Kunming Institute of Zoology CAS
Recent publications
Background Previous cytogenetic studies show that the karyotypes of species in Ciconiiformes vary considerably, from 2n = 52 to 78. Their karyotypes include different numbers of small to minute bi-armed chromosomes that have evolved probably by fusions of two ancestral microchromosomes, besides macrochromosomes and dot-like microchromosomes. However, it is impossible to define the inter-species homologies of such small-sized bi-armed chromosomes based on chromosome morphology and banding characteristics. Although painting probes from the chicken ( Gallus gallus , GGA) chromosomes 1–9 and Z have been widely used to investigate avian chromosome homologies, GGA microchromosome probes are rarely used in these studies because most GGA microchromosome probes generated by flow sorting often contain multiple GGA microchromosomes. In contrast, the stone curlew ( Burhinus oedicnemus , BOE, Charadriiformes) has an atypical low diploid chromosome number (42) karyotype and only 4 pairs of dot-like microchromosomes; a set of chromosome-specific painting probes that cover all BOE chromosomes has been generated. To get a genome-wide view of evolutionary chromosomal rearrangements in different lineages of Ciconiiformes, we used BOE painting probes instead of GGA painting probes to analyze the karyotypes of three ciconiiform species belonging to two different families: the eastern grey heron ( Ardea cinerea , ACI, 2n = 64, Ardeidae), the little egret ( Egretta garzetta , EGA, 2n = 64, Ardeidae) and the crested ibis ( Nipponia nippon , NNI, 2n = 68, Threskiornithidae). Results BOE painting probes display the same hybridization pattern on chromosomes of ACI and EGA, while a different hybridization pattern is observed on chromosomes of NNI. BOE autosome probes detected 21 conserved homologous segments and 5 fusions on the sixteen pairs of recognizable chromosomes of ACI and EGA, while 16 conserved homologous segments and 4 fusions were found on the twelve pairs of recognizable chromosomes of NNI. Only a portion of smaller bi-armed chromosomes in the karyotypes of the ciconiiform species could have evolved from fusions of ancestral microchromosomes. In particular BOE 5, which is the result of a fusion between two segments homologous to GGA 7 and 8 respectively, was retained also as either a single chromosome in ACI (ACI 5) and EGA (EGA 5) or had fused with a part of the BOE 10 equivalent in NNI (NNI 5). Conclusion Our painting results indicate that different chromosome rearrangements occur in different ciconiiform lineages. Some of the small-sized bi-armed chromosomes in ACI, EGA and NNI are derived from the fusions of two microchromosomes, indicating that microchromosome fusions play an important role in ciconiiform chromosome evolution. The fusion segment homologous to GGA 7 and 8 is a potential cytogenetic signature that unites Ardeidae and Threskiornithidae.
Objective How do birds navigate their way? It is one of the interesting question about homing pigeons, however the genetic of navigation has reminded as a puzzle. Optic lobe, olfactory bulb, hippocampus and cere were collected for RNA sampling. The generated RNA-seq represent RNA resequencing data for racing homer (homing) pigeon and other rock pigeon breeds. The obtained data set can provide new insight about hippocampus role and GSR contribution to pigeon magnetoreception. Data description To investigate the navigation ability of rock pigeon breeds, 60 whole transcriptome sequence data sets related to homing pigeon, Shiraz tumblers, feral pigeons and Persian high flyers were obtained. RNA extraction was performed from three brain regions (optic lobe, olfactory bulb, hippocampus) and cere. Paired-end 150 bp short reads (Library size 350 bp) were sequenced by Illumina Hiseq 2000. In this way, about 342.1 Gbp and 130.3 Gb data were provided. The whole transcriptome data sets have been deposited at the NCBI SRA database (PRJNA532674). The submitted data set may play critical role to describe the mechanism of navigation ability of rock pigeon breeds.
