus isolate. The SBMV^SP RNA encodes four overlapping open reading frames (ORF1, ORF2a, ORF2b, ORF4) and has a genome organization similar to that of the Cocksfoot mottle sobemovirus .     

蚕豆萎蔫病毒2中国分离物全基因组结构及可能的基因表达方式

报道了蚕豆萎蔫病毒2的B935分离物全基因组序列。RNA1和RNA2分别由5956和3601个核苷酸组成[不包括3‘端未知长度的poly（A）尾巴]。RNA1和RNA2均包含单个阅读框,分别编码分子量为210063（210kD）和119002（119kD）的蛋白质。对外壳蛋白N端氨基酸序列测定表明,外壳蛋白大、小亚基（LCP、SCP）为119kD蛋白质在466／467位的Q／C和868／869位的Q／A位点切割形成的中间和C端蛋白,而端蛋白与豇豆花叶病毒58kD/48kD移动蛋白具有一定的同源性,并且包含一个类似病毒移动蛋白特有的rNTP结合域,推断为移动蛋白。通过与豇豆花叶病毒科病毒RNA1编码的多聚蛋白的同源性比较及功能蛋白保守序列的查找,表明210kd蛋白质可切割形成RdRp、蛋白酶、包含NTP结合域蛋白（NTBM）、蛋白酶辅助因子和Vpg等成熟蛋白,并进一步对其切割位 作了分析,根据LCP和SCP氨基酸序列所作的系统关系树充分证明了蚕豆萎蔫病毒（BBWV）两个血清型,确应命名为两个不同的病毒。     

Characterization and Complete Nucleotide Sequence of Two Isolates of Tomato mosaic virus

Two virus isolates, designated S1 and TL, were obtained from tomato and camellia root in China, respectively, and their host ranges, symptomatology, serological reactions and complete nucleotide sequences were determined. Isolate TL systemically infected Chenopodium amaranticolor causing leaf chlorosis, but the isolate S1 induced only local necrotic lesions. The complete nucleotide sequences of S1 and TL were determined and consisted of 6384 and 6383 nucleotides (Genbank accessions AJ132845 and AJ417701 ), respectively. Sequence analysis revealed that both isolates have the highest nucleotide sequence identity (over 92%) with Tomato mosaic virus (ToMV), but less (80%) with other tobamoviruses. Phylogenetic analyses based on the amino acid sequences of 30‐kD and 17.5‐kD proteins also indicated that both the isolates form a cluster with the isolates of ToMV. These data suggest that S1 and TL are isolates of ToMV. The possible reasons that TL infected C. amaranticolor systemically but S1 induced only local necrotic lesions are discussed.     

Factors affecting the survival of Bradyrhizobium applied in liquid cultures to soya bean [Glycine max (L.) Merr.] seeds

AIMS: To determine the impact of medium composition, bacterial strain, trehalose accumulation, and relative humidity during seed storage on the survival of Bradyrhizobium japonicum on soya bean [Glycine max (L.) Merr.] seeds. METHODS AND RESULTS: Bacteria in liquid cultures were applied to seeds, and the number of survivors was quantified after 2, 24, 48, or 96 h. Addition of yeast extract to a defined medium increased on-seed survival 50- to 80-fold. Addition of 40 mmol l(-1) of NaCl to the medium doubled or tripled the accumulation of trehalose in cells and increased survival several fold, and the addition of both salt and trehalose had an additive effect. There was a threefold difference among strains in survival, and survival of the various strains was significantly correlated with differences in the accumulation of trehalose. The correlation between trehalose accumulation by bacteria and survival was also highly significant in other experiments. Studies in controlled humidity environments showed 100-fold or more differences in survival. CONCLUSIONS: The consistently significant correlation of trehalose content of cells with survival on seed suggests that trehalose is an important component of the survival mechanisms. When some of the factors (salt and trehalose in the medium plus humidity control) were studied in combination, several 100-fold increases in survival of bacteria on seeds were recorded. SIGNIFICANCE AND IMPACT OF THE STUDY: It is possible by manipulation of several parameters--strain selection, salt and trehalose content of the medium, control of relative humidity--to achieve substantial improvements in survival of Bradyrhizobium on soya bean seeds.     

