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BackgroundGenesis of novel gene regulatory modules is largely responsible for morphological and functional evolution. De novo generation of novel cis-regulatory elements (CREs) is much rarer than genomic events that alter existing CREs such as transposition, promoter switching or co-option. Only one case of de novo generation has been reported to date, in fish and without involvement of phenotype alteration. Yet, this event likely occurs in other animals and helps drive genetic/phenotypic variation.ResultsUsing a porcine model of spontaneous hearing loss not previously characterized we performed gene mapping and mutation screening to determine the genetic foundation of the phenotype. We identified a mutation in the non-regulatory region of the melanocyte-specific promoter of microphthalmia-associated transcription factor (MITF) gene that generated a novel silencer. The consequent elimination of expression of the MITF-M isoform led to early degeneration of the intermediate cells of the cochlear stria vascularis and profound hearing loss, as well as depigmentation, all of which resemble the typical phenotype of Waardenburg syndrome in humans. The mutation exclusively affected MITF-M and no other isoforms. The essential function of Mitf-m in hearing development was further validated using a knock-out mouse model.ConclusionsElimination of the MITF-M isoform alone is sufficient to cause deafness and depigmentation. To our knowledge, this study provides the first evidence of a de novo CRE in mammals that produces a systemic functional effect.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-016-0273-2) contains supplementary material, which is available to authorized users.

The Cephalopoda are a group of highly diverse marine species in the phylum Mollusca, which are distributed worldwide. They have evolved some vertebrate-like biological traits and exhibit complicated behavioural repertoires. Thus, they are interesting species for studying the mechanisms of evolutionary convergence, innovational functional structures and evolutionary adaptation to a highly active, predatory lifestyle in diverse marine environments. Despite the evolutionary placement and biological significance of cephalopods, genomic data on these organisms remain limited. Here, we assembled a chromosome-level genome of a female East Asian common octopus (Octopus sinensis) by combining Pacific Bioscience (PacBio) single-molecule realtime sequencing, Illumina paired-end sequencing and Hi-C technology. An O. sinensis genome of 2.72 Gb was assembled from a total of 245.01 Gb high-quality PacBio sequences. The assembled genome represents 80.2% completeness (BUSCO) with a contig N50 of 490.36 Kb and a scaffold N50 of 105.89 Mb, showing a considerable improvement compared with other sequenced cephalopod genomes. Hi-C scaffolding of the genome resulted in the construction of 30 pseudochromosomes in Cephalopoda, representing 96.41% of the assembled sequences. The genome contained 42.26% repeat sequences and 5,245 noncoding RNAs. A total of 31,676 protein-coding genes were predicted, of which 82.73% were functionally annotated. The comparative genomic analysis identified 17,020 orthologous gene families, including 819 unique gene families and 629 expanded gene families. This genomic information will be an important molecular resource for further investigation of biological function and evolutionary adaptations in octopuses, and facilitate research into their population genetics and comparative evolution. K E Y W O R D S chromosome-level genome assembly, genome annotation, Octopus sinensis, PacBio sequencing | 1573 LI et aL. Group Contig number Contig length (bp)

The greenfin horse-faced filefish, Thamnaconus septentrionalis, is a valuable commercial fish species that is widely distributed in the Indo-West Pacific Ocean. This fish has characteristic blue-green fins, rough skin and a spine-like first dorsal fin. Thamnaconus septentrionalis is of conservation concern because its population has declined sharply, and it is an important marine aquaculture fish species in China. Genomic resources for the filefish are lacking, and no reference genome has been released. In this study, the first chromosome-level genome of T. septentrionalis was constructed using nanopore sequencing and Hi-C technology. A total of 50.95 Gb polished nanopore sequences were generated and were assembled into a 474.31-Mb genome, accounting for 96.45% of the estimated genome size of this filefish. The assembled genome contained only 242 contigs, and the achieved contig N50 was 22.46 Mb, a surprisingly high value among all sequenced fish species. Hi-C scaffolding of the genome resulted in 20 pseudochromosomes containing 99.44% of the total assembled sequences. The genome contained 67.35 Mb of repeat sequences, accounting for 14.2% of the assembly. A total of 22,067 protein-coding genes were predicted, 94.82% of which were successfully annotated with putative functions. Furthermore, a phylogenetic tree was constructed using 1,872 single-copy orthologous genes, and 67 unique gene families