Shaili Johri

All Publications

• The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome Doane, M. P., Morris, M. M., Papudeshi, B., Allen, L., Pande, D., Haggerty, J. M., Johri, S., Turnlund, A. C., Peterson, M., Kacev, D., Nosal, A., Ramirez, D., Hovel, K., Ledbetter, J., Alker, A., Avalos, J., Baker, K., Bhide, S., Billings, E., Byrum, S., Clemens, M., Demery, A. J., Lima, L. F., Gomez, O., Gutierrez, O., Hinton, S., Kieu, D., Kim, A., Loaiza, R., Martinez, A., McGhee, J., Nguyen, K., Parlan, S., Pham, A., Price-Waldman, R., Edwards, R. A., Dinsdale, E. A. 2020; 8 (1): 93

  Abstract

  BACKGROUND: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes.RESULTS: We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes.CONCLUSION: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence ofextant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.

  View details for DOI 10.1186/s40168-020-00840-x

  View details for PubMedID 32534596

• The pandemic push: can COVID-19 reinvent conferences to models rooted in sustainability, equitability and inclusion? Socio Ecological Practice Niner, H. J., Johri, S., Meyer, J., Wasserman, S. N. 2020: 253–256

  View details for DOI 10.1007/s42532-020-00059-y

• Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations DIVERSITY-BASEL Johri, S., Doane, M. P., Allen, L., Dinsdale, E. A. 2019; 11 (4)

  View details for DOI 10.3390/d11040049

  View details for Web of Science ID 000467289800002

• 'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market SCIENTIFIC REPORTS Johri, S., Solanki, J., Cantu, V., Fellows, S. R., Edwards, R. A., Moreno, I., Vyas, A., Dinsdale, E. A. 2019; 9: 4476

  Abstract

  Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.

  View details for DOI 10.1038/s41598-019-40940-9

  View details for Web of Science ID 000461151800060

  View details for PubMedID 30872700

  View details for PubMedCentralID PMC6418218

• Complete mitochondrial genome of the gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae) MITOCHONDRIAL DNA PART B-RESOURCES Dunn, N., Johri, S., Curnick, D., Carbone, C., Dinsdale, E. A., Chapple, T. K., Block, B. A., Savolainen, V. 2020; 5 (3): 2080–82

  View details for DOI 10.1080/23802359.2020.1765208

  View details for Web of Science ID 000536092800001

• Mitochondrial genome of the Smoothnose wedgefish Rhynchobatus laevis from the Western Indian Ocean MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Tiwari, A., Kerr, E. N., Dinsdale, E. A. 2020; 5 (3): 2083–84

  View details for DOI 10.1080/23802359.2020.1765209

  View details for Web of Science ID 000536126500001

• Mitochondrial genome of the silky sharkCarcharhinus falciformisfrom the British Indian Ocean Territory Marine Protected Area MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Chapple, T. K., Dinsdale, E. A., Robert, S., Block, B. A. 2020; 5 (3): 2416–17

  View details for DOI 10.1080/23802359.2020.1775147

  View details for Web of Science ID 000546839100001

• Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus from the British Indian Ocean Territory Marine Protected Area MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Chapple, T. K., Robert, S., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2347–49

  View details for DOI 10.1080/23802359.2020.1775148

  View details for Web of Science ID 000540548600001

• Mitochondrial genome of the Silvertip shark, Carcharhinus albimarginatus, from the British Indian Ocean Territory MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Dunn, N., Chapple, T. K., Curnick, D., Savolainen, V., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2085–86

  View details for DOI 10.1080/23802359.2020.1765210

  View details for Web of Science ID 000536091800001

• Mitochondrial genome of the silky shark Carcharhinus falciformis from the British Indian Ocean Territory Marine Protected Area. Mitochondrial DNA. Part B, Resources Johri, S., Chapple, T. K., Dinsdale, E. A., Schallert, R., Block, B. A. 2020; 5 (3): 2416-2417

  Abstract

  We present the first mitochondrial genome of Carcharhinus falciformis from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area (MPA). The mitochondrial genome of C. falciformis is 16,701 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 1063 bp in length. The complete mitogenome sequence of C. falciformis from the BIOT MPA will enable improved conservation measures of the CITES listed species through studies of species distribution, population abundance, fishing pressure and wildlife trade.

