Indica rice genome assembly, annotation and mining of blast disease resistance genes

Sequence data size for rice cultivars. (XLSX 15 kb

Genome-Wide Comparison of <i>Magnaporthe</i> Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements

<div><p>Blast disease caused by the <i>Magnaporthe</i> species is a major factor affecting the productivity of rice, wheat and millets. This study was aimed at generating genomic information for rice and non-rice <i>Magnaporthe</i> isolates to understand the extent of genetic variation. We have sequenced the whole genome of the <i>Magnaporthe</i> isolates, infecting rice (leaf and neck), finger millet (leaf and neck), foxtail millet (leaf) and buffel grass (leaf). Rice and finger millet isolates infecting both leaf and neck tissues were sequenced, since the damage and yield loss caused due to neck blast is much higher as compared to leaf blast. The genome-wide comparison was carried out to study the variability in gene content, candidate effectors, repeat element distribution, genes involved in carbohydrate metabolism and SNPs. The analysis of repeat element footprints revealed some genes such as naringenin, 2-oxoglutarate 3-dioxygenase being targeted by <i>Pot</i>2 and Occan, in isolates from different host species. Some repeat insertions were host-specific while other insertions were randomly shared between isolates. The distributions of repeat elements, secretory proteins, CAZymes and SNPs showed significant variation across host-specific lineages of <i>Magnaporthe</i> indicating an independent genome evolution orchestrated by multiple genomic factors.</p></div

Genetic relatedness based on genome-wide SNPs of rice and non-rice isolates.

<p>(a) Chromosome-wise distribution of SNP density in rice and non-rice <i>Magnaporthe</i> isolates. The outer circle represents seven chromosomes of reference genome 70–15. The subsequent circles in inward order represent SNP density of rice isolates (MG01, MG02, and MG10), finger millet isolates (MG03, MG04, and MG12), foxtail millet isolates (MG05 and MG08) and buffel grass isolate MG07. (b) Genome-wide SNP based dendrogram was constructed based on UPGMA method.</p

Assembly statistics and repeat content of rice and non-rice <i>Magnaporthe</i> isolates.

<p>Assembly statistics and repeat content of rice and non-rice <i>Magnaporthe</i> isolates.</p

Cross-infection assay of rice and non-rice isolates.

<p>The spores of <i>Magnaporthe</i> isolates were artificially inoculated on various varieties of rice, finger millet and buffel grass.</p

Distribution of secretory genes coding for carbohydrate-active enzymes in <i>Magnaporthe</i>.

<p>Distribution of secretory genes coding for carbohydrate-active enzymes in <i>Magnaporthe</i>.</p

Distribution of transposable elements (a) and genic insertion of <i>Pot</i>2 and Occan (b) in rice and non-rice <i>Magnaporthe</i> isolates.

<p>Thick black bars indicate UTRs, and bars with crossed lines indicate Intron.</p

Host-wise clustering of proteomes (a) and secretome (b) of rice and non-rice <i>Magnaporthe</i> isolates.

<p>The number of gene families shared between the <i>Magnaporthe</i> species from different hosts (Rice, finger millet, foxtail millet, and Buffel grass) and a total number of clustered genes (numbers in parentheses) are indicated in Venn diagram. The numbers outside Venn diagram indicate, the isolate name from respective hosts, a total number of genes and singletons contributed by each isolate in parentheses.</p

Genes under positive selection.

<p>Genes under positive selection.</p