Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat.

Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.

Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups-rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed ß-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats-freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism's genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe's respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium.

Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading bacterium Sphingobium ummariense strain RL-3, which was isolated from the HCH dumpsite located in Lucknow, India (27°00'N and 81°09'E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of 139 contigs, 4,645 coding sequences, and 65% G+C content.

Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane.

Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and degraded HCH isomers rapidly. The draft genome sequence of HDIPO4 (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of 65%.

Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03T.

Sphingobium baderi strain LL03(T) was isolated from hexachlorocyclohexane (HCH)-contaminated soil from Spolana, Czech Republic. Strain LL03(T) is a mutant that is deficient in linB and linC (genes that encode hexachlorocyclohexane haloalkane dehalogenase and dehydrogenase, respectively). The draft genome sequence of LL03(T) (~4.85 Mb) consists of 92 contigs and 4,914 coding sequences, with a G+C content of 63.5%.

Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated from a Hexachlorocyclohexane Dumpsite.

Sphingobium lactosutens DS20(T) has been isolated from the hexachlorocyclohexane (HCH) dumpsite in Lucknow, India, but does not degrade any of the HCH isomers. Here, we present the ~5.36-Mb draft genome sequence of strain DS20(T), which consists of 110 contigs and 5,288 coding sequences, with a G+C content of 63.1%.

Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from a Hexachlorocyclohexane Dumpsite.

Novosphingobium lindaniclasticum LE124(T) is a hexachlorocyclohexane (HCH)-degrading bacterium isolated from a high-dosage-point HCH dumpsite (450 mg HCH/g soil) located in Lucknow, India (27°00'N and 81°09'E). Here, we present the annotated draft genome sequence of strain LE124(T), which has an estimated size of 4.86 Mb and is comprised of 4,566 coding sequences.

Draft Genome Sequence of Sphingobium quisquiliarum Strain P25T, a Novel Hexachlorocyclohexane (HCH)-Degrading Bacterium Isolated from an HCH Dumpsite.

Here, we report the draft genome sequence (4.2 Mb) of Sphingobium quisquiliarum strain P25(T), a natural lin (genes involved in degradation of hexachlorocyclohexane [HCH] isomers) variant genotype, isolated from a heavily contaminated (450 mg HCH/g of soil) HCH dumpsite.

Draft Genome Sequence of Sphingobium chinhatense Strain IP26T, Isolated from a Hexachlorocyclohexane Dumpsite.

Sphingobium chinhatense strain IP26(T) is a conducive hexachlorocyclohexane (HCH) degrader isolated from a heavily contaminated (450 mg HCH/g soil) HCH dumpsite. IP26(T) degrades α-, ß-, γ-, and δ-HCH, which are highly persistent in the environment. Here we report the draft genome sequence (~5.8 Mbp) of this strain.

Mapping of a major QTL for pre-harvest sprouting tolerance on chromosome 3A in bread wheat.

Quantitative trait loci (QTL) analysis was conducted for pre-harvest sprouting tolerance (PHST) in bread wheat for a solitary chromosome 3A, which was shown to be important for this trait in earlier studies. An inter-varietal mapping population in the form of recombinant inbred lines (RILs) developed from a cross between SPR8198 (a PHS tolerant genotype) and HD2329 (a PHS susceptible cultivar) was used for this purpose. The parents and the RIL population were grown in six different environments and the data on PHS were collected in each case. A framework linkage map of chromosome 3A with 13 markers was prepared and used for QTL analysis. A major QTL (QPhs.ccsu-3A.1) was detected on 3AL at a genetic distance of approximately 183 cM from centromere, the length of the map being 279.1 cM. The QTL explained 24.68% to 35.21% variation in individual environments and 78.03% of the variation across the environments (pooled data). The results of the present study are significant on two counts. Firstly, the detected QTL is a major QTL, explaining up to 78.03% of the variation and, secondly, the QTL showed up in all the six environments and also with the pooled data, which is rather rare in QTL analysis. The positive additive effects in the present study suggest that a superior allele of the QTL is available in the superior parent (SPR8198), which can be used for marker-aided selection for the transfer of this QTL allele to obtain PHS-tolerant progeny. It has also been shown that the red-coloured grain of PHS tolerant parent is not associated with the QTL for PHST identified during the present study, suggesting that PHS tolerant white-grained cultivars can be developed.

