Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (FOL) are characterized by the presence of AVR1 in their genomes. The product of this gene, Avr1, triggers resistance in tomato cultivars carrying resistance gene I. In FOL race 2 and race 3 isolates, AVR1 is absent, and hence they are virulent on tomato cultivars carrying I. In this study, we analyzed an approximately 100-kb genomic fragment containing the AVR1 locus of FOL race 1 isolate 004 (FOL004) and compared it to the sequenced genome of FOL race 2 isolate 4287 (FOL4287). A genomic fragment of 31 kb containing AVR1 was found to be missing in FOL4287. Further analysis suggests that race 2 evolved from race 1 by deletion of this 31-kb fragment due to a recombination event between two transposable elements bordering the fragment. A worldwide collection of 71 FOL isolates representing races 1, 2, and 3, all known vegetative compatibility groups (VCGs), and five continents was subjected to PCR analysis of the AVR1 locus, including the two bordering transposable elements. Based on phylogenetic analysis using the EF1-␣ gene, five evolutionary lineages for FOL that correlate well with VCGs were identified. More importantly, we show that FOL races evolved in a stepwise manner within each VCG by the loss of function of avirulence genes in a number of alternative ways.IMPORTANCE Plant-pathogenic microorganisms frequently mutate to overcome disease resistance genes that have been introduced in crops. For the fungus Fusarium oxysporum f. sp. lycopersici, the causal agent of Fusarium wilt in tomato, we have identified the nature of the mutations that have led to the overcoming of the I and I-2 resistance genes in all five known clonal lineages, which include a newly discovered lineage. Five different deletion events, at least several of which are caused by recombination between transposable elements, have led to loss of AVR1 and overcoming of I. Two new events affecting AVR2 that led to overcoming of I-2 have been identified. We propose a reconstruction of the evolution of races in FOL, in which the same mutations in AVR2 and AVR3 have occurred in different lineages and the FOL pathogenicity chromosome has been transferred to new lineages several times.

The Plant Genome C hloroplasts are important organelles that are responsible for photosynthesis and play a vital role in plant physiology and development in green plants and algae (Raven and Allen, 2003). Chloroplasts have their own DNA, and for most of the land plants, the chloroplast genome exists in circular form with a quadripartite structure comprised of a large single copy (LSC) and a small single copy (SSC) region separated by two inverted repeats (IR; Sugiura, 2003; Wicke et al., 2011). The size of the chloroplast genome varies from 120 to 170 Kb and possessed 60 to 130 genes which are primarily involved in photosynthesis and other metabolic process (Sugiura, 2003; Wicke et al., 2011). The haploid nature, low level of recombination, and maternal inheritance of the chloroplast genome, as well as its low substitution rate compared with the nuclear genome, present chloroplast genomes as valuable

Half hourly data of soil moisture content, soil temperature, solar irradiance, and reflectance are measured during April 2010 to March 2011 at a tropical station, viz., Astronomical Observatory, Thiruvananthapuram, Kerala, India (76 • 59'E longitude and 8 • 29'N latitude). The monthly, seasonal and seasonal mean diurnal variation of soil moisture content is analyzed in detail and is correlated with the rainfall measured at the same site during the period of study. The large variability in the soil moisture content is attributed to the rainfall during all the seasons and also to the evaporation/movement of water to deeper layers. The relationship of surface albedo on soil moisture content on different time scales are studied and the influence of solar elevation angle and cloud cover are also investigated. Surface albedo is found to fall exponentially with increase in soil moisture content. Soil thermal diffusivity and soil thermal conductivity are also estimated from the subsoil temperature profile. Log normal dependence of thermal diffusivity and power law dependence of thermal conductivity on soil moisture content are confirmed.

Mitogenome sequencing provides an understanding of the evolutionary mechanism of mitogenome formation, mechanisms driving plant gene order, genome structure, and migration sequences. Data on the mitochondrial genome for family Convolvulaceae members is lacking. E. alsinoides, also known as shankhpushpi, is an important medicinal plant under the family Convolvulaceae, widely used in the Ayurvedic system of medicine. We identified the mitogenome of E. alsinoides using the Illumina mate-pair sequencing platform, and annotated using bioinformatics approaches in the present study. The mitogenome of E. alsinoides was 344184 bp in length and comprised 46 unique coding genes, including 31 protein-coding genes (PCGs), 12 tRNA genes, and 3 rRNA genes. The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC. Measurement of the skewness of the nucleotide composition showed that the AT and GC skew is positive, indicating higher A’s and G’s in the mitogenome of E. alsinoides. The Ka/Ks ratios of 11 protein-coding genes (atp1, ccmC, cob, cox1, rps19, rps12, nad3, nad9, atp9, rpl5, nad4L) were <1, indicating that these genes were under purifying selection. Synteny and gene order analysis were performed to identify homologous genes among the related species. Synteny blocks representing nine genes (nad9, nad2, ccmFc, nad1, nad4, nad5, matR, cox1, nad7) were observed in all the species of Solanales. Gene order comparison showed that a high level of gene rearrangement has occurred among all the species of Solanales. The mitogenome data obtained in the present study could be used as the Convolvulaceae family representative for future studies, as there is no complex taxonomic history associated with this plant.