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Topmouth culter (Culter alburnus) is an ecologically and economically important species belonging to the subfamily Culterinae that is native to and widespread in East Asia. Intraspecific variation of semi‐buoyant and adhesive eggs in topmouth culter provides an ideal opportunity to investigate the genetic mechanisms of spawning habits underlying the adaptive radiation of cyprinids in East Asia. In this study, we present a chromosome‐level genome assembly of topmouth culter and re‐sequenced 158 individuals from six locations in China covering three geographical groups and two egg type variations. The topmouth culter genome size was 1.05 Gb, with a contig N50 length of 17.8 Mb and anchored onto 24 chromosomes. Phylogenetic analysis showed that the divergence time of the Culterinae was coinciding with the time of initiation of the Asian monsoon intensification. Gene family evolutionary analysis indicated that the expanded gene families in topmouth culter were associated with dietary adaptation. Population‐level genetic analysis indicated clear differentiation among the six populations, which were clustered into three distinct clusters, consistent with their geographical divergence. The historical effective population size of topmouth culter correlated with the Tibetan Plateau uplifting according to the demographic history reconstruction. A selective sweep analysis between adhesive and semi‐buoyant egg populations revealed the genes associated with the hydration and adhesiveness of eggs, indicating divergent selection towards different hydrological environments. This study offers a high‐resolution genetic resource for further studies on evolutionary adaptation, genetic breeding and conservation of topmouth culter, providing insights into the molecular mechanisms for egg type variation of East Asian cyprinids. [ABSTRACT FROM AUTHOR]

The zebrafish (Danio rerio) is one of the most widely used model organisms for studying vertebrate gene function and human disease, given the 70% conserved protein‐coding genes between zebrafish and human. Two of the most common laboratory zebrafish strains are Tuebingen and AB. Despite the fact that the zebrafish reference genome is derived from the Tuebingen strain, the AB strain is still widely used although a high‐quality genome comparable to Tuebingen is lacking. Here, we report a 1.40‐Gb representative de novo genome assembly of the AB strain (DrAB1), with contig N50 length of 21 Mb, by integrating Illumina short‐read sequencing, Nanopore long‐read sequencing and HiC‐based chromatin mapping. Compared with the published zebrafish Zv11 reference genome (GRCz11), this genome assembly shows considerable improvements in both contiguity and completeness. In addition, substantial structural differences and extensive sequence divergence of unprecedented resolution have been uncovered, especially with respect to 9,029,929 single nucleotide polymorphisms, 2,376,812 InDels, 32,623 insertions, 22,089 deletions and 220 inversions, which constitute ~2.6% of the DrAB1 genome. Many of these variants may have potential functional effects on phenotype, which should be considered in further experimental designs. Consequently, our study provides additional genomic resources and a high‐resolution structural variation map based on whole‐genome alignment for the zebrafish community, which could also be an indispensable reference genome from a model species in future research on fish phylogenetic genomics, comparative genomics and adaptive evolution. [ABSTRACT FROM AUTHOR]

Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448.52‐Mb genome assembly with contig N50 length of 5.53 Mb by integrating Illumina short‐read sequencing, Nanopore long‐read sequencing and HiC‐based chromatin map. Demographic history reconstruction of the butterfly hillstream loach reveals that the population dynamics is correlated with the different stages of uplifting of the Tibetan Plateau. Comparative genomic analysis finds evidence of six keratin genes in butterfly hillstream loach evolving under positive selection. Within these genes, two keratin genes exhibit species‐specific and divergent amino acid changes, suggesting a role in the formation of the unculi. Additionally, a series of positively selected genes, rapid evolving genes, specific variant genes and expanded gene families are found, including genes related to Hedgehog, Notch and BMP pathways, which may be involved in craniofacial development. These findings may have important implications for understanding the genetic basis of phenotypic adaptation to torrential mountain stream life. [ABSTRACT FROM AUTHOR]