Structural characterization, expression analysis and evolution of the red/far-red sensing photoreceptor gene, phytochrome C (PHYC), localized on the 'B' genome of hexaploid wheat (Triticum aestivum L.).

Phytochromes are a family of red/far-red light perceiving photoreceptors. The monocot phytochrome family is represented by three members, PHYA, PHYB and PHYC. We have isolated and characterized the first PHY gene member (TaPHYC) from common wheat, Triticum aestivum var. CPAN1676. It codes for a species of the photoreceptor, phyC, which is known to be light-stable in all plants analyzed so far. A sequence of 7.2 kb has been determined, which includes 3.42 kb of coding region. This is the second full-length PHYC gene sequenced from a monocot (first was from rice). TaPHYC gene shares structural similarities with the rice PHYC containing four exons and three introns in the coding region. The 5' UTR is 1.0-kb-long and harbors an upstream open reading frame (URF) encoding 28 aa. Southern blot analysis of TaPHYC indicates that it represents single locus in the wheat genome, although the possibility of additional loci cannot be completely ruled out. Chromosomal localization using nullisomic-tetrasomic lines of Triticum aestivum var. Chinese Spring places TaPHYC on chromosome 4B. PHYC represents a constitutively expressed gene in all the organs tested and under light/dark conditions. However, PHYC was found to be developmentally regulated showing maximal expression in 3-day-old dark-grown seedlings, which declined thereafter. In silico analysis has also been done to compare TaPHYC gene with the partial sequences known from other wheat species and cultivars. The presence of a topoisomerase gene immediately downstream of the PHYC gene, both in rice and wheat genomes, presents yet another example of synteny in cereals and its possible significance has been discussed.

Isolation and molecular characterization of the COP1 gene homolog from rice, Oryza sativa L. subsp. Indica var. Pusa Basmati 1.

The COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) gene has been identified earlier from dicot species namely Arabidopsis, tomato and pea. The protein encoded by this gene acts as a molecular switch that negatively regulates the transition from the skotomorphogenic to the photomorphogenic mode of plant development. We have isolated and characterized the COP1 homolog from a monocot species, i.e. rice (var. Pusa Basmati 1). All the functional domains (Zn-binding RING finger motif, coiled-coil region, WD-40 repeats, cytoplasmic/nuclear localization sequences and protein-protein interaction domains) that are known in the COP1 proteins from dicots are conserved in COP1 from rice as well. The transcript levels of COP1 vary in various tissues of the rice plant. These variations were found to be development-dependent and do not solely depend on the light conditions.

OsIAA1, an Aux/IAA cDNA from rice, and changes in its expression as influenced by auxin and light.

The Aux/IAA class of genes are rapidly induced by exogenous auxins and have been characterized extensively from many dicot species like Arabidopsis, Glycine max and Pisum sativum. We report here the isolation and characterization of rice (Oryza sativa L. subsp. Indica) OsIAA1 cDNA as a monocot member of the Aux/IAA gene family. The predicted amino acid sequence of OsIAA1 corresponds to a protein of ca. 26 kDa, which harbors all four characteristic domains known to be conserved in Aux/IAA proteins. The conservation of these Aux/IAA genes indicates that auxins have essentially a similar mode of action in monocots and dicots. Northern blot analysis revealed that the OsIAA1 transcript levels decrease in the excised coleoptile segments on auxin starvation, and the level is restored when auxin is supplemented; the increase in OsIAA1 transcript level was apparent within 15 to 30 min of auxin application. Auxin-induced OsIAA1 expression appears to be correlated with the elongation of excised coleoptile segments. In light-grown rice seedlings, OsIAA1 is preferentially expressed in roots and basal segment of the seedling, whereas in the etiolated rice seedlings, the OsIAA1 transcripts are most abundant in the coleoptile. A comparative analysis in light- and dark-grown seedling tissues indicates that the OsIAA1 transcript levels decrease on illumination.

