Description of a novel taxon associated with Sugarcane Grassy Shoot (SCGS) disease

Phytoplasma is a group of extremely small bacteria (mollicutes). They don’t have a cell wall and any particular shape (pleomorphic). Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects. Phytoplasmas reside in plant’s phloem tissue while insects serve as vectors for the transmission of infection from plant to plant. Once disease caused by phytoplasma is established, entire fields of crops might be wiped out. Sugarcane is the world’s fourth largest and commercially important crop. Sugarcane Grassy Shoot disease is related to Rice Yellow Dwarf (RYD) phytoplasma which occurs in sugarcane growing countries throughout the world.

The major characteristic of SCGS disease are stunting, profuse tillering, side shoots, chlorotic stripes and bleached white leaf blades. The common symptoms of SCGS in sugarcane plant are narrowing and partially or almost chlorotic leaf lamina, excessive tillering and witches’ broom symptoms. Severely infected younger plants appear yellowish. The phytoplasma infection often leads to stunted growth, reduction in leaf size, and excessive proliferation of shoots.

Complete leaf chlorosis in SCGS disease &
Grassy appearance of phytoplasma-infected sugarcane plant

It’s important to study the genome of phytoplasma to understand how this tiny microbe causes infection in plants and gets transmitted through insect vectors. Phytoplasma DNA is difficult to isolate and then sequence it further, as researchers have not yet been active in this organism’s laboratory cultivation. Recently, the researchers at NCMR Pune successfully isolated and sequenced sugarcane phytoplasma. In this study, researchers demonstrated the phylogenetic position of 16SrXI-B group phytoplasmas by characterizing the phytoplasma strain associated with Sugarcane Grassy Shoot (SCGS) disease based on comparative genome features and phylogenetic analyses with its closely related phytoplasma taxa and proposed a novel ‘Ca. Phytoplasma’ taxon. This study is the first description of phytoplasma from India and the first description of phytoplasma species based on genome sequences.

Reference: https://pubmed.ncbi.nlm.nih.gov/33289626/

First Phytoplasma whole genome sequence from India

-By Kranti Karande

Phytoplasma is a group of extremely small bacteria. They don’t have a cell wall and any particular shape. Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects. 

Sugarcane Grassy Shoot (SCGS) is a disease caused by phytoplasma and the disease leads to 5% to 20% crop loss. SCGS phytoplasma causes severe proliferation of tillers leading to the typical grassy appearance of sugarcane, hence the name grassy shoot is given. Another disease called Bermuda Grass White leaf (BGWL) disease is a destructive phytoplasma disease of Bermuda grass.

Research group of Dr. Amit Yadav at NCMR, NCCS Pune performed whole genome sequencing of two phytoplasma associated with these two diseases. This is the first whole genome sequence of phytoplasma published from India. This sequence data might help in taxonomical characterization of other phytoplasma belonging to the same group.

A sugarcane plant sample (strain SCGS) exhibiting grassy shoot symptoms and a Bermuda grass sample (strain LW01) showing white leaf symptoms were collected from Pune, Maharashtra, India. The presence of phytoplasma was confirmed by 16S rRNA gene sequencing. Researcher confirmed that these phytoplasma strains belonged to the 16SrXI and 16SrXIV phytoplasma groups, respectively. Both genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline

The final SCGS assembly contained 29 scaffolds corresponding to 505,173 base pairs of DNA. The genome was found to be 95.43% complete and the GC content was 19.86%.The SCGS genome was predicted to have 404 protein-coding genes, 12 tRNA and two rRNA genes.

Similarly, the LW01 assembly contained 21 scaffolds corresponding to 483,935 base pairs of DNA. This genome was found to be 91.32 % complete and the GC content was 20.46 %. The LW01 genome was predicted to have 425 protein-coding genes, 13 tRNA and three rRNA genes.

Reference: https://www.ncbi.nlm.nih.gov/pubmed/32040378