  View details for DOI 10.1080/23802359.2020.1775147

  View details for PubMedID 33457810

  View details for PubMedCentralID PMC7782099

• Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus from the British Indian Ocean Territory Marine Protected Area. Mitochondrial DNA. Part B, Resources Johri, S., Chapple, T. K., Schallert, R., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2347-2349

  Abstract

  We present the first mitochondrial genome of Trianenodon obesus from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area. The mitogenome was 16,702 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 38.9%. The control region was 1064 bp in length. This mitogenome for the BIOT MPA T. obesus differed from the previously published T. obesus genome by 15 bp and the differences include a 2 bp insertion and 13 single nucleotide polymorphisms distributed across the mitogenome in the BIOT MPA sequence. Whole mitogenome sequence of T. obesus from the Chagos archipelago presented here fills existing gaps in genetic information on marine species from the BIOT MPA and provides additional tools for species specific assessments as to the effectiveness of MPA management. In addition, methods presented here lay the framework for genetic studies in remote locations with limited infrastructure.

  View details for DOI 10.1080/23802359.2020.1775148

  View details for PubMedID 33457786

  View details for PubMedCentralID PMC7783066

• Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus) META GENE Johri, S., Fellows, S. R., Solanki, J., Busch, A., Livingston, I., Mora, M., Tiwari, A., Cantu, V., Goodman, A., Morris, M. M., Doane, M. P., Edwards, R. A., Dinsdale, E. A. 2020; 24

  View details for DOI 10.1016/j.mgene.2020.100648

  View details for Web of Science ID 000525750700044

• Mitochondrial genome of the Silvertip shark, Carcharhinus albimarginatus, from the British Indian Ocean Territory. Mitochondrial DNA. Part B, Resources Johri, S., Dunn, N., Chapple, T. K., Curnick, D., Savolainen, V., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2085-2086

  Abstract

  The Chagos archipelago in the British Indian Ocean Territory (BIOT) has been lacking in detailed genetic studies of its chondrichthyan populations. Chondrichthyes in Chagos continue to be endangered through illegal fishing operations, necessitating species distribution and abundance studies to facilitate urgent monitoring and conservation of the species. Here, we present a complete mitochondrial genome of the Silvertip Shark, Carcharhinus albimarginatus sampled in the Chagos archipelago. The mitochondrial genome of C. albimarginatus was 16,706 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, a replication origin and a D-loop region. GC content was at 38.7% and the control region was 1,065 bp in length. We expect that mitogenomes presented here will aid development of molecular assays for species distribution studies. Overall these studies will promote effective conservation of marine ecosystemes in the BIOT.

  View details for DOI 10.1080/23802359.2020.1765210

  View details for PubMedID 33457752

  View details for PubMedCentralID PMC7782225

• Complete mitochondrial genome of the gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. Part B, Resources Dunn, N., Johri, S., Curnick, D., Carbone, C., Dinsdale, E. A., Chapple, T. K., Block, B. A., Savolainen, V. 2020; 5 (3): 2080-2082

  Abstract

  We report the first mitochondrial genome sequences for the gray reef shark, Carcharhinus amblyrhynchos. Two specimens from the British Indian Ocean Territory were sequenced independently using two different next generation sequencing methods, namely short read sequencing on the Illumina HiSeq and long read sequencing on the Oxford Nanopore Technologies' MinION sequencer. The two sequences are 99.9% identical and are 16,705 base pairs (bp) and 16,706 bp in length. The mitogenome contains 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two non-coding regions; the control region and the origin of light-strand replication (OL).

  View details for DOI 10.1080/23802359.2020.1765208

  View details for PubMedID 33457750

  View details for PubMedCentralID PMC7782339

• Mitochondrial genome of the Smoothnose wedgefish Rhynchobatus laevis from the Western Indian Ocean. Mitochondrial DNA. Part B, Resources Johri, S., Tiwari, A., Kerr, E. N., Dinsdale, E. A. 2020; 5 (3): 2083-2084

  Abstract

  We present the first mitogenome sequence of the Smoothnose Wedgefish, Rhynchobatus laevis obtained through field sequencing on the MinION handheld sequencer. The mitochondrial genome of R. laevis is 16,560 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 867 bp in length. Whole mitochondrial genome sequence of R. laevis will enable improved understanding of distribution, abundance, catch and trade rates of the Critically Endangered species.

  View details for DOI 10.1080/23802359.2020.1765209

  View details for PubMedID 33457751

  View details for PubMedCentralID PMC7782167