The psbO gene for 33-kDa precursor polypeptide of the oxygen-evolving complex in Arabidopsis thaliana--nucleotide sequence and control of its expression.

The 33-kDa polypeptide of the oxygen-evolving complex of photosystem II is nuclear-encoded. The single psbO gene of Arabidopsis thaliana, as suggested by Southern hybridization, has been isolated from the genomic library and sequenced. The sequence analysis has revealed that the psbO gene harbors two introns and encodes a precursor polypeptide of 332 amino acid residues; the first 85 amino acid residues represent the transit peptide and the following 247 amino acids constitute the mature polypeptide. The hydrophilic nature of the 33-kDa protein is confirmed by the presence of 27% charged residues. Northern analysis of the total RNA from Arabidopsis indicates that a 1.2-kb transcript represents the psbO gene. It is expressed in a tissue-specific manner -- the steady-state transcript levels being highest in the leaves and virtually undetectable in the roots. Also, expression of the psbO gene is development-dependent and regulated by light in young Arabidopsis seedlings. In a constitutively photomorphogenic mutant of Arabidopsis, pho2 (plumular hook open 2), the psbO gene is de-repressed in young, dark-grown seedlings, resulting in increased transcript abundance compared to the wild-type. These studies, thus, define the influence of at least one regulatory component for psbO expression.

Mutants of Arabidopsis as tools to understand the regulation of phenylpropanoid pathway and UVB protection mechanisms.

Plants accumulate certain phenylpropanoid compounds in the vacuoles of their epidermal and subepidermal cell layers thereby protecting the underlying tissue against UVB-induced damage. However, a number of mutants of Arabidopsis thaliana are known that fail to synthesize these protective pigments, thereby allowing harmful UVB radiation to penetrate into their dermal layers. Study of several of these nonlethal mutants, defective in various aspects of flavonoid and lignin biosynthesis, has led to a better understanding of the coordinate regulation and expression of important genes as well as of mechanisms involved in plant defense against UVB radiation. The characteristics of the various phenylpropanoid mutants of Arabidopsis, viz. flavonoid mutants (banyuls [ban]; increased chalcone synthase expression 1 [icx1]; transparent testa [tt] and ultraviolet sensitive [uvs]) and hydroxycinnamic acid ester mutants (ferulic acid hydroxylase 1 [fah1] and sinapoylglucose accumulator 1 [sng1]) are discussed in detail. We have briefly touched upon, wherever relevant, the unique aspects in other plant species too.

Nucleotide sequence of the psbP gene encoding precursor of 23-kDa polypeptide of oxygen-evolving complex in Arabidopsis thaliana and its expression in the wild-type and a constitutively photomorphogenic mutant.

The psbP gene encoding the precursor of 23-kDa polypeptide of the oxygen-evolving complex of photosystem II has been isolated from Arabidopsis thaliana genomic library and sequenced. The gene harbors three introns and encodes a mature polypeptide of 186 amino acid residues and a transit peptide of 77 amino acid residues. The deduced molecular mass of the mature polypeptide is 23.5-kDa and it contains 22.6% charged amino acid residues which may contribute to the hydrophilic nature of the protein. The transcript encoded by psbP gene of Arabidopsis is approximately 1.3-kb long. In wild-type Arabidopsis seedlings, its expression is organ-specific and is regulated by endogenous developmental cues, light and sucrose. In a constitutively photomorphogenic mutant of Arabidopsis, designated as pho1, the psbP gene is partly derepressed in young, dark-grown seedlings, resulting in a slightly higher level of the transcript. Additionally, the pho1 mutant shows slow accumulation of psbP transcript upon illumination of young, dark-grown seedlings. However, the derepression is not markedly displayed on dark-adaptation of pho1 plants grown in continuous light. These studies, therefore, define the activity of at least one cellular effector involved in regulation of psbP expression.

