BioGenomics2017 - Global Biodiversity Genomics Conference
February 21-23, 2017
Smithsonian National Museum of Natural History | Washington, D.C.

Program - Single Session


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12
Ecological Genomics

Room: Salon 3, Marriott Hotel

14:00 - 15:30

Moderator: Bill Wcislo, STRI



12.1  14:10  Genomic and chemical consequences of different levels of Gene Flow in the Fig- Wasp Pollination Mutualism. Herre A*, Smithsonian Institution- STRI

Figs and their pollinator wasps present a model system for understanding the patterns and processes underlying co-adaptation and co-evolution. Both figs and wasps are species-rich, and it is the pollinator wasps recognition and choice of host that determines the potential paths of fig gene flow, and ultimately, fig species boundaries. In turn, wasp choices are based in part on host volatile chemical production. Our previous studies undermined the existing paradigms of strict one to one host-pollinator specificity and tight co-speciation of figs and their pollinator wasps, and have been subsequently corroborated by studies across the globe. I will discuss results from ongoing studies of the mechanistic role of the figs chemical signals in mediating co-evolutionary processes, and the genetics that both underly and reflect them.


12.2  14:10  Genomic changes associated with sockeye salmon ecotype divergence provide insights into life history evolution and tools for fisheries management. Veale AJ, University of British Columbia; Russello MA*, University of British Columbia

Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here we used paired migratory [anadromous vs. resident (kokanee)] and reproductive (shore- vs. stream-spawning kokanee) ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena drainages) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms (SNPs), 219 of which were identified as outlier loci and candidates for divergent selection between resident and anadromous forms. Of the 126 outlier SNPs identified between shore- and stream-spawning kokanee population pairs, one was shared across multiple comparisons and was uniformly the most highly differentiated SNP. In order to further investigate the association of this locus with sockeye salmon reproductive life history variation, we genotyped 1519 anadromous sockeye and resident kokanee from 47 shore- and stream-spawning populations across their pan-Pacific distribution using a newly-developed TaqMan assay, revealing directional divergence associated with spawning habitat. Subsequent sequencing of ~23,000 base pairs surrounding the SNP revealed evidence for an ancient selective sweep underlying divergence of the shore-spawning and stream-spawning alleles, likely pre-dating the Pleistocene. Overall, the identified SNPs and genomic regions offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide new tools for informing management applications that require identifying individuals to ecotype.


12.3  14:50  Host and habitat differences of Labyrinthula parasites: a metabarcode approach. Pagenkopp Lohan KM*, Smithsonian Environmental Research Center; DiMaria R, Smithsonian Environmental Research Center; Martin D; Ross C, University of North Florida; Paul V, Smithsonian Marine Station Ft. Pierce; Duffy JE, Smithsonian Environmental Research Center; Harvell D, Cornell University; Ruiz G, Smithsonian Environmental Research Center

Seagrass beds are among the most productive and widespread ecosystems in the world; unfortunately, they are also one of the most threatened. Though many stressors impact seagrasses, one reason for their decline is attributed to a wasting disease caused by protistan parasites in the genus Labyrinthula. To begin assessing the potential for host specificity and habitat preference among Labyrinthula species, we collected samples from six seagrass species, as well as ambient water and sediment, across multiple locations within the Indian River Lagoon, Florida. We designed primers for the small subunit (SSU) gene and first internal transcribed spacer (ITS1) region of the ribosomal gene complex to target species within the genus Labyrinthula that previous studies had shown were pathogenic. Applying these primers in a two-step PCR protocol, we generated amplicon libraries for Illumina sequencing from all positive seagrass hosts (n=91, SSU only) and environmental samples (n=24, SSU and ITS1). Bioinformatic analyses were conducted using a combination of USEARCH, QIIME, mothur, and the statistical program R. We found 19 OTUs identified as Labyrinthulea, of which 6 were identified as Labyrinthula spp., from 462,594 sequences that were generated from 115 samples. OTUs identified as Labyrinthulea were detected from 108 samples, including 84 seagrass samples and all environmental samples. OTUs identified as Labyrinthula spp. were detected from 64 samples, including 42 seagrass samples and 22 environmental samples. Preliminary phylogenetic analyses indicate that the diversity of Labyrinthula is higher than previously recognized, with multiple OTUs forming distinct clades apart from sequences of previously known Labyrinthula. The relative abundance of the six OTUs identified as Labyrinthula spp. varied from 164 sequences for OTU_50 up to 19,038 sequences for OTU_9. Occurrence of these OTUs also varied, with OTU_9 occurring in 32 samples, followed by OTU_15 in 19 samples. Two OTUs (OTU_44, OTU_50) each occurred in only one sample. Two of the OTUs were detected in three hosts and both water and sediment samples. Only one OTU occurred in both rivers and in five sampling locations. Further examination of the distribution of these clades across hosts and environmental reservoirs, determination of which OTUs represent pathogenic species, and which are associated with disease symptoms is ongoing.


