Phased genome assemblies reveal haplotype-specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae).

While haplotype-specific genetic load shapes the evolutionary trajectory of natural and captive populations, mixed-haplotype assembly and genotyping hindered its characterization in diploids. Herein, we produced two phased genome assemblies of the critically endangered fish Chinese Bahaba (Bahaba taipingensis, Sciaenidae, Teleostei) and resequenced 20 whole genomes to quantify population genetic load at a haplotype level. We identified frame-shifting variants as the most deleterious type, followed by mutations in the 5'-UTR, 3'-UTR and missense mutations at conserved amino acids. Phased haplotypes revealed gene deletions and high-impact deleterious variants. We estimated ~1.12% of genes missing or interrupted per haplotype, with a significant overlap of disrupted genes (30.35%) between haplotype sets. Relative proportions of deleterious variant categories differed significantly between haplotypes. Simulations suggested that purifying selection struggled to purge slightly deleterious genetic load in captive breeding compared to genotyping interventions, and that higher inter-haplotypic variance of genetic load predicted more efficient purging by artificial selection. Combining the knowledge of haplotype-resolved genetic load with predictive modelling will be immensely useful for understanding the evolution of deleterious variants and guiding conservation planning.

Application of cofactors in the regulation of microbial metabolism: A state of the art review.

Cofactors are crucial chemicals that maintain cellular redox balance and drive the cell to do synthetic and catabolic reactions. They are involved in practically all enzymatic activities that occur in live cells. It has been a hot research topic in recent years to manage their concentrations and forms in microbial cells by using appropriate techniques to obtain more high-quality target products. In this review, we first summarize the physiological functions of common cofactors, and give a brief overview of common cofactors acetyl coenzyme A, NAD(P)H/NAD(P)+, and ATP/ADP; then we provide a detailed introduction of intracellular cofactor regeneration pathways, review the regulation of cofactor forms and concentrations by molecular biological means, and review the existing regulatory strategies of microbial cellular cofactors and their application progress, to maximize and rapidly direct the metabolic flux to target metabolites. Finally, we speculate on the future of cofactor engineering applications in cell factories. Graphical Abstract.

The complete mitochondrial genome of Mastacembelus aculeatus (Cypriniformes, Mastacembelidae) from the Pearl River, China.

In this paper, the complete mitochondrial DNA (mtDNA) sequence of Mastacembelus aculeatus was determined. The mitochondrial genome is 16 543 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region as those found in other vertebrates, with the gene identical to that of typical vertebrates. The overall base composition of the heavy strand is 30.0% A, 26.4% T, 14.8% C, and 28.7% G, with an AT bias of 56.49%. Phylogeny of M. aculeatus suggested more close relationship with Mastacembelus armatus and Mastacembelus favus. The complete mitogenome may add new information to existing mitogenome data for Mastacembelidae, providing further information that may contribute to their taxonomy, evolution, and phylogeny.

The mitochondrial genome of Sinibotia robusta of pearl river (Cypriniformes: Cobitidae).

We present the complete mitochondrial genome of Sinibotia robusta in this study. The mitochondrial genome is 16 575 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 31.9% A, 25.7% T, 26.9% C and 15.5% G. Except ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The genus most related to Botia Gray was Leptobotia Bleeker and Parabotia Sauvage, as revealed by phylogenetic relationships derived using a maximum likelihood tree. This mitogenome will help elucidate the morphological systematic complexity and phylogenetic structure of Cobitidae and related species.

Spatial transformation-enabled electromagnetic devices: from radio frequencies to optical wavelengths.

Transformation optics provides scientists and engineers with a new powerful design paradigm to manipulate the flow of electromagnetic waves in a user-defined manner and with unprecedented flexibility, by controlling the spatial distribution of the electromagnetic properties of a medium. Using this approach, over the past decade, various previously undiscovered physical wave phenomena have been revealed and novel electromagnetic devices have been demonstrated throughout the electromagnetic spectrum. In this paper, we present versatile theoretical and experimental investigations on designing transformation optics-enabled devices for shaping electromagnetic wave radiation and guidance, at both radio frequencies and optical wavelengths. Different from conventional coordinate transformations, more advanced and versatile coordinate transformations are exploited here to benefit diverse applications, thereby providing expanded design flexibility, enhanced device performance, as well as reduced implementation complexity. These design examples demonstrate the comprehensive capability of transformation optics in controlling electromagnetic waves, while the associated novel devices will open up new paths towards future integrated electromagnetic component synthesis and design, from microwave to optical spectral regimes.