title: Genome wide comprehensive analysis and web resource development on cell wall degrading enzymes from phyto-parasitic nematodes.
abstract: BACKGROUND
  The plant cell wall serves as a primary barrier against pathogen invasion. The success of a plant pathogen largely depends on its ability to overcome this barrier. During the infection process, plant parasitic nematodes secrete cell wall degrading enzymes (CWDEs) apart from piercing with their stylet, a sharp and hard mouthpart used for successful infection. CWDEs typically consist of cellulases, hemicellulases, and pectinases, which help the nematode to infect and establish the feeding structure or form a cyst. The study of nematode cell wall degrading enzymes not only enhance our understanding of the interaction between nematodes and their host, but also provides information on a novel source of enzymes for their potential use in biomass based biofuel/bioproduct industries. Although there is comprehensive information available on genome wide analysis of CWDEs for bacteria, fungi, termites and plants, but no comprehensive information available for plant pathogenic nematodes. Herein we have performed a genome wide analysis of CWDEs from the genome sequenced phyto pathogenic nematode species and developed a comprehensive publicly available database.
  
  
  RESULTS
  In the present study, we have performed a genome wide analysis for the presence of CWDEs from five plant parasitic nematode species with fully sequenced genomes covering three genera viz. Bursaphelenchus, Glorodera and Meloidogyne. Using the Hidden Markov Models (HMM) conserved domain profiles of the respective gene families, we have identified 530 genes encoding CWDEs that are distributed among 24 gene families of glycoside hydrolases (412) and polysaccharide lyases (118). Furthermore, expression profiles of these genes were analyzed across the life cycle of a potato cyst nematode. Most genes were found to have moderate to high expression from early to late infectious stages, while some clusters were invasion stage specific, indicating the role of these enzymes in the nematode's infection and establishment process. Additionally, we have also developed a Nematode's Plant Cell Wall Degrading Enzyme (NCWDE) database as a platform to provide a comprehensive outcome of the present study.
  
  
  CONCLUSIONS
  Our study provides collective information about different families of CWDEs from five different sequenced plant pathogenic nematode species. The outcomes of this study will help in developing better strategies to curtail the nematode infection, as well as help in identification of novel cell wall degrading enzymes for biofuel/bioproduct industries.
authors.affiliation: Department of Plant & Soil Science, Texas Tech University, 2802, 15th street, Lubbock, TX, 79409, USA. krishan.m.rai@ttu.edu.
authors.forename: Krishan Mohan
authors.initials: KM
authors.lastname: Rai
authors.affiliation: Department of Plant & Soil Science, Texas Tech University, 2802, 15th street, Lubbock, TX, 79409, USA. vimal-kumar.balasubramanian@ttu.edu.
authors.forename: Vimal Kumar
authors.initials: VK
authors.lastname: Balasubramanian
authors.affiliation: Department of Plant & Soil Science, Texas Tech University, 2802, 15th street, Lubbock, TX, 79409, USA. cassie.welker@ttu.edu.
authors.forename: Cassie Marie
authors.initials: CM
authors.lastname: Welker
authors.affiliation: Department of Plant & Soil Science, Texas Tech University, 2802, 15th street, Lubbock, TX, 79409, USA. mingxiong.pang@ttu.edu.
authors.forename: Mingxiong
authors.initials: M
authors.lastname: Pang
authors.affiliation: Department of Plant & Soil Science, Texas Tech University, 2802, 15th street, Lubbock, TX, 79409, USA. meimei@sbc.org.my.|Current address Sarawak Biodiversity Centre, KM20, Jalan Borneo Heights, Semengoh, Locked Bag No. 3032, Kuching, Sarawak, 93990, Malaysia. meimei@sbc.org.my.
authors.forename: Mei Mei
authors.initials: MM
authors.lastname: Hii
authors.affiliation: Department of Plant & Soil Science, Texas Tech University, 2802, 15th street, Lubbock, TX, 79409, USA. venugopal.mendu@ttu.edu.
authors.forename: Venugopal
authors.initials: V
authors.lastname: Mendu
mesh_terms: D000818:Animals; D002473:Cell Wall / Q000502:physiology*; D055106:Genome-Wide Association Study; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism; D015801:Helminth Proteins / Q000235:genetics* / Q000378:metabolism; D059828:Plant Cells / Q000502:physiology*; D011133:Polysaccharide-Lyases / Q000235:genetics / Q000378:metabolism; D017187:Tylenchida / Q000201:enzymology / Q000235:genetics*
chemical_list: D015801:Helminth Proteins; D006026:Glycoside Hydrolases; D011133:Polysaccharide-Lyases