12.4  15:10  The genome of the white shark, Carcharodon carcharias: Insights on genome size evolution, repeat content, and shark biology. Marra NJ*, Save Our Seas Shark Research Center; Wang M, Cornell University; Pavinski Bitar PD, Cornell University; Sun Q, Cornell University; Komissarov A, St. Petersburg State University; Jorgensen S, Monterey Bay Aquarium; Jue N, California State University Monterey Bay; O\'Brien SJ, Save Our Seas Shark Research Center; Shivji M, Save Our Seas Shark Research Center; Stanhope MJ, Cornell University

Elasmobranch fishes (sharks, skates, rays; Elasmobranchii), are woefully underrepresented in terms of their genomic resources. To date there exists only one well-annotated genome sequence in the Chondrichthyes, the elephant shark, a member of the Holocephali, a separate subclass from the Elasmobranchii. To address this deficiency we sequenced, assembled and annotated the genome of the white shark, Carcharodon carcharias. Through the use of single end, paired end, overlapping paired end, and mate paired sequencing libraries we constructed an initial assembly of the white shark genome using SOAPdenovo2. This resulted in a sequence of 4.076 Gbp (> 100x depth). Subsequently, five Chicago libraries were sequenced and used in conjunction with our SOAPdenovo2 assembly by Dovetail Genomics and their HiRise pipeline. This more than doubled the n50 scaffold length to 2.77 Mbp in a 4.079 Gbp assembly. CEGMA analyses indicated that greater than 92% of core eukaryotic genes are present in this final assembly. The genome was annotated with the MAKER2 pipeline and yielded roughly 29,900 predicted protein coding genes with an average gene length of 24.35 Kbp. Of these, 28,950 coded for protein sequences with significant blast hits in either the Swiss-Prot or nr databases and allowed us to investigate various aspects of shark biology. We have, for example, identified multiple genes that play a likely role in shark electroreception, including the genes Eya1, Eya2, Eya4, and Six1, the latter two having been previously identified as expressed in developing electroreception organs of another shark, Scyliorhinus canicula. We also identified white shark sequences for 45/73 apoptosis and cell cycle related genes present in the Deathbase database for the human, mouse, and zebrafish genomes. For many of these genes there appear to be multiple copies in the white shark genome and we are currently validating the functional copy number and searching for patterns of adaptive molecular evolution. Resolving the genetic repertoire for cell cycle control is significant, given that apoptosis, tumor formation, and wound healing have long been areas of focus in elasmobranchs. The white shark genome appears to have a large degree of sequence duplication. K-mer based analyses have identified the possibility of a genome or segmental duplication that we are now exploring with additional Ks distribution based analyses (synonymous distance between paralogues). Characterization of the repeat content in the genome has identified a large number of repeat elements with 57% of the genome consisting of interspersed repeats. This includes roughly 30% of the genome consisting of LINE elements. As one of the first, and the largest shark genome sequenced to date, the white shark genome provides a valuable resource for understanding various aspects of shark biology (e.g. sensory biology and immunity) as well as the evolution of large genome size and repeat content in an ancient vertebrate lineage.




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