Digestion is driven by digestive enzymes and digestive enzyme gene copy number can provide insights on the genomic underpinnings of dietary specialization. The “Adaptive Modulation Hypothesis” (AMH) proposes that digestive enzyme activity, which increases with increased gene copy number, should correlate with substrate quantity in the diet. To test the AMH and reveal some of the genetics of herbivory vs carnivory, we sequenced, assembled, and annotated the genome of
- Award ID(s):
- 1942681
- NSF-PAR ID:
- 10292294
- Date Published:
- Journal Name:
- Frontiers in Microbiology
- Volume:
- 12
- ISSN:
- 1664-302X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Anoplarchus purpurescens , a carnivorous prickleback fish in the family Stichaeidae, and compared the gene copy number for key digestive enzymes to that ofCebidichthys violaceus , a herbivorous fish from the same family. A highly contiguous genome assembly of high quality (N50 = 10.6 Mb) was produced forA. purpurescens , using combined long-read and short-read technology, with an estimated 33,842 protein-coding genes. The digestive enzymes that we examined include pancreatic α-amylase, carboxyl ester lipase, alanyl aminopeptidase, trypsin, and chymotrypsin.Anoplarchus purpurescens had fewer copies of pancreatic α-amylase (carbohydrate digestion) thanC. violaceus (1 vs. 3 copies). Moreover,A. purpurescens had one fewer copy of carboxyl ester lipase (plant lipid digestion) thanC. violaceus (4 vs. 5). We observed an expansion in copy number for several protein digestion genes inA. purpurescens compared toC. violaceus , including trypsin (5 vs. 3) and total aminopeptidases (6 vs. 5). Collectively, these genomic differences coincide with measured digestive enzyme activities (phenotypes) in the two species and they support the AMH. Moreover, this genomic resource is now available to better understand fish biology and dietary specialization. -
Abstract Background Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes the tomato pathogen
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