Purpose Breast cancer is now the most common malignant tumor worldwide. About one-fourth of female cancer patients all over the world suffer from breast cancer. And about one in six female cancer deaths worldwide is caused by breast cancer. In terms of absolute numbers of cases and deaths, China ranks first in the world. The CACA Guidelines for Holistic Integrative Management of Breast Cancer were edited to help improve the diagnosis and comprehensive treatment in China. Methods The Grading of Recommendations Assessment, Development and Evaluation (GRADE) was used to classify evidence and consensus. Results The CACA Guidelines for Holistic Integrative Management of Breast Cancer include the epidemiology of breast cancer, breast cancer screening, breast cancer diagnosis, early breast cancer treatment, advanced breast cancer treatment, follow-up, rehabilitation, and traditional Chinese medicine treatment of breast cancer patients. Conclusion We to standardize the diagnosis and treatment of breast cancer in China through the formulation of the CACA Guidelines.
The Elateridae family (click beetles) represents a highly diverse lineage that possesses a specialized clicking mechanism to startle predators. At present, however, phylogenetic relationships, especially among recognized subfamilies, remain contentious. Mitochondrial genomes (mitogenomes) can help resolve previously intractable phylogenetic relationships using morphological or limited molecular data. Here, we report the complete mitogenome of Pectocera sp. (Elateridae: Dendrometrinae: Oxynopterini), which was 15,962 bp in length and showed a typical gene number and order as most beetle mitogenomes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 noncoding control region (AT-rich region). Comparative genomic analyses showed a high degree of feature similarity among Pectocera sp. and other click beetles. Evolutionary analysis of all PCGs based on the nonsynonymous/synonymous substitution rate ratio (ω) indicated that cox1 and atp8 exhibited the lowest and highest evolutionary rates, respectively, and that the evolutionary rates of all PCGs, except for cox3, nad2, and nad3, were lower than the average ω of click beetles. Phylogenetic analyses based on concatenated and coalescent approaches indicated that Pectocera sp. was sister to Campsosternus auratus in the same tribe (Oxynopterini) with high support. This study offers insight into the mitogenomic basis of Pectocera sp. and provides an important data resource for exploring the taxonomy, phylogeny, and evolution of click beetles.
Bears are fascinating mammals because of their complex pattern of speciation and rapid evolution of distinct phenotypes. Interspecific hybridization has been common and has shaped the complex evolutionary history of bears. In this study, based on the largest population-level genomic dataset to date involving all Ursinae species and recently developed methods for detecting hybrid speciation, we provide explicit evidence for the hybrid origin of Asiatic black bears, which arose through historical hybridization between the ancestor of polar bear/brown bear/American black bears and the ancestor of sun bear/sloth bears. This was inferred to have occurred soon after the divergence of the two parental lineages in Eurasia due to climate-driven population expansion and dispersal. In addition, we found that the intermediate body size of this hybrid species arose from its combination of relevant genes derived from two parental lineages of contrasting sizes. This and alternate fixation of numerous other loci that had diverged between parental lineages may have initiated the reproductive isolation of the Asiatic black bear from its two parents. Our study sheds further light on the evolutionary history of bears and documents the importance of hybridization in new species formation and phenotypic evolution in mammals.
In 2014–2015 and 2019–2021, teleost fishes off Galindez Island (Antarctic Peninsula) were examined for trematodes. Combined morphological and molecular analyses revealed the presence of eight trematode species of four families (Hemiuridae, Lecithasteridae, Opecoelidae, Lepidapedidae) from five fish species. Only adult trematodes were found and all of them are Antarctic endemics with their congeners occurring on other continents. The hemiuroids, Elytrophalloides oatesi (Leiper & Atkinson, 1914), Genolinea bowersi (Leiper & Atkinson, 1914), and Lecithaster macrocotyle Szidat & Graefe, 1967 belong to the most common Antarctic species and together with Lepidapedon garrardi (Leiper & Atkinson, 1914) and Neolebouria georgiensis Gibson, 1976 they were recorded as the least host-specific parasites. The originally sub-Antarctic Neolepidapedon macquariensis Zdzitowiecki, 1993 is a new record for the Antarctic Peninsula and Parachaenichthys charcoti (Vaillant), is a new host record. Neolebouria terranovaensis Zdzitowiecki, Pisano & Vacchi, 1993 is considered a synonym of N. georgiensis because of identical morphology and dimensions. The currently known phylogenetic relationships within the studied families are supported, including the polyphyly of Macvicaria Gibson & Bray, 1982 with the future need to accommodate its Antarctic species in a new genus. The validity of M. georgiana (Kovaleva & Gaevskaja, 1974) and M. magellanica Laskowski, Jezewski & Zdzitowiecki, 2013 needs to be confirmed by further analyses. Genetic sequence data are still scarce from Antarctica, and more studies applying integrative taxonomic approaches and large-scale parasitological examinations of benthic invertebrates are needed to match sequences of larval stages to those of well-characterised adults and to elucidate trematode life-cycles.