The endangered Aral barbel Luciobarbus brachycephalus is endemic to the water systems of the Caspian Sea and Aral Sea. Given the scarcity of genetic data for the species, we present a draft assembly based on PacBio long-read sequencing technology. Approximate 299.4 Gb of long reads representing 166× of the estimated genome size were generated, and the final assembly was composed of 653 contigs totaling approximately 1,698.3 Mb, with a contig N50 length of 4.5 Mb. A total of 807.6 Mb represented approximately 47.6% of the assembly and were identified as repeats. Fifty-four thousand and six hundred possible protein genes were predicted, among which 50,727, representing approximately 92.9%, could be annotated by at least one database. Evolutionary analysis showed that L. brachycephalus and Labeo rohita diverged by approximately 42.6 Ma, and the obvious expansion of gene families residing in the L. brachycephalus genome may be attributed to the specific whole-genome duplication of the species. The first genome assembly of L. brachycephalus can not only provide a foundation for genetic conservation and molecular breeding of this species but also contribute to comparative analyses of genome biology and evolution within Cyprinidae. [ABSTRACT FROM AUTHOR]

• We reported the first complete mitochondrial genome sequence of N. hainanensis. • Highly conserved genome organization and phylogeny between N. hainanensis and P. glenii. • The divergence of Neodontobutis and Perccotus was later than that of Odontobutis. • Stronger selective constraints in PCGs for P. glenii compared with other Odontobitidae. To investigate the molecular evolution of mitochondrial genomes among the family Odontobutidae, the complete mitochondrial genomes of Neodontobutis hainanensis and Perccottus glenii were sequenced and compared with seven odontobutids species. The genome organization, base composition, codon usage, and gene arrangement of N. hainanensis exhibited high similarity to P. glenii compared to those of other Odontobutidae species. Reconstructed phylogenetic analyses of Odontobutidae strongly supported that Neodontobutis and Perccottus formed a unifying group sister to Odontobutis. Our molecular dating time revealed that the two species diverged approximately 21.7 Ma during Miocene, later than that of Odontobutis. Selection analyses showed stronger selective constraints in mitochondrial genes for P. glenii. However, two positively selected sites in NADH4 and NADH6 genes were respectively detected in N. hainanensis and P. glenii , indicating that they might evolve different metabolic performance in response to the contrasting environments. [ABSTRACT FROM AUTHOR]

The Aral barbel (Luciobarbus brachycephalus) is an important commercial species in Aral sea basin and its population is decreasing rapidly. However, the genetic resource available for this species as well as other barbels in barbinae is limited. In this study, we described the complete mitochondrial genome of L. brachycephalus. The mitochondrial genome is 16,603 bp in length containing 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 tRNAs and a control region. The overall base composition of L. brachycephalus mtDNA is: 31.2% for A, 27.8% for C, 16.5% for G, 24.4% for T. [ABSTRACT FROM AUTHOR]

Lungfishes are the closest extant relatives of tetrapods and preserve ancestral traits linked with the water-to-land transition. However, their huge genome sizes have hindered understanding of this key transition in evolution. Here, we report a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 Mb and 2.81 Gb, respectively. The large size of the lungfish genome is due mainly to retrotransposons. Genes with ultra-long length show similar expression levels to other genes, indicating that lungfishes have evolved high transcription efficacy to keep gene expression balanced. Together with transcriptome and experimental data, we identified potential genes and regulatory elements related to such terrestrial adaptation traits as pulmonary surfactant, anxiolytic ability, pentadactyl limbs, and pharyngeal remodeling. Our results provide insights and key resources for understanding the evolutionary pathway leading from fishes to humans. • Chromosome-level assembly of the largest vertebrate genome reported to date • Continuous expansion of transposons contributed to the huge lungfish genome • Genetic changes enhanced respiration, locomotion, and anxiolytic ability • Three genetic innovation steps from bony fishes to lungfishes and then tetrapods Genome assembly and analysis of the massive African lungfish genome has shed light on genetic innovations required for the water-to-land transition [ABSTRACT FROM AUTHOR]