This year for DNA day, we wanted to highlight papers reporting new genome sequences of organisms from peanuts to Papilio butterflies published in Nature Genetics over the last year. All reference genomes are published open access under a CC-BY licence.
In reverse chronological order:
The spotted gar (Lepisosteus oculatus) genome was published last month by Ingo Braasch, John Postlethwait and colleagues. The gar occupies an important evolutionary position between teleosts and tetrapods. It diverged from the teleost lineage before the teleost genome duplication and its genome is thus an excellent resource for understanding post-duplication evolution and the evolution of vertebrates more generally. See also the great News & Views by David Parichy here.
In February of this year, we published two new genome papers. Taisei Kikuchi, Mark Viney, Matthew Berriman and colleagues reported the genomes of six nematode species from the Strongyloides clade (see previous blog post here). Analysis of these genomes has shed light on the evolution of parasitism and will be valuable for further research into the unique biology of these species.
The second genome paper published in February, by David Bertioli and colleagues, reported the genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of the cultivated peanut. The peanuts that we know and love from our grocery stores are allotetraploids, meaning that the assembly and understanding of their genome is extremely difficult. The genomes of these two progenitor species can help to understand peanut biology and identify disease resistance genes to improve peanut cultivation.
Late last year, we published the pineapple genome and two papers reporting the genome sequences of the ruff (Philomachus pugnax).
The pineapple genome (actually, 3 genomes) was published by Ray Ming, Robert Paull and Qingyi Yu in November 2015. The authors sequenced 2 cultivated varieties and a wild relative species to better understand the basis and evolution of CAM photosynthesis (see earlier blog posts here and here). Qing Xu and Zhong-Jian Liu also published a News & Views article to accompany the paper.
The ruff, a species of wading bird with a fascinating reproductive strategy, was sequenced independently by Xin Liu, Leif Andersson and colleagues and by Mark Blaxter, David Lank, Terry Burke and colleagues. The papers were covered quite elegantly in a News & Views article by Chris Jiggins (here). The males of this species can take one of 3 different forms: Independents, which are dominant and fight for females; Satellites, which are submissive to Independents, but are still obviously male; and Faeders, which look like slightly larger females and gain matings by going unnoticed by the aggressive Independent males. Analysis of the genome sequence led to the discovery of a large inversion that determines the male’s type, including his appearance and behavior. For more on these amazing birds, see our previous blog post here. We also published an editorial to accompany the publication of these papers, which outlined our editorial criteria for reference genomes.
In May of last year, we published the genome of the grass carp Ctenopharyngodon idellus . by Yaping Wang, Haoran Lin, Bin Han, Zuoyan Zhu and colleagues. This fish switches from a carnivorous to vegetarian diet after the larval stage and its genome provides insights into this dietary change. The grass carp is an economically important fish, accounting for 16% of global aquaculture. The availability of the genome opens the door for using genomic information to improve grass carp breeding programs.
The genome of the zoonotic hookworm Ancylostoma ceylanicum was published by Erich Schwarz and colleagues in March 2015. This species is significant because it can infect both humans and other animals, making it an excellent laboratory model for hookworm infections. The authors also sequenced the transcriptomes of these worms during different infection stages and identified genes that are essential for it to parasitize its host. These genes are potential drug or vaccine targets that can be studied in more depth in the future.
In March 2015, we published the sequences of two butterfly species by Haruhiko Fujiwara and colleagues. Females of the swallowtail butterfly Papilio polytes come in two forms, one of which mimics an unpalatable species, allowing them to evade predation. The authors also sequenced a related species, Papilio xuthus, which lacks the mimetic form (see also the News & Views by James Mallet). A previous paper had identified the sex determination gene doublesex as the mimicry locus, but the molecular structure and mechanism underlying the genetics of this trait were not reported in that paper. Fujiwara and colleagues found that a large inversion underlies this trait and used RNAi knockdown experiments to further understand the female-limited mimicry in this species.
Finally, early last year David Hibbett, Francis Martin and colleagues reported the genome sequences of 18 fungal species, including 13 ectomycorrhizal (or plant symbiotic) species. They found that ectomycorrhizal species have a reduced number of plant cell wall degrading enzymes. They further used these and other sequenced genomes to understand the evolution of symbiosis in fungi and to identify genes important for these key interactions. Luca Venturini and Massimo Delledonne nicely summarized this work and its importance for evolution and ecology in their News & Views article (here).
Do you have a favorite genome paper, from the above list or elsewhere? Tell us below in the comments!