蚕豆萎蔫病毒2号山西分离株的全基因组序列测定与分析

本试验在生物学接种的基础上,利用非序列依赖性PCR扩增（sequence-independent amplification,SIA）对感病青椒（Capsicum annuum）进行了分子鉴定. 序列测定及分析发现,侵染青椒的病毒为蚕豆萎蔫病毒2号（Broad bean wilt virus 2, BBWV2）. 为明确BBWV2青椒分离物（BBWV2 Ca）的分类地位,对BBWV2 Ca的全基因组序列进行了分段克隆、序列测定和分析. BBWV2-Ca RNA1全长5 929 bp,含有1个ORF. BBWV2 Ca RNA2全长3 559 bp,含有1个ORF,编码3种蛋白：VP53/VP37、外壳蛋白大亚基（large coat protein, LCP）和外壳蛋白小亚基(small coat protein, SCP). 全序列核苷酸同源性分析显示,BBWV2-Ca RNA1与BBWV2其它分离物核苷酸同源性在77.9%～93.7%之间|RNA2与BBWV2其它分离物核苷酸同源性在80.2%～93.8%之间. 全序列系统进化分析显示,BBWV2-Ca RNA1与BBWV2-XJ14-3以及BBWV2-RP3株系聚为一簇,亲缘关系最近|RNA2与BBWV2-Am形成一个独立分支,亲缘关系最近.     

The Nucleotide Sequence and Genome Structure of Mung Bean Yellow Mosaic Geminivirus

Complete nucleotide sequences of the infectious cloned DNA components (DNA 1 and DNA 2) of mung bean yellow mosaic virus (MYMV) were determined. MYMV DNA 1 and DNA 2 consists of 2,723 and 2,675 nucleotides respectively. DNA 1 and DNA 2 have little sequence similarity except for a region of approximately 200 bases which is almost identical in the two molecules. Analysis of open reading frames revealed nine potential coding regions for proteins of mol. wt. > 10,000, six in DNA 1 and three in DNA 2. The nucleotide sequence of MYMV DNA was compared with that of bean golden mosaic virus (BGMV), tomato golden mosaic virus (TGMV) and African cassava mosaic virus (ACMV). The 200-base region common to the two DNAs of each virus had little sequence similarity, except for a highly conserved 33-36 base sequence potentially capable of forming a stable hairpin structure. The potential coding regions in the MYMV DNAs had counterparts in the BGMV, TGMV and ACMV, suggesting an overall similarity in genome organization, except for absence of 1L3 in MYMV DNA 1. The most highly conserved ORFs, MYMV 1R1, BGMV 1R1, TGMV 1R1 and ACMV 1R1, are the putative genes for the coat proteins of MYMV, BGMV, TGMV and ACMV, respectively. MYMV 1L1 has also a high degree of sequence similarity with BGMV 1L1, TGMV 1L1 and ACMV 1L1.     

Complete Nucleotide Sequence and Genome Organization of Soybean Crinkle Leaf Virus

The genomic DNA of soybean crinkle leaf virus (SCLV) from Thailand has been sequenced. The single circular DNA molecule comprises 2737 nucleotides, and contains eight open reading frames each capable of encoding a protein with a molecular weight greater than 10 kDa. A 39‐base potential stem‐loop forming region occurs in the intergenic region (IR) that also includes the conserved nonanucleotide sequence TAATATTAC. The iterative sequence (TCAATCGGTGT), which is specific to SCLV, is also found in the IR. SCLV is most closely related (90% identity) to the monopartite geminivirus ageratum yellow vein virus. As the two viruses differ in host range, and the iterative sequence is specific to SLCV, the virus is a distinct monopartite geminivirus of soybean.     

Complete Nucleotide Sequence of the RNA 3 of Bacopa chlorosis virus and Production of Polyclonal Antibodies to a Recombinant Coat Protein

The complete sequence of the RNA 3 of a virus causing chlorosis in Impatiens in Germany was determined and identified as an isolate of Bacopa chlorosis virus (BaCV, genus Ilarvirus). BaCV has previously only been reported from bacopa in the USA, but no coat protein (CP) sequence has been previously available. Both RNA 3 encoded proteins, CP and movement protein, showed highest sequence identity to Parietaria mottle virus, a subgroup 1 ilarvirus. Attempts to purify BaCV failed, so an antiserum was raised against a recombinant CP. The polyclonal antiserum so produced allowed specific detection of BaCV but showed no serological cross‐reaction with other ilarviruses and was unsuitable for immunoelectron microscopy. The host range includes many important flowering plant species, highlighting the potential threat BaCV might pose for the horticultural industry. This is the first report of BaCV occurring in Germany and outside the US.     