Ant colonies with permanent division of labour between castes and highly distinct roles of the sexes have been conceptualized to be superorganisms, but the cellular and molecular mechanisms that mediate caste/sex-specific behavioural specialization have remained obscure. Here we characterized the brain cell repertoire of queens, gynes (virgin queens), workers and males of Monomorium pharaonis by obtaining 206,367 single-nucleus transcriptomes. In contrast to Drosophila, the mushroom body Kenyon cells are abundant in ants and display a high diversity with most subtypes being enriched in worker brains, the evolutionarily derived caste. Male brains are as specialized as worker brains but with opposite trends in cell composition with higher abundances of all optic lobe neuronal subtypes, while the composition of gyne and queen brains remained generalized, reminiscent of solitary ancestors. Role differentiation from virgin gynes to inseminated queens induces abundance changes in roughly 35% of cell types, indicating active neurogenesis and/or programmed cell death during this transition. We also identified insemination-induced cell changes probably associated with the longevity and fecundity of the reproductive caste, including increases of ensheathing glia and a population of dopamine-regulated Dh31-expressing neurons. We conclude that permanent caste differentiation and extreme sex-differentiation induced major changes in the neural circuitry of ants. Using single-cell transcriptomics, the authors generate a brain cell atlas for the pharaoh ant including individuals of different sexes and castes and show changes in cell composition underlying division of labour and reproductive specialization.
Three undescribed jatrophane diterpenoids, named euphpepluones P-R (1–3), were isolated from the whole plant Euphorbia peplus. The structures of these compounds were elucidated by spectroscopic methods. The absolute configuration of 1 was further assigned by X-ray crystallographic analysis. All compounds were evaluated for bioactivity towards autophagic flux by flow cytometry using HM mCherry-GFP-LC3 cells. Compounds 2 and 6 exhibited significant inhibition of autophagic flux.
Papilio machaon was assigned as the type species for all butterflies by Linnaeus and P. bianor is a congener but exhibits a great difference in morphology (especially larva and adult color pattern) and larval host plants from P. machaon. Thus, they are the ideal models to investigate genetic mechanisms underlying morphology and plasticity between congeners. The reference genomes of both species were dissected in our previous studies, but little is known about their regulatory genome and the epigenetic regulation of gene expression throughout developmental stages. Here, we profiled the chromatin accessibility and gene expression of three developmental stages (the 4th instar larva [L4], the 5th instar larva [L5], and pupa [P]) using transposase accessible chromatin sequencing (ATAC-seq) and RNA-seq. Results showed that many accessible chromatin peaks were identified at three developmental stages (peak number, P. machaon: 44,977 [L4], 36,919 [L5], 47,147 [P]; P. bianor: 20,341 [L4], 44,668 [L5], 62,249 [P]). Moreover, the number of differentially accessible peaks and differentially expressed genes between larval stages of each butterfly species are significantly fewer than that between larval and pupal stages, suggesting a higher similarity within larvae and a significant difference between larvae and pupae. This study added the annotated information of chromatin accessibility genome-wide of the two papilionid species and will promote the investigation of gene regulation in butterfly evolution.
