Vishal Singh Somvanshi and Uma Rao
Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012 Email: [email protected]; [email protected]
Nematodes are one of the largest groups of metazoans. They are ubiquitous in nature and are found in almost all possible ecosystems. It is estimated that 1 – 10 million species of nematodes could be present in the environment, but only~27000 species have been described. Although popular as animal, humanor plant parasites, majority of nematodes are beneficial for the environment and play critical role in nutrient recycling. The life cycle of nematodescomprise of an embryonicstage, followed by four larval and adult stages. In some nematode species, an alternative 3rd larval stage known as dauer stage, which isable of survive adverse environmental conditions is also found. In parasitic nematodes, some or all stages can be parasitic. The life span of nematodes may vary greatly from a few days to several years. Phylum Nematoda has traditionally been classified into two classes- Adenophoreaand Secernentea. However, the molecular analysis of phylogenetic evolution in Phylum Nematoda revealed that Adenophorea was ancestral, and Secernentea arose from Adenophorea. As per the new analysis, Phylum Nematoda has been classified into three major lineages, Chromadoria, Enoplia and Dorylaimia, distributed into 5 major clades. It was also suggested that animal- and plant-parasitism evolved at least four and three different times, respectively, during the course of nematode evolution.
Plant-parasitic nematodes (PPNs) cause an estimated annual global crop yield loss of about 10%, amounting to US $173 billion.The globally identified top ten most dangerous plant- parasitic nematode are:(1) root‐knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heteroderaand Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholussimilis; (5) Ditylenchusdipsaci; (6) the pine wilt nematode Bursaphelenchusxylophilus; (7) the reniform nematode Rotylenchulusreniformis;
(8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbusaberrans;
and (10) Aphelenchoidesbesseyi.In India, a recent estimate indicated that plant-parasitic nematodes cause an approximate yield loss of ₹102,039.79 million (US$1577 million) to various crops. The top plant nematode threats to Indian agriculture are Meloidogyne spp., Rotylenchulusreniformis, Globodera and Heteroderaspp., Pratylenchusspp., Aphelenchoidesbesseyi, Ditylenchusangustus, Radopholussimilis, Tylenchulussemipenetrans, Hirschmanniella spp., Helicotylenchusmulticinctus, and Tylenchorhynchusbrevilineatus. Also, two extremely dangerous nematodes not present in India are pinewood nematode (Bursaphelenchusxylophilus) and red ring nematode of coconut (B. cocophilus).
Despite the fact that PPNs are an enormous threat to the crops, there is an acute scarcity of management options for these parasites. Most of the chemical pesticides used for PPN
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Thegenome of nematode Caenorhabditis elegans was sequenced in 1998. It is the only nematode for which the genome sequence is complete. Since then genomes of 131 nematodes have been sequenced and published on WormBase, the primary nematode genome repository.
In 2019 the C. elegans genome was re-sequenced using long read sequencing approach and newer genes were discovered. Nematode genomes show several interesting features. Nematode genomes are compact andrange from 19.67 Mb to 265 Mb in size. In spite of such a major size difference, the number of genes in Nematodes is almost comparable to that of humans. On an average, the ematode genomes also show high gene density. The nematodesshow a large number of genes for which no homologues could be recognized outside the same nematode genus, indicating high rates of gene gain and loss through horizontal gene transfer. In addition, the nematode genes are organised in operons. Comparative genomic analysis has revealed that nematode genomes do not show any genomic featurewhich could be used to differentiate parasitic nematodes from free-living nematodes. Several novel genes are also known to arise in Phylum Nematoda.
A list of all the sequenced plant parasitic nematodes, the technologies used for sequencing and their genome statistics is provided in Table 1.
Table 1: A comparison of publishedplant-parasitic nematode genomes (Modifoed from Somvanshi et al., 2018)
S.
No.
Nematode Assembly
Size
No. of Scaffolds
N50 value (kbp)
CEGMA score (Complete/
Partial %) or Complete%
Year
1 Meloidogyne incognita 86.1 2995 62.5 77/80.6 2008
2 Meloidogyne hapla 53.0 3452 37.6 94.8/96.8 2008
3 Bursaphelenchusxylophilus 74.6 5527 949.8 97.6/98.4 2011 4 Meloidogyne floridensis 96.7 58696 3.7 58.1/77.4 2014
5 Globoderapallida 124.6 6873 122 74.19/80.65 2014
6 Pratylenchuscoffeae 19.7 5821 10 NA 2015
7 Globoderarostochiensis 95.9 4377 89 93.55/95.56 2016
8 Meloidogyne enterolobii 162.4 46090 9.2 81 /NA 2017
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9 Meloidogyne floridensis SJF1
74.9 9134 13.2 84 2017
10 Meloidogyne incognita W1 122.1 33735 16.4 83 2017
11 Globoderaellingtonae 119.1 2248 360 92/96 2017
12 Meloidogyne javanicaVW4 142.6 34394 14.2 90 2017
13 Meloidogyne arenaria HarA
163.7 46509 10.5 91 2017
14 Ditylenchus destructor 112 1761 570 91 2016
15 Meloidogyne incognita 183.5 12091 38.6 97 2017
16 Meloidogyne javanica 256.3 31341 10.4 96 2017
17 Meloidogyne arenaria 235.5 26196 16.4 95 2017
18 Meloidogyne graminicola 38.18 4304 20.4 84.27/90.73 2018
Recent advancements in PPN genomics and transcriptomics has made it possible to identify promising molecular targets and metabolic choke points that may be exploited for their management through transgenic approaches or target-based drug discovery.Although new drugs or chemicals designed using genomic information are still awaited, the transgenic crop- based approaches, such as host delivered RNAi has been very successfully used for nematode management.It is expected that increased use of genomic information would give a major boost to find smarter options for animal- and plant-parasitic nematode managemen.
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