Complete Genome Sequence of a Novel Wild tomato mosaic virus Isolate Infecting Nicotiana tabacum in China

Virus particles of approximately 740–760 nm in length and 13 nm in diameter were observed from a diseased Nicotiana tabacum (tobacco) plant in Sichuan Province, China. The complete genomic sequence of the virus isolate XC1 was determined to contain 9659 nucleotides without 3′ terminal poly(A) tail. XC1 has a genome typical of members of the genus Potyvirus, encoding a large polyprotein of 3075 amino acids. Putative proteolytic cleavage sites and a number of well characterized functional motifs were identified by sequence comparisons with those of known potyviruses. Sequence comparison revealed that XC1 shared the highest level of nucleotide sequence identity (76.5%) with Wild tomato mosaic virus (WTMV). Phylogenetic analysis showed that XC1 was closely related to the WTMV Guangdong isolate with an identity of 94.3% between CP gene sequence of the two viruses. We thus named XC1 WTMV‐XC‐1 as a novel isolate of WTMV. The full sequence of WTMV‐XC‐1 may serve as a basis for future investigations on the gene diversity of WTMV.     

侵染花生的辣椒褪绿病毒SRNA全序列分析

番茄斑萎病毒属(Tospovirus)是布尼亚病毒科(Bunyaviridae)中植物病毒组成的一个属,病毒粒子为球状,直径80~110nm,粒体外层由一层脂质包裹。基因组属于负单链RNA,由三个片段组成,分别被称为L RNA、M RNA、和S RNA。L RNA为负链、含单个开放阅读框架(ORF),M RNA和S RNA均为双义R     

CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula

Processing of double‐stranded RNA precursors into small RNAs is an essential regulator of gene expression in plant development and stress response. Small RNA processing requires the combined activity of a functionally diverse group of molecular components. However, in most of the plant species, there are insufficient mutant resources to functionally characterize each encoding gene. Here, mutations in loci encoding protein machinery involved in small RNA processing in soya bean and Medicago truncatula were generated using the CRISPR/Cas9 and TAL‐effector nuclease (TALEN) mutagenesis platforms. An efficient CRISPR/Cas9 reagent was used to create a bi‐allelic double mutant for the two soya bean paralogous Double‐stranded RNA‐binding2 (GmDrb2a and GmDrb2b) genes. These mutations, along with a CRISPR/Cas9‐generated mutation of the M. truncatula Hua enhancer1 (MtHen1) gene, were determined to be germ‐line transmissible. Furthermore, TALENs were used to generate a mutation within the soya bean Dicer‐like2 gene. CRISPR/Cas9 mutagenesis of the soya bean Dicer‐like3 gene and the GmHen1a gene was observed in the T₀ generation, but these mutations failed to transmit to the T₁ generation. The irregular transmission of induced mutations and the corresponding transgenes was investigated by whole‐genome sequencing to reveal a spectrum of non‐germ‐line‐targeted mutations and multiple transgene insertion events. Finally, a suite of combinatorial mutant plants were generated by combining the previously reported Gmdcl1a, Gmdcl1b and Gmdcl4b mutants with the Gmdrb2ab double mutant. Altogether, this study demonstrates the synergistic use of different genome engineering platforms to generate a collection of useful mutant plant lines for future study of small RNA processing in legume crops.     

Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]

Determinate growth habit is an agronomically important trait associated with domestication in soya bean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four nonsynonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb, were identified, which constitute the soft sweeps for the adaptation. These variable‐sized sweeps substantially reflected the strength and timing of selection and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures of extensive long‐range LD and haplotype homozygosity, and multiple frequent adaptive haplotypes. A haplotype network constructed for Dt1 and a phylogenetic tree based on its extended haplotype block implied independent sources of the adaptive alleles through de novo mutations or rare standing variation in quick succession during the selective phase, strongly supporting multiple origins of the determinacy. We propose that the adaptation of soya bean determinacy is guided by a model of soft sweeps and that this model might be indispensable during crop domestication or evolution.     