Ten new icetexane diterpenoids, salpratins E–N (1–10) and a known analogue (11) were characterized from Salvia prattii Hemsl. Structurally, 1 is the first 19(4→3)-abeo-icetexane diterpenoid featuring with a 6/7/6 ring system. The structures of isolated compounds were determined by comprehensive analyses of spectroscopic data, ECD calculation, and single-crystal X-ray diffraction. Biological studies initially revealed that 1, 7, 10, and 11 are notable Cav3.2 T-type Ca²⁺ channel (TTCC) inhibitors with IC50 values of 2.9, 5.1, 2.3, and 3.2 μM, respectively. Five icetexane related derivatives (13–17) were synthesized from an abietane type precursor, (+)-carnosic acid (12), for the purpose of overcoming the poor water solubility of aforementioned active compounds and further investigating diverse diterpenes with valuable activity. Among them, 13 and 14 showed potent inhibitions on Cav3.2, having IC50 values of 6.7 and 2.4 μM. Significantly, they exhibited dose-dependent (1, 3, and 10 mg/kg) and comparable analgesic effects as that of Z944, a TTCCs inhibitor under clinical trial for pain management, in the mouse acetic acid writhing test. These findings further enrich structural diversity and bioactivity of Salvia diterpenoids, as well as provide promising structural templates for the development of Cav3.2 analgesics.
Metastasis is the leading cause of cancer-related death. The interactions between circulating tumor cells and endothelial adhesion molecules in distant organs is a key step during extravasation in hematogenous metastasis. Surgery is a common intervention for most primary solid tumors. However, surgical trauma-related systemic inflammation facilitates distant tumor metastasis by increasing the spread and adhesion of tumor cells to vascular endothelial cells (ECs). Currently, there are no effective interventions to prevent distant metastasis. Here, we show that HECTD3 deficiency in ECs significantly reduces tumor metastasis in multiple mouse models. HECTD3 depletion downregulates expression of adhesion molecules, such as VCAM-1, ICAM-1 and E-selectin, in mouse primary ECs and HUVECs stimulated by inflammatory factors and inhibits adhesion of tumor cells to ECs both in vitro and in vivo. We demonstrate that HECTD3 promotes stabilization, nuclear localization and kinase activity of IKKα by ubiquitinating IKKα with K27- and K63-linked polyubiquitin chains at K296, increasing phosphorylation of histone H3 to promote NF-κB target gene transcription. Knockout of HECTD3 in endothelium significantly inhibits tumor cells lung colonization, while conditional knockin promotes that. IKKα kinase inhibitors prevented LPS-induced pulmonary metastasis. These findings reveal the promotional role of the HECTD3-IKKα axis in tumor hematogenous metastasis and provide a potential strategy for tumor metastasis prevention.
Oakleaf butterflies in the genus Kallima have a polymorphic wing phenotype, enabling these insects to masquerade as dead leaves. This iconic example of protective resemblance provides an interesting evolutionary paradigm that can be employed to study biodiversity. We integrated multi-omic data analyses and functional validation to infer the evolutionary history of Kallima species and investigate the genetic basis of their variable leaf wing patterns. We find that Kallima butterflies diversified in the eastern Himalayas and dispersed to East and Southeast Asia. Moreover, we find that leaf wing polymorphism is controlled by the wing patterning gene cortex, which has been maintained in Kallima by long-term balancing selection. Our results provide macroevolutionary and microevolutionary insights into a model species originating from a mountain ecosystem.
Wound treatment remains one of the most prevalent healthcare issues. Tylotoin is a skin repair peptide identified from salamander (Tylototriton verrucosus) and exhibits skin wound healing properties. Noticeably, the easy degradation and frequent administration limit its application in wound healing. Chitosan (CS) -PLGA-Tylotoin nanoparticles (CPT NPs) were prepared to circumvent this limitation and deliver Tylotoin for the promotion of the healing of skin wounds. Results showed that optimized CPT NPs particle size, zeta potential, encapsulation efficiency and drug loading were 297.80 ± 5.37 nm, 20.37 ± 0.83 mV, 81.00 % and 1.74 %, respectively. In vitro, CPT NPs exhibited good antibacterial properties and biocompatibility and persistently promoted the cell migration of HaCaT cells and HUVECs due to the long-term sustained release of Tylotoin within 14 days (64.81 %). In vivo, the scarless healing of skin wound promotion was evaluated in mouse back full-thickness wound models. We demonstrated that mouse back full-thickness wounds topically treated with CPT NPs once every two weeks exhibited better scarless healing than those treated with Tylotoin once daily. We envision that CPT NPs, as a Tylotoin delivery platform might, may be potentially utilized to in skin wounds healing in clinics in the future.
