Sequence analysis of a soilborne wheat mosaic virus isolate from Italy shows that it is the same virus asEuropean wheat mosaic virus andSoilborne rye mosaic virus

The complete sequence of the two RNAs of a furovirus isolate from durum wheat in Italy was determined. Sequence comparisons and phylogenetic analysis were done to compare the Italian virus withSoilborne wheat mosaic virus (SBWMV) from the USA and with furovirus sequences recently published asEuropean wheat mosaic virus (EWMV), from wheat in France, andSoilborne rye mosaic virus (SBRMV), from rye and wheat in Germany. Over the entire genome, the Italian isolate RNA1 and RNA2 had respectively 97.5% and 98.6% nucleotide identity with EWMV, 95.5% and 85.8% with SBRMV-G and 70.6% and 64.5% with SBWMV. The Italian isolate was therefore clearly distinct from SBWMV The European isolates all appear to belong to the same virus and the nameSoilborne cereal mosaic virus may resolve earlier ambiguities.     

Sequence analysis of a soil-borne wheat mosaic virus isolate from Italy shows that it is the same virus as European wheat mosaic virus and Soil-borne rye mosaic virus

The complete sequence of the two RNAs of a furovirus isolate from durum wheat in Italy was determined. Sequence comparisons and phylogenetic analysis were done to compare the Italian virus with Soil-borne wheat mosaic virus (SBWMV) from the USA and with furovirus sequences recently published as European wheat mosaic virus (EWMV), from wheat in France, and Soil-borne rye mosaic virus (SBRMV), from rye and wheat in Germany. Over the entire genome, the Italian isolate RNA1 and RNA2 had respectively 97.5% and 98.6% nucleotide identity with EWMV, 95.5% and 85.8% with SBRMV-G and 70.6% and 64.5% with SBWMV. The Italian isolate was therefore clearly distinct from SBWMV. The European isolates all appear to belong to the same virus and the name Soil-borne cereal mosaic virus may resolve earlier ambiguities.     

Evidence that soilborne wheat mosaic virus moves long distance through the xylem in wheat

Summary Soilborne wheat mosaic virus (SBWMV) is a member of the genusFurovirus of plant viruses. SBWMV is transmitted to wheat roots by the plasmodiophorid vectorPolymyxa graminis. Experiments were conducted to determine the path for SBWMV transport from roots to leaves. The results of immunogold labeling suggest that SBWMV enters and moves long distance through the xylem. SBWMV may enter primary xylem elements before cell death occurs and then move upward in the plant after the xylem has matured into hollow vessels. There is also evidence for lateral movement between adjacent xylem vessels.Abbreviations SBWMV Soilborne wheat mosaic virus - TMV Tobacco mosaic virus - BMV Brome mosaic virus - PMTV Potato mop-top virus - BNYVV Beet necrotic yellow vein virus - WSSMV Wheat spindle streak mosaic virus - WSMV Wheat streak mosaic virus     

Analysis of nucleotide sequence of wheat yellow mosaic virus genomic RNAs

Wheat yellow mosaic virus (WYMV) isolate HC was used for viral cDNA synthesis and sequencing. The results show that the viral RNA1 is 7629 nueleotides encoding a polyprotein with 2407 amino acids, from which seven putative proteins may be produced by an autolytie cleavage processing besides the viral coat protein. The RNA2 is 3639 nueleotides and codes for a polypretein of 903 amino acids, which may contain two putative non-structural proteins. Although WYMV shares a similarity in genetic organization to wheat spindle streak mosaic virus (WSSMV), the identities in their nucleotide sequences or deduced amino acid sequences are as low as 70% and 75 % respectively. Based on this result, it is confirmed that WYMV and WSSMV are different species within Bymovirus.     

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.     

The complete sequence of a sugarcane mosaic virus isolate causing maize dwarf mosaic disease in China

The complete sequence of a potyvirus from maize in Zhejiang Province was determined. The RNA was 9596 nucleotides long, excluding the 3′-poly (A) tail, and there was a single long open reading frame (ORF) of 9192 nts encoding a 346.1 ku polyprotein. The polyprotein had substantial amino acid sequence homology with those encoded by the RNAs of a Chinese isolate of sorghum mosaic virus (SrMV-C) and a Bulgarian isolate of maize dwarf mosaic virus, but it was most closely related to sugarcane mosaic virus (SCMV) isolates, for which only partial sequences have been published. According to the published criteria for distinguishing potyviruses, the sequence reported here is clearly a strain of SCMV, but it also showed a surprisingly high amino acid homology with SrMV-C in the HC-Pro, P3 and Cl proteins.     

