Stahlke, Amanda R Chang, Jennifer Tembrock, Luke R Sim, Sheina B Chudalayandi, Sivanandan Geib, Scott M Scheffler, Brian E Perera, Omaththage P Gilligan, Todd M Childers, Anna K
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Published in
Genome biology and evolution
Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist yea...
Walden, Nora Schranz, M Eric
Published in
Genome biology and evolution
Large genomic datasets are becoming the new normal in phylogenetic research, but the identification of true orthologous genes and exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with ortholog detection...
Laine, Veronika N Sävilammi, Tiina Wahlberg, Niklas Meramo, Katarina Ossa, Gonzalo Johnson, Joseph S Blomberg, Anna S Yeszhanov, Aidyn B Yung, Veronica Paterson, Steve
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Published in
Genome biology and evolution
Understanding mechanisms involved in speciation can be challenging, especially when hybridization or introgression blurs species boundaries. In bats resolving relationships of some closely related groups has proven difficult due subtle interspecific variation both in morphometrics and molecular datasets. The endemic South American Histiotus bats, c...
Borges, Rui Boussau, Bastien Szöllősi, Gergely J Kosiol, Carolin
Published in
Genome biology and evolution
Despite the importance of natural selection in species' evolutionary history, phylogenetic methods that take into account population-level processes typically ignore selection. The assumption of neutrality is often based on the idea that selection occurs at a minority of loci in the genome and is unlikely to compromise phylogenetic inferences signi...
Martinez-Gomez, Laura Cerdán-Vélez, Daniel Abascal, Federico Tress, Michael L
Published in
Genome biology and evolution
The mutually exclusive splicing of tandem duplicated exons produces protein isoforms that are identical save for a homologous region that allows for the fine tuning of protein function. Tandem duplicated exon substitution events are rare, yet highly important alternative splicing events. Most events are ancient, their isoforms are highly expressed,...
Koritnik, Neža Gerdol, Marco Šolinc, Gašper Švigelj, Tomaž Caserman, Simon Merzel, Franci Holden, Ellie Benesch, Justin L P Trenti, Francesco Guella, Graziano
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Published in
Genome biology and evolution
Pore-forming toxins are an important component of the venom of many animals. Actinoporins are potent cytolysins that were first detected in the venom of sea anemones; however, they are occasionally found in animals other than cnidarians and are expanded in a few predatory gastropods. Here, we report the presence of 27 unique actinoporin-like genes ...
Yoshida, Masa-Aki Hirota, Kazuki Imoto, Junichi Okuno, Miki Tanaka, Hiroyuki Kajitani, Rei Toyoda, Atsushi Itoh, Takehiko Ikeo, Kazuho Sasaki, Takenori
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Published in
Genome biology and evolution
The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the d...
Fong, Sarah L Capra, John A
Published in
Genome biology and evolution
Thousands of human gene regulatory enhancers are composed of sequences with multiple evolutionary origins. These evolutionarily "complex" enhancers consist of older "core" sequences and younger "derived" sequences. However, the functional relationship between the sequences of different evolutionary origins within complex enhancers is poorly underst...
Hu, Qing-Ling Ye, Yu-Xuan Zhuo, Ji-Chong Huang, Hai-Jian Li, Jun-Min Zhang, Chuan-Xi
Published in
Genome biology and evolution
In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with ...
Ge, Xinyu Jin, Jianfeng Peng, Lang Zang, Haoming Wang, Beixin Sun, Changhai
Published in
Genome biology and evolution
Trichoptera is a highly adapted group of freshwater insects. They are generally more sensitive to dissolved oxygen and water quality than most freshwater organisms, and this sensitivity allows them to be used as reliable biological indicators of water quality. At present, there exists no chromosome-level genome of a hydropsychid species. Cheumatops...
