Cetaceans evolution: insights from the genome sequences of common minke whales

Abstract

BackgroundWhales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water.ResultsWe present four common minke whale (Balaenoptera acutorostrata) genomes with depth of ×13 ~ ×17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 – 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales.ConclusionsThis whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1213-1) contains supplementary material, which is available to authorized users.

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

“…Our data showed that ATZ treatment does not affect the relative proportion of cell types in the testes (Supplementary Figure S3A–E). Furthermore, we did not observe any significant changes in body or organ weights (Supplementary Figure S4A and B) or any decrease in testosterone and Follicle-stimulating hormone (FSH) levels (Supplementary Figure S4C), which are the expected outcomes of ATZ treatment in adult males (42). We cannot exclude the possibility that a subtle phenotype exists in F3 ATZ-lineage males that is not detectable by these methods.…”

“…Nr5a2 is highly expressed during development and the knockdown of Nr5a2 in zygote leads to downregulation of Pou5f1 expression (24). In our previous work we showed that mice exposed to ATZ have a higher number of H3K4me3 peaks that contain Nr5a2 motif (42). It has also been shown before that ATZ activates NR5A receptors (35).…”

“…Chromatin immunoprecipitation was conducted as previously described (42). An Illumina Hiseq2000 Genome Analyzer was used to perform massively parallel 50-bp sequencing in Single End mode.…”

“…Recent study showed that ATZ also affects DNA methylation in plants (38). In mammals, ATZ exposure affects many tissues, including testes (39–42), ovaries (43–47), brain (48,49), liver (50–54) and the presence of low dose metabolites of ATZ is associated with low birth weight in human (55). …”

A transcriptional view on somatic embryogenesis

“…Although we have a good idea about the types of cells that form somatic embryos in vitro (Filonova, Bozhkov, & Arnold, 2000; Toonen et al., 1994) and the cellular characteristics of these cells (Emons, 1994; Verdeil et al., 2007; Yeung, 1995), the process remains largely undescribed at the molecular level. High throughput expression analyses have been used to identify characteristics of embryogenic explants (Salvo, Hirsch, Buell, Kaeppler, & Kaeppler, 2014; Trontin, Klimaszewska, Morel, Hargreaves, & Lelu‐Walter, 2016; Wickramasuriya & Dunwell, 2015; Yang et al., 2012), but most studies use whole explants, which contain a complex mixture of tissues and cell types, making it difficult to specifically assign molecular identities to embryogenic cells. In situ gene expression analyses would help to resolve the sometimes contradictory relationship between expression of developmental marker genes and cell fate in different culture systems (Miguel & Marum, 2011) and provide a more exact description of when and how embryogenic cells are formed in culture (Li et al., 2014; Soriano et al., 2014).…”