Role of Salicylic Acid and Benzoic Acid in Flowering of a Photoperiod-Insensitive Strain, Lemna paucicostata LP6.

Lemna paucicostata LP6 does not normally flower when grown on basal Bonner-Devirian medium, but substantial flowering is obtained when 10 mum salicylic acid (SA) or benzoic acid is added to the medium. Benzoic acid is somewhat more effective than SA, and the threshold level of both SA and benzoic acid required for flower initiation is reduced as the pH of the medium is lowered to 4.0. SA- or benzoic acid-induced flowering is enhanced in the simultaneous presence of 6-benzylaminopurine (BAP), although BAP per se does not influence flowering in strain LP6. Continuous presence of SA or benzoic acid in the culture medium is essential to obtain maximal flowering. A short-term treatment of the plants (for first 24 h) with 10 mum SA or benzoic acid, followed by culture in the basal medium containing 1 mum BAP can, however, stimulate profuse flowering. Benzoic acid is more effective than SA, and the effect is more pronounced at pH 4 than at 5.5. Thus, under these conditions, flowering is of an inductive nature. Experiments with [(14)C]SA and [(14)C]benzoic acid have provided evidence that at pH 4 there is relatively more uptake of benzoic acid than SA, thus leading to an increased flowering response. The data obtained from the experiments designed to study the mobility of [(14)C]SA and [(14)C]-benzoic acid from mother to daughter fronds indicate that there is virtually no mobility of SA or benzoic acid between fronds.

Analysis of multiple photoreceptor pigments for phototropism in a mutant of Arabidopsis thaliana.

The shape of the fluence-response relationship for the phototropic response of the JK224 strain of Arabidopsis thaliana depends on the fluence rate and wavelength of the actinic light. At low fluence rate (0.1 micromole m-2 s-1), the response to 450-nm light is characterized by a single maximum at about 9 micromoles m-2. At higher fluence rate (0.4 micromole m-2 s-1), the response shows two maxima, at 4.5 and 9 micromoles m-2. The response to 510-nm light shows a single maximum at 4.5 micromoles m-2. Unilateral preirradiation with high fluence rate (25 micromoles m-2 s-1) 510-nm light eliminates the maximum at 4.5 micromoles m-2 in the fluence response curve to a subsequent unilateral 450-nm irradiation, while the second maximum at 9 micromoles m-2 is unaffected. Based on these results, it is concluded that a single photoreceptor pigment has been altered in the JK224 strain of Arabidopsis thaliana.

Identification of 3',5'-cyclic AMP in axenic cultures of Lemna paucicostata by high-performance liquid chromatography.

Nucleotides were purified from the extract of aseptically grown Lemna paucicostata 6746 by low-pressure column chromatography and thin-layer chromatography. In this partially purified sample, a compound has been identified, using a highly sensitive HPLC-fluorometric detection method, with chromatographic properties and substrate specificity for cyclic nucleotide phosphodiesterase similar to authentic 3',5'-cyclic AMP. The level of cAMP has been estimated to be 70-80 pmol/g fresh wt.

Influence of hook position on phototropic and gravitropic curvature by etiolated hypocotyls of Arabidopsis thaliana.

Phototropic and gravitropic curvature by hypocotyls of Arabidopsis thaliana is minimal when the side of the hook with the cotyledons attached is positioned toward the direction of tropistic curvature, and maximal when that side of the hook is positioned away from the direction of tropistic curvature. Based on these data, it is proposed that the position of the hook with attached cotyledons affects curvature and not stimulus perception. A randomly oriented population of plants exhibited considerable heterogeneity in tropistic curvature. This heterogeneity arises at least in part from the dependence of curvature on the position of the hook.