Chromosome-level genome provides insight into the evolution and conservation of the threatened goral (Naemorhedus goral).

BACKGROUND: Gorals Naemorhedus resemble both goats and antelopes, which prompts much debate about the intragenus species delimitation and phylogenetic status of the genus Naemorhedus within the subfamily Caprinae. Their evolution is believed to be linked to the uplift of the Qinghai-Tibet Plateau (QTP). To better understand its phylogenetics, the genetic information is worth being resolved. RESULTS: Based on a sample from the eastern margin of QTP, we constructed the first reference genome for Himalayan goral Naemorhedus goral, using PacBio long-read sequencing and Hi-C technology. The 2.59 Gb assembled genome had a contig N50 of 3.70 Mb and scaffold N50 of 106.66 Mb, which anchored onto 28 pseudo chromosomes. A total of 20,145 protein-coding genes were predicted in the assembled genome, of which 99.93% were functionally annotated. Phylogenetically, the goral was closely related to muskox on the mitochondrial genome level and nested into the takin-muskox clade on the genome tree, rather than other so-called goat-antelopes. The cladogenetic event among muskox, takin and goral occurred sequentially during the late Miocene (~ 11 - 5 Mya), when the QTP experienced a third dramatic uplift with consequent profound changes in climate and environment. Several chromosome fusions and translocations were observed between goral and takin/muskox. The expanded gene families in the goral genome were mainly related to the metabolism of drugs and diseases, so as the positive selected genes. The Ne of goral continued to decrease since ~ 1 Mya during the Pleistocene with active glaciations. CONCLUSION: The high-quality goral genome provides insights into the evolution and valuable information for the conservation of this threatened group.

High-fat diet aggravates the severity of the in vitro posttraumatic osteoarthritis model through macrophagic FBW7.

Osteoarthritis (OA) is a prevalent and distressing chronic degenerative joint disorder characterized by damaged articular cartilage and inflamed joints. Among risk factors, obesity has emerged as the second-leading contributor to OA after age. Obesity is believed to play a key role in the development and progression of OA. This study aimed to investigate the role and underlying mechanisms of high-fat diet (HFD)-induced obesity in the development of OA. Our findings revealed that HFD could aggravate the destabilization of the medial meniscus (DMM)-induced damage in the mouse model of obesity. Similar results were observed when macrophages obtained from HFD-fed mice were cocultured with cartilage and subsequently stimulated with interleukin-1ß (IL-1ß). Mechanistically, we observed a decrease in the expression of intraarticular macrophagic FBW7, which was implicated in the aggravation of OA in the HFD-fed animal. Furthermore, by modulating the immune status of macrophages, we found that reversing the macrophagic expression of FBW7 in these cells can alleviate the chondrocyte damage. In conclusion, this study provides novel insights into the pathological mechanisms underlying HFD-related OA development by identifying the role of FBW7 in synovial macrophages. These findings open up new avenues for research and therapeutic interventions targeting HFD-related OA.

Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish.

Triploids are rare in nature because of difficulties in meiotic and gametogenic processes, especially in vertebrates. The Carassius complex of cyprinid teleosts contains sexual tetraploid crucian carp/goldfish (C. auratus) and unisexual hexaploid gibel carp/Prussian carp (C. gibelio) lineages, providing a valuable model for studying the evolution and maintenance mechanism of unisexual polyploids in vertebrates. Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each set is derived from a different ancestor. Resequencing data from different strains of C. gibelio show that unisexual reproduction has been maintained for over 0.82 million years. Comparative genomics show intensive expansion and alterations of meiotic cell cycle-related genes and an oocyte-specific histone variant. Cytological assays indicate that C. gibelio produces unreduced oocytes by an alternative ameiotic pathway; however, sporadic homologous recombination and a high rate of gene conversion also exist in C. gibelio. These genomic changes might have facilitated purging deleterious mutations and maintaining genome stability in this unisexual amphitriploid fish. Overall, the current results provide novel insights into the evolutionary mechanisms of the reproductive success in unisexual polyploid vertebrates.

Mitochondrial genome and phylogenetic relationship of Gymnocypris eckloni (Schizothoracinae) in Qaidam river basin.

Genomic data can improve our understanding on the phylogenetic relationship among Tibetan highland fishes. The whole mitochondrial genome of Gymnocypris eckloni generated in this study is 16,784 bp in length, containing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and one non-coding control region (D-Loop). Phylogenetic analysis recovers a non-monophyetic population of G. eckloni in the Qaidam basin, representing two distinct lineages designated 'Qiadam A' and 'Qaidam B', within Qaidam A clustering with Chuanchia labiosa and Schizopygopisis pylzovi captured in the Yellow River and Qaidam B grouping with G. eckloni from the Yellow River. Our research may helpful to further reconsideration of clearer taxonomy and improvement of biodiversity conservation strategy of Tibetan highland fishes.

A new species of Triplophysa (Cypriniformes, Nemacheilidae) from Weihe River in Gansu Province, China.

A new species of Tibetan loach, Triplophysa weiheensis sp. nov., is described from the Weihe River in Gansu Province, China, based on morphological and molecular analyses. The new species can be distinguished from all known congeners by a unique combination of the following characters: scaleless; snout abruptly sloping downward, anterior to anterior nostril; lower jaw crescentic, not sharp; body without obvious mottling; lateral line interrupted on posterior trunk at pelvic-fin distal extremity; caudal-peduncle length 2.0-2.7 times its depth; branched rays of pectoral fin 10-11; branched rays of pelvic fin 5-6; inner gill rakers on 1 st gill arch 14-16; vertebrae 4+34-36; intestine with 6-7 loops, length ca. 1.8 times SL ( n=3); bony capsule of air bladder small and thin; posterior chamber of air bladder absent.

Taxonomic status of a population of Gymoncypris waddelli Regan, 1905 (Cypriniformes: Schizothoracinae) distributed in Pengqu River, Tibet, China.

Gymnocypris waddelli, a highland cold-water fish, is distributed among rivers and lakes of the southern Qinghai-Tibet Plateau. Although previously described as G. waddelli, specimens from the Pengqu River are morphologically distinguishable from those from Lake Yamzhog Yumco, which is the type locality of G. waddelli. We investigated morphological variations of G. waddelli specimens from Pengqu River and Lake Yamzhog Yumco using not only traditional morphological methods but also newly-developed geometric morphometric analysis; furthermore, mitochondrial Cytochrome b (Cyt b) gene analysis was employed to explore the phylogenetic position of the Pengqu River population. Our morphological analyses suggested that G. waddelli from the Pengqu River had an obtuse snout, nearly straight oral fissure, shorter lower jaw than upper jaw, broad mouth and sparse inside gill rakers of the first arch relative to the Lake Yamzhog Yumco population. The strongly supported monophyly of Pengqu population according to mitochondrial datasets was obtained, indicating genetic differences between Pengqu River and Lake Yamzhog Yumco populations. Given their substantial genetic and morphological divergence, specimens from Pengqu River warrant recognition as a distinct species, here described and named Gymnocypris pengquensis.