skip to main content

Attention:

The NSF Public Access Repository (PAR) system and access will be unavailable from 8:00 PM ET on Friday, March 21 until 8:00 AM ET on Saturday, March 22 due to maintenance. We apologize for the inconvenience.


Title: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: Birth, death and adaptation
Abstract

Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP) gene superfamily varies widely.CYPome size variation has been attributed to reciprocal adaptive radiations in insect detoxification genes in response to plant biosynthetic gene radiations driven by co‐evolution between herbivores and their chemically defended hostplants. Alternatively, variation inCYPome size may be due to random “birth‐and‐death” processes, whereby exponential increase via gene duplications is limited by random decay via gene death or transition via divergence. We examinedCYPome diversification in the genomes of seven Lepidoptera species varying in host breadth from monophagous (Bombyx mori) to highly polyphagous (Amyelois transitella).CYPome size largely reflects the size of Clan 3, the clan associated with xenobiotic detoxification, and to some extent phylogenetic age. Consistently across genomes, familiesCYP6,CYP9 andCYP321 are most diverse andCYP6AB,CYP6AE,CYP6B,CYP9A andCYP9G are most diverse among subfamilies. Higher gene number in subfamilies is due to duplications occurring primarily after speciation and specialization (“P450 blooms”), and the genes are arranged in clusters, indicative of active duplicating loci. In the parsnip webworm,Depressaria pastinacella, gene expression levels in large subfamilies are high relative to smaller subfamilies. Functional and phylogenetic data suggest a correlation between highly dynamic loci (reflective of extensive gene duplication, functionalization and in some cases loss) and the ability of enzymes encoded by these genes to metabolize hostplant defences, consistent with an adaptive, nonrandom process driven by ecological interactions.

 
more » « less
PAR ID:
10043606
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley-Blackwell
Date Published:
Journal Name:
Molecular Ecology
Volume:
26
Issue:
21
ISSN:
0962-1083
Page Range / eLocation ID:
p. 6021-6035
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Summary

    Plant smallRNAs (sRNAs) modulate key physiological mechanisms through post‐transcriptional and transcriptional silencing of gene expression. SmallRNAs fall into two major categories: those are reliant onRNA‐dependentRNApolymerases (RDRs) for biogenesis and those that are not. KnownRDR1/2/6‐dependentsRNAs include phased and repeat‐associated short interferingRNAs, while knownRDR1/2/6‐independentsRNAs are primarily microRNAs (miRNA) and other hairpin‐derivedsRNAs. In this study we produced and analyzedsRNA‐seq libraries fromrdr1/rdr2/rdr6triple mutant plants. We found 58 previously annotated miRNAloci that were reliant onRDR1, ‐2, or ‐6function, casting doubt on their classification. We also found 38RDR1/2/6‐independentsRNAloci that are notMIRNAs or otherwise hairpin‐derived, and did not fit into other known paradigms forsRNAbiogenesis. These 38sRNA‐producing loci have as‐yet‐undescribed biogenesis mechanisms, and are frequently located in the vicinity of protein‐coding genes. Altogether, our analysis suggests that these 38 loci represent one or more undescribed types ofsRNAinArabidopsis thaliana.

     
    more » « less
  2. Abstract

    A whole‐genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalysed adaptive radiation in some polyploid‐origin lineages. However, little is known about general consequences of aWGDbecause gene duplicates (i.e., paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid‐origin species. We demonstrate a new method that enables genome‐wide scans for signatures of selection at both nonduplicated and duplicated loci by taking locus‐specific copy number into account. We apply this method toRADsequence data from different ecotypes of a polyploid‐origin salmonid (Oncorhynchus nerka) and reveal signatures of divergent selection that would have been missed if duplicated loci were filtered. We also find conserved signatures of elevated divergence at pairs of homeologous chromosomes with residual tetrasomic inheritance, suggesting that joint evolution of some nondiverged gene duplicates may affect the adaptive potential of these genes. These findings illustrate that including duplicated loci in genomic analyses enables novel insights into the evolutionary consequences ofWGDs and local segmental gene duplications.

