Amphioxus functional genomics and the origins of vertebrate gene regulation.

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that-in vertebrates-over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations

Structural studies of the four-way helical DNA junction

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Size of and damage on shoots of Passiflora suberosa (Passifloraceae) influence oviposition site selection of Heliconius erato phyllis (Fabricius) (Lepidoptera, Nymphalidae)

Oviposition site selection of Heliconius erato phyllis (Fabricius, 1775) (Lepidoptera, Nymphalidae) was studied when size of and damage on shoots were variable in a natural population of Passiflora suberosa Linnaeus (Passifloraceae), and through sequential and simultaneous choice experiments performed under insectary conditions. Females showed marked oviposition preference for undamaged and largest shoots of P. suberosa. Eggs were mostly laid on the terminal buds of intact shoots under natural conditions. In simultaneous choice trials, females preferred to oviposit on shoots from which leaves (ten) were removed but the terminal bud maintained to those where leaves were kept but the terminal bud was cut out. In sequential choice trials, they did not lay eggs on shoots from which the terminal bud was removed. Females preferred to oviposit on large to short intact shoots in both sequential and simultaneous choice trials. Females laid eggs preferentially on shoots with the greatest leaf area when most plants were intact in the field during early spring. Later in fall, when mostly large, old shoots were damaged or in a reproductive stage (less desirable for oviposition), oviposition intensity was highest on the shortest, youngest shoots of P. suberosa. Thus, females might rank these quality attributes higher than size while selecting shoots for oviposition. The consequences of ovipositing selectively on intact, large shoots of P. suberosa are discussed from the view point of H. erato phyllis larval performance