Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family

The Huaibei grey donkey (HGD) is an endangered species and a vital native breed in Anhui Province, China. However, its complete mitogenome, phylogeny, and maternal origin remain unclear. The objectives of this study were to detect the genetic diversity of the HGD and investigate its phylogenetic relationship with other breeds to inform conservation management. The complete mitogenome of the HGD was sequenced through next-generation sequencing, and the most variable region in the mitochondrial DNA displacement-loop (D-loop) was amplified via a polymerase chain reaction (PCR). Next, we used the median-joining network (MJN) to calculate the genetic relationships among populations and the neighbor-jointing method to build a phylogenetic tree and speculate as to its origin. The results showed that the mitogenome contains 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. Analyzing the D-loop region of the HGDs, we identified 23 polymorphic sites and 11 haplotypes. The haplotype and nucleotide diversity were 0.87000 (Hd) and 0.02115 (Pi), respectively. The MJN analysis indicated that the HGD potentially has two maternal lineages, and phylogenetic analysis indicated that the Somali lineage could be the most probable domestication center for this breed. Therefore, our mitogenome analysis highlights the high genetic diversity of the HGD, which may have originated from the Somali wild ass, as opposed to the Asian wild ass. This study will provide a useful resource for HGD conservation and breeding

1D to 2D Growth of NaF Crystals in Photothermo-Refractive Glasses

International audienceThe precipitation of NaF crystals with a low refractive index only in the UV exposure region is essential to obtain high refractive index change in photothermo-refractive (PTR) glass for producing high-performance volume Bragg gratings (VBGs). However, the precision control of the growth of NaF crystals in the UV exposure region of PTR glass remains challenging. In this work, the effect of Al2O3 on the crystallization behavior of NaF crystals in PTR glass was investigated using the nonisothermal crystallization kinetic method. After photothermal-induced nucleation, the crystallization activation energy (Ea) of PTR glass decreased first and then increased with the rise in the Al2O3 content. The appropriate amount of Al2O3 (4 mol %) is helpful for reducing the Ea and promoting the formation of NaF crystals. The crystal growth index (n) and crystal growth dimension (m) suggest that the crystallization behavior of NaF crystals was photothermally induced nucleation and crystallization of 1D growth. The increasing trend of the m values indicates that the crystals tend to transit from 1D to 2D growth with the increase in Al2O3 content. When Al2O3 is 6 mol %, n equals m + 1, which implies the NaF crystals crystallize spontaneously rather than growing on the Ag nuclei. The crystals observed using scanning electron microscopy images showed that irregular precursors appeared first and then grew into needle-like crystals. When the NaF crystals grew sufficiently long, they transformed into lamellar crystals. This work elucidates the crystallization process of NaF crystals in PTR glass and provides guidance for the production of high-performance VBGs

Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9

Genome editing by the well-established CRISPR/Cas9 technology has greatly facilitated our understanding of many biological processes. However, a complete whole-genome knockout for any species or model organism has rarely been achieved. Here, we performed a systematic knockout of all the genes (1333) on Chromosome 1 in zebrafish, successfully mutated 1029 genes, and generated 1039 germline-transmissible alleles corresponding to 636 genes. Meanwhile, by high-throughput bioinformatics analysis, we found that sequence features play pivotal roles in effective gRNA targeting at specific genes of interest, while the success rate of gene targeting positively correlates with GC content of the target sites. Moreover, we found that nearly one-fourth of all mutants are related to human diseases, and several representative CRISPR/Cas9-generated mutants are described here. Furthermore, we tried to identify the underlying mechanisms leading to distinct phenotypes between genetic mutants and antisense morpholino-mediated knockdown embryos. Altogether, this work has generated the first chromosome-wide collection of zebrafish genetic mutants by the CRISPR/Cas9 technology, which will serve as a valuable resource for the community, and our bioinformatics analysis also provides some useful guidance to design gene-specific gRNAs for successful gene editing