     
    more » « less
  3. Abstract

    Major habitat transitions, such as those from marine to freshwater habitats or from aquatic to terrestrial habitats, have occurred infrequently in animal evolution and may represent a barrier to diversification. Identifying genomic events associated with these transitions can help us better understand mechanisms that allow animals to cross these barriers and diversify in new habitats. Study of theCapitella telataandHelobdella robustagenomes allows examination of one such habitat transition (marine to freshwater) in Annelida. Initial examination of these genomes indicated that the freshwater leechH. robustacontains many more copies (12) of the sodium–potassium pump alpha‐subunit (Na+/K+ATPase) gene than does the marine polychaeteC. telata(2). The sodium–potassium pump plays a key role in maintenance of cellular ionic balance and osmoregulation, and Na+/K+ATPase duplications may have helped annelids invade and diversify in freshwater habitats. To assess whether the timing of Na+/K+ATPase duplications coincided with the marine‐to‐freshwater transition in Clitellata, we used transcriptomic data from 18 annelid taxa, along with the two genomes, to infer a species phylogeny and identified Na+/K+ATPase gene transcripts in order to infer the timing of gene duplication events using tree‐based methods. The inferred timing of Na+/K+ATPase duplication events is consistent with the timing of the initial marine‐to‐freshwater transition early in the history of clitellate annelids, supporting the hypothesis that gene duplications may have played a role in the annelid diversification into freshwater habitats.

     
    more » « less
  4. Summary

    Distyly is an intriguing floral adaptation that increases pollen transfer precision and restricts inbreeding. It has been a model system in evolutionary biology since Darwin. Although theS‐locus determines the long‐ and short‐styled morphs, the genes were unknown inTurnera. We have now identified these genes.

    We used deletion mapping to identify, and then sequence,BACclones and genome scaffolds to constructS/shaplotypes. We investigated candidate gene expression, hemizygosity, and used mutants, to explore gene function.

    Thes‐haplotype possessed 21 genes collinear with a region of chromosome 7 of grape. TheS‐haplotype possessed three additional genes and two inversions.TsSPH1was expressed in filaments and anthers,TsYUC6in anthers andTsBAHDin pistils. Long‐homostyle mutants did not possessTsBAHDand a short‐homostyle mutant did not expressTsSPH1.

    Three hemizygous genes appear to determine S‐morph characteristics inT. subulata. Hemizygosity is common to all distylous species investigated, yet the genes differ. The pistil candidate gene,TsBAHD, differs from that ofPrimula, but both may inactivate brassinosteroids causing short styles.TsYUC6is involved in auxin synthesis and likely determines pollen characteristics.TsSPH1is likely involved in filament elongation. We propose an incompatibility mechanism involvingTsYUC6andTsBAHD.

     
    more » « less
  5. Proliferating cell nuclear antigen (PCNA) plays critical roles in eukaryoticDNAreplication and replication‐associated processes. It is typically encoded by one or two gene copies (pcna) in eukaryotic genomes. Recently reported higher copy numbers ofpcnain some dinoflagellates raised a question of how this gene has uniquely evolved in this phylum. Through real‐timePCRquantification, we found a wide range ofpcnacopy number (2–287 copies) in 11 dinoflagellate species (n = 38), and a strong positive correlation betweenpcnacopy number and genome size (log10–log10transformed). Intraspecificpcnadiverged up to 21% and are dominated by nonsynonymous substitutions, indicating strong purifying selection pressure on and hence functional necessity of this gene. By surveyingpcnacopy numbers in eukaryotes, we observed a genome size threshold at 4 pgDNA, above which more than twopcnacopies are found. To examine whether retrotransposition is a mechanism ofpcnaduplication, we measured the copy number of retroposedpcna, taking advantage of the 22‐nt dinoflagellate‐specific spliced leader (DinoSL) capping the 5′ end of dinoflagellate nuclear‐encodedmRNAs, which would exist in the upstream region of a retroposed gene copy. We found that retroposedpcnacopy number increased with totalpcnacopy number and genome size. These results indicate co‐evolution of dinoflagellatepcnacopy number with genome size, and retroposition as a major mechanism ofpcnaduplication in dinoflagellates. Furthermore, we posit that the demand of faithful replication and maintenance of the large dinoflagellate genomes might have favored the preservation of the retroposedpcnaas functional genes.

     
    more » « less