The complete sequence of a sugarcane mosaic virus isolate causing maize dwarf mosaic disease in China

The complete sequence of a potyvirus from maize in Zhejiang Province was determined. The RNA was 9596 nucleotides long, excluding the 3'-poly (A) tail, and there was a single long open reading frame (ORF) of 9192 nts encoding a 346.1 ku polyprotein. The polyprotein had substantial amino acid sequence homology with those encoded by the RNAs of a Chinese isolate of sorghum mosaic virus (SrMV-C) and a Bulgarian isolate of maize dwarf mosaic virus, but it was most closely related to sugarcane mosaic virus (SCMV) isolates, for which only partial sequences have been published. According to the published criteria for distinguishing potyviruses, the sequence reported here is clearly a strain of SCMV, but it also showed a surprisingly high amino acid homology with SrMV-C in the HC-Pro, P3 and Cl proteins.     

Sequence analysis of the conserved protamine gene cluster shows that it contains a fourth expressed gene

Structural data are presented on the protamine gene cluster (PGC) of human, mouse, rat, and bull. By restriction mapping we demonstrate that the organization of the protamine cluster is conserved throughout all four species, i.e., the genes are situated in a head to tail arrangement in the order: protamine l-protamine 2-transition protein 2. Further, we established the nucleotide sequence of the entire human PGC (25 kb in total) and the 3′ portion of the rat protamine cluster (PRM2 and TNP2 genes and intergenic region). In addition, a 1 kb fragment of the bovine and murine protamine cluster, situated between PRM2 and TNP2, was sequenced. This fragment is conserved regarding sequence, position, and orientation in all species examined, and was classified as likely coding region by gene recognition program GRAIL. Using the rat fragment as a probe in RNA blots, we detected a testis-specific signal of about 0.5 kb. Finally, we demonstrate a high density of Alu elements, both full and fragmented copies, in the human PGC and discuss their localization with respect to evolutionary and functional aspects. © 1996 Wiley-Liss, Inc.     

Molecular analysis of the capsid protein gene of a german isolate of barley mild mosaic virus

Summary Barley mild mosaic virus (BaMMV) is one of the agents causing the barley yellow mosaic disease. The sequence corresponding to the 3end of the BaMMV RNA1 of a German isolate was sequenced and the coding sequence for the 251 amino acid containing capsid protein was determined. Comparison of this sequence to other potyviral sequences and to the corresponding sequence of two Japanese isolates of BaMMV was done. The three different isolates of BaMMV show a high degree of similarity.Abbrevations BaMMV barley mild mosaic virus - BaYMV barley yellow mosaic virus; bp: base pair - IPTG isopropyl -D thiogalactopyranoside - kb kilo base - NTR nontranslated region - ORF open reading frame - PVDF polyvinylidene difluoride     

Complete nucleotide sequence and genome organization of tobacco mosaic virus isolated from Viciafaba

Based on reported TMV-U1 sequence, primers were designed and fragments covering the entire genome of TMV broad bean strain (TMV-B) were obtained with RT-PCR. These fragments were cloned and sequenced and the 5' and 3' end sequences of genome were confirmed with RACE. The complete sequence of TMV-B comprises 6 395 nucleotides (nt) and four open reading frames, which correspond to 126 ku (1 116 amino acids), 183 ku (1 616 amino acids), 30 ku (268 amino acids) and 17.5 ku proteins (159 amino acids). The complete nucleotide sequence of TMV-B is 99.4% identical to that of TMV-U1. The two virus isolates share the same sequence of 5', 3' non-coding region and 17.5 K ORF, and 6, 1 and 3 amino acid changes are found in 126 K protein, 54 K protein and 30 K protein, respectively. The possible mechanism on the infection of TMV-B in Vicia faba is discussed.     

Sequence analysis of two tandemly linked Em genes from wheat

DNA sequences are presented for two members of the wheat Em gene family. The sequences correspond to the two linked genes at the Xem-1AL locus. Comparisons of these sequences with that of another wheat Em gene and two Em cDNA clones reveals substantial homology within the protein-coding regions, and the presence in the 5-flanking regions of the genomic sequences of motifs characteristic of ABA-responsive cis-acting elements.     

Sequence analysis of WIS-2-1A,a retrotransposon-like element from wheat

WIS-2-1A, a 8624 bp insertion in the Glu-1A-2 locus of chromosome 1A of wheat, consists of two 1755 bp long terminal repeats enclosing a 5114 bp internal region. No long open reading frames could be found, but inspection of the predicted amino acid sequence showed regions with homology to retrotransposon structures, including a methionine tRNA initiator binding site, a nucleotide binding domain, a protease, an integrase and a polymerase. DNA replication errors have resulted in frame-shifts in the protein coding region, suggesting that retrotransposition of WIS-2-1A, if it occurs, must be mediated by trans-acting factors.     

