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Shah, Tejas M.
- Analysis of Community Structure and Species Richness of Protozoa-Enriched Rumen Metagenome from Indian Surti by Shotgun Sequencing
Abstract Views :220 |
PDF Views:80
Authors
Ravi K. Shah
1,
Amrutlal K. Patel
1,
Tejas M. Shah
1,
Krishna M. Singh
1,
Neelam M. Nathani
1,
Chaitanya G. Joshi
1
Affiliations
1 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
1 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
Source
Current Science, Vol 111, No 1 (2016), Pagination: 184-191Abstract
The present study applies metagenomics to characterize the diversity and relative abundance of protozoa residing in the rumen of Indian Surti buffalo (Bubalus bubalis). To increase protozoa representation in the metagenome, protozoa enrichment was performed by density sedimentation and confirmed by quantitative real time PCR. The highly enriched metagenome sample was subjected to shotgun sequencing by Ion Torrent PGM which resulted in 10,303,375 reads total-ling 1.6 gigabases. The taxonomic profile obtained by comparison with SILVA SSU database showed pre-dominance of the class Litostomatea (99.78%) fol-lowed by Coccidia (0.10%) and Aconoidasida (0.06%). At the genus level Isotricha (48.06%) followed by Polyplastron (9.90%), Dasytricha (9.87%) and Eudiplodinium (7.47%) were predominant. The taxo-nomic assignment based on protein coding regions showed discrepancy with the SSU-based assignments, possibly due to the absence of most eukaryotic ge-nomes in public databases. According to the SEED subsystems annotation database, genes for protein me-tabolism were the most abundant followed by genes for RNA metabolism, regulation and cell signalling. The present study offers a preliminary snapshot of di-versity, functional potential and relative abundance of protozoa within the Indian Surti buffalo rumen and al-so expands our knowledge of these unicellular eukary-otes present in the rumen ecosystem.Keywords
Buffalo Rumen, Metagenome, Protozoa Enrichment, Quantitative Real Time PCR, Shotgun Sequencing.Full Text
- Identification of Genetic Variants in PDC, RHO, PDE6A and PDE6B in Dogs with Progressive Retinal Atrophy
Abstract Views :211 |
PDF Views:77
Authors
Dipal Y. Pandya
1,
Divyesh N. Kelawala
2,
Namrata V. Patel
1,
Tejas M. Shah
1,
Anand B. Patel
1,
Nidhi R. Parmar
1,
Bhaskar Reddy
1,
Deepak B. Patil
2,
Chaitanya G. Joshi
1
Affiliations
1 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
2 Department of Veterinary Surgery and Radiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
1 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
2 Department of Veterinary Surgery and Radiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
Source
Current Science, Vol 111, No 10 (2016), Pagination: 1640-1648Abstract
The progressive retinal atrophy (PRA) is an inherited eye disease and characterized by progressive retinal degeneration which leads to impaired vision in dogs. Using targeted next generation sequencing of nine PRA cases and six controls, we have identified SNPs in PDC, PDE6A and PDE6B, which were not previously associated with PRA. The gene in which the highest mutations found was PDE6A (113 and 104 SNPs), followed by PDE6B, PDC and RHO in all dog breeds and Spitz-only respectively. Five SNPs identified in PDC gene of Spitz-only breed showed significant association with PRA. However, no pathogenetically relevant mutations were found in RHO gene for PRA. The SNP in PDE6B chr3: 91763017 (G/A) in Spitz-only breed, and PDE6A chr4: 5912574 (T/C) and PDC chr7: 19511750 (T/A) were associated with PRA in the breeds of dog studied. Our results show that PRA is genetically heterogeneous and is caused by multiple, distinct mutations.Keywords
Genome-Wide Association, Next Generation Sequencing, Progressive Retinal Atrophy, Single Nucleotide Polymorphisms.Full Text
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