Isolation and Complete Nucleotide Sequence of the Measles Virus IMB-1 Strain in China

The complete nucleotide sequence of the measles virus strain IMB-1,which was isolated in China,was determined.As in other measles viruses,its genome is 15,894 nucleotides in length and encodes six proteins.The full-length nucleotide sequence of the IMB-1 isolate differed from vaccine strains (including wild-type Edmonston strain) by 4%-5% at the nucleotide sequence level.This isolate has amino acid variations over the full genome,including in the hemagglutinin and fusion genes.This report is the first to de...     

Biological Characterization and Complete Genome Sequence of a Possible Strain of Indian cassava mosaic virus from Jatropha curcas in India

The outbreak of a severe mosaic disease with a significant incidence was noticed on Jatropha curcas plants growing in Lucknow, Northern India. The causal virus was successfully transmitted by whiteflies (Bemisia tabaci) and grafting from naturally infected to healthy J. curcas plants. The association of Begomovirus with the mosaic disease of J. curcas was detected by PCR using primers specific to DNA‐A of Begomoviruses. Further, full‐length DNA‐A genome of ～2.7 kb was amplified by RCA followed by digestion with Bam HI restriction enzyme. Cloning and sequencing of obtained amplicons resulted in 2740 nucleotides of complete DNA‐A consisting of six ORFs and IR region (GenBank Accession HM230683 ). The sequence analysis revealed highest 85% similarities with Jatropha curcas mosaic virus, 77–84% with Indian cassava mosaic virus and 73–76% with Sri Lankan cassava mosaic virus isolates. Phylogenetic analysis of the Begomovirus isolate also showed a clear‐cut distinct relationship with earlier reported Begomoviruses from Jatropha curcas and other Begomoviruses. On the basis of the guidelines of the International Committee on Taxonomy of Viruses (ICTV‐2008), our virus isolate was identified as a possible strain of Indian cassava mosaic virus, and its name Jatropha mosaic India virus (JMIV) is proposed.     

Characterization and Experimental Host Range of a Brazilian Tomato Isolate of Tomato severe rugose virus

We report the complete molecular characterization of the DNA‐A and DNA‐B of a Brazilian tomato isolate of Tomato severe rugose virus (ToSRV) and the experimental host range of the virus determined using whitefly transmission tests. Genome analysis showed that ToSRV has a close evolutionary relationship with Tomato rugose mosaic virus. Of 33 plants species inoculated with viruliferous Bemisia tabaci biotype B, 13 species were susceptible to ToSRV, nine asymptomatically. Therefore, ToSRV disease management strategy should include the control of infected weeds close to tomato fields.     

Complete Nucleotide Sequence and Construction of an Infectious Clone of a Tunisian Isolate of Tomato yellow leaf curl Sardinia virus

The full‐length genome of a Tunisian isolate of Tomato yellow leaf curl Sardinia virus (TYLCSV) was engineered and submitted to sequence analysis. The Tunisian isolate has 99% sequence identity with TYLCSV‐Sicilian (Sic), results thus providing further evidence for the inclusion of this isolate in the TYLCSV‐Sic group. A 1.7‐mer construct of the virus was obtained and efficiently agroinfiltrated into tomato and tobacco plants to induce symptoms indistinguishable from those of natural infection.     

The Complete Nucleotide Sequence of the RNA 1 of a Chinese Isolate of Tomato chlorosis virus

Interveinal leaf chlorosis, brittleness, limited necrotic flecking or bronzing developed on greenhouse‐grown tobacco and tomato plants at Nanjing Agricultural University from 2010 to 2013. A positive RT‐PCR using a pair of degenerate primers for Crinivirus confirmed the diseased plants were infected with Tomato chlorosis virus (ToCV). The complete RNA 1 genomic sequence of this ToCV isolate was determined; it comprises of 8596 nucleotides with four open reading frames. Phylogenetic analysis of ToCV isolates from diverse geographical regions categorized the ToCV isolates into two main groups. Group one consisted of Chinese, American‐Florida, Greek and Brazilian isolates, while Group two contained only the Spanish isolate. The first group had two subgroups, one of Chinese and American‐Florida isolates, while the other subgroup had Greek and Brazilian isolates. This is the first study of the complete nucleotide sequence of the RNA 1 of ToCV isolated from China.