Cellular senescence is a dynamic process driven by epigenetic and genetic changes. Although some transcriptomic signatures of senescent cells have been discovered, how these senescence-related signals change over time remains largely unclear. Here, we profiled the transcriptome dynamics of human dermal fibroblast (HDF) cells in successive stages of growth from proliferation to senescence. Based on time-series expression profile analysis, we discovered four trajectories (C1, C2, C3, C4) that are dynamically expressed as senescence progresses. While some genes were continuously up-regulated (C4) or down-regulated (C2) with aging, other genes did not change linearly with cell proliferation, but remained stable until entering the senescent state (C1, C3). Further analysis revealed that the four modes were enriched in different biological pathways, including regulation of cellular senescence. These findings provide a new perspective on understanding the dynamic regulatory mechanism of cellular senescence.
Background Breast cancer is the most common malignancy in women worldwide, and its treatment largely depends on mastectomy. Patients after mastectomy suffer from crippled body image, self-esteem, and quality of life. Post-mastectomy breast reconstruction can improve patients’ psychosocial health. Although silicone and fat have been widely used for breast reconstruction, they have remarkable limitations. Our study aimed to establish an improved method for breast reconstruction from human-induced pluripotent stem cells (iPSCs). Methods We used a two-step procedure to induce mammary-like organoids (MLOs) from iPSCs and applied transcriptome sequencing to analyze the gene expression profiles during the development process from embryoid bodies (mEBs) to MLOs. Moreover, we evaluated the in vitro effect of fibroblasts cell line HFF (human foreskin fibroblasts) on the size and morphology of MLOs and explored the in vivo effect of HFF on regeneration rate of MLOs. Results MLOs had a similar gene expression profile and morphogenesis as the normal mammary glands. Furthermore, the addition of HFF increases the branching ratio and organoid diameters and facilitates the formation of multiple cell layers duct-like structures in MLOs in vitro. Finally, orthotopical transplantation of the MLOs to cleared mammary gland fad pad of NSG mice showed that HFF increases the formation of mammary gland-like structures. Conclusions Fibroblasts facilitate iPSC-derived MLOs to generate mammary gland-like structures in both in vitro and in vivo conditions. Our findings lay a foundation for breast reconstruction by using iPSCs.
Background Cannabis is an important industrial crop species whose fibre, seeds, flowers and leaves are widely used by humans. The study of cannabinoids extracted from plants has been popular research topic in recent years. China is one of the origins of cannabis and one of the few countries with wild cannabis plants. However, the genetic structure of Chinese cannabis and the degree of adaptive selection remain unclear. Results The main morphological characteristics of wild cannabis in China were assessed. Based on whole-genome resequencing SNPs, Chinese cannabis could be divided into five groups in terms of geographical source and ecotype: wild accessions growing in the northwestern region; wild accessions growing in the northeastern region; cultivated accessions grown for fibre in the northeastern region; cultivated accessions grown for seed in northwestern region, and cultivated accessions in southwestern region. We further identified genes related to flowering time, seed germination, seed size, embryogenesis, growth, and stress responses selected during the process of cannabis domestication. The expression of flowering-related genes under long-day (LD) and short-day (SD) conditions showed that Chinese cultivated cannabis is adapted to different photoperiods through the regulation of Flowering locus T-like (FT-like) expression. Conclusion This study clarifies the genetic structure of Chinese cannabis and offers valuable genomic resources for cannabis breeding.
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273 members
Xueyan Li
  • State Key Laboratory of Genetic Resources and Evolution
Bing Su
  • State Key Laboratory of Genetic Resources and Evolution
Kong-wah Sing
  • State Key Laboratory of Genetic Resources and Evolution
Xue-Long Jiang
  • State Key Laboratory of Genetic Resources and Evolution
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Kunming, China