Serological and molecular characterisations of the Egyptian isolate of Bean common mosaic virus

Bean common mosaic virus (BCMV) was isolated from the naturally infected bean plants collected from the Kafr El-Sheikh and El-Gharbia Governorates. BCMV induced sever mosaic, vein banding, malformation, leaf curling and stunting on bean plants cv. Giza 6. The isolated virus was propagated in bean plants cv. Giza 6. The identification of BCMV was carried out serologically by an indirect enzyme-linked immunosorbent assay using BCMV antiserum. Positive reaction indicated that the virus under study was related serologically to Potyvirus. The molecular biology techniques were used to identify and characterise the coat protein gene of BCMV. Oligonucleotide primers were designed for BCMV according to the published nucleotide sequences of BCMV and were successfully amplified with a DNA fragment (300 bp) from BCMV CP gene by RT-PCR. The total RNA was extracted from bean leaves and was reverse-transcribed and amplified using the oligonucleotide primer. The amplified product was analysed by gel electrophoresis. Also, Southern and dot blot hybridisations were used to establish the authenticity and specificity to the RT-PCR-amplified products of BCMV. The nucleotide sequences of the Egyptian isolate of BCMV/CP showed similarity with an isolate (BCMV-NY 15) which belongs to Puerto Rico.     

Molecular Diversities of Sugarcane mosaic virus and Sorghum mosaic virus Isolates from Yunnan Province,China

Degenerate Potyviridae primers were used to amplify and sequence the 3′‐terminal regions of viruses from traditional and modern cultivars of sugarcane with mosaic disease growing in different areas of Yunnan province, China. Seven samples contained Sugarcane mosaic virus (SCMV), 11 contained Sorghum mosaic virus (SrMV) and two contained both viruses. SCMV was only isolated from traditional cultivars. In a phylogenetic analysis of the partial NIb and complete coat protein coding regions, most SCMV isolates formed a distinctive phylogenetic cluster (named SO) that otherwise contained only three Vietnamese isolates. SCMV variation seems mostly related to host genotype. In the same analysis, the SrMV isolates formed three major groups, one of which is reported for the first time, but the significance of the grouping is unclear.     

X染色体的DNA序列结构不同于6、7、8、10、11、12号染色体

雌性哺乳动物X染色体上的大部分基因均因X染色体失活作用而失去表达能力 ,X染色体长臂表现失活更明显。虽然对X染色体失活的许多方面都有所了解 ,但是仍然不清楚失活信号沿着X染色体全长扩散的机制。为了了解X染色体是否有不同于其他染色体的基因组学特征 ,这些特征是否关系到X染色体的失活扩散和维持 ,分析 6、7、8、1 0、1 1、1 2号染色体和X染色体DNA序列 7碱基 (7nt)组合水平的结构是否显示差异。从NCBI基因库(http :∥www .ncbi.nlm .nih .gov genome guide)下载 7条染色体长臂各 6 0Mb区域。将这 6 0Mb区域分为 0 5Mb (或 5 0kb)一段 ,对每一段DNA做 7nt字符串组合分析 ,如 1～ 7,2～ 8,3～ 9…… ,记录每种 7nt字符串的频率 ,A、C、G和T4个硷基的 7nt字符串共有 4 7=1 6 384种组合。根据数字差异显示的结果 (http :∥www .ncbi.nlm .nih .gov genome guide) ,选择在扁桃腺生发中心B细胞中高表达的基因 70个 ,用以计算所有内含子 (有义链 )的 7nt频率值。每个内含子被记录为一组 7nt频率值 ,求和相同基因中的所有内含子相同 7nt字符串的频率值 ,再用该和乘以该基因的表达频率得该基因 7nt字符串的频率值 ,求和 70个基因的 7nt字符串的频率值称做intron 7nt,该值试图模拟细胞中RNA小片段的总和。     

Sequence analysis of the Czech Potato mop-top virus (PMTV) isolate Korneta-Nemilkov

The nucleotide sequence was determined for Czech potato mop-top virus (PMTV) isolate Korneta-Nemilkov, found in the potato field situated in South Bohemia. The nucleotide and amino acid sequences were compared with other PMTV isolates available in databases. The sequence identity was always >99% when Czech isolate RNA 2 and RNA 3 sequences were compared with each of the 3 Danish isolates and with Sw isolate, and slightly lower when compared to Scottish isolates. Similarity of deduced proteins was 100% for 5 out of 6 proteins used in comparison of Czech isolate with Danish isolate 54-15. The only difference between 2 isolates was found in coat protein (CP) gene. Interestingly, the CP of the Czech isolate seems to be 100% identical to the one of Sw, while many changes were found in the region encoding TGBp2, TGBp3 and cysteine-rich protein (CRP) for these 2 isolates. The lowest similarity scores were found when comparing the Czech isolate CRP with CRP of Scottish isolates.