2022 Vol. 43, No. 3
2022, 43(3): 301-318. doi: 10.24272/j.issn.2095-8137.2021.397
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Hyperproteinemia is a metabolic disorder associated with increased plasma protein concentration (PPC) and is often clinically complicated by malignant diseases or severe infections. At present, however, research on the molecular mechanism underlying high PPC (HPPC) is scant. Here, an animal model of primary hyperproteinemia was constructed in an invertebrate (Bombyx mori) to investigate the effects of HPPC on circulating blood cells. Results showed that HPPC affected blood cell homeostasis, leading to increased reactive oxygen species levels, and induced programmed cell death dependent on the endoplasmic reticulum-calcium ion signaling pathway. HPPC induced the proliferation of blood cells, mainly granulocytes, by activating the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway. Supplementation with the endocrine hormone active substance 20E significantly reduced the impact of HPPC on blood cell homeostasis. Thus, we identified a novel signaling pathway by which HPPC affects blood cell homeostasis, which differs from hyperglycemia, hyperlipidemia, and hypercholesterolemia. In addition, we showed that down-regulation of gene expression of the hematopoietic factor Gcm could be used as a potential early detection indicator for hyperproteinemia.
Chinese tongue sole (Cynoglossus semilaevis) is an economically important marine fish species with a ZZ/ZW sex determination mechanism, which can be influenced by temperature. Alternative splicing (AS) is an important mechanism regulating the expression of genes related to sex determination and gonadal differentiation, but has rarely been reported in fish. In this study, to explore the molecular regulatory mechanisms of sex determination and gonadal differentiation, we combined isoform and RNA sequencing (Iso-Seq and RNA-Seq) to perform transcriptome profiling of male and female gonads in C. semilaevis. In total, 81 883 and 32 341 full-length transcripts were obtained in males and females, respectively. A total of 8 279 AS genes were identified, including 2 639 genes showing differential AS (DAS) between males and females. Many intersecting DAS genes and differentially expressed genes (DEGs) were enriched in the meiotic cell cycle pathway, and genes related to gonadal differentiation, such as esrrb and wt1a, were found to have sex-specific isoforms. Thus, this study revealed AS events in the gonadal transcriptomes of male and female C. semilaevis, described the characteristics of active transcription in the testes, and identified candidate genes for studying the regulatory mechanisms of AS during gonadal differentiation.
Phylogenetic relationships of the zokor genus Eospalax (Mammalia, Rodentia, Spalacidae) inferred from whole-genome analyses, with description of a new species endemic to Hengduan Mountains
2022, 43(3): 331-342. doi: 10.24272/j.issn.2095-8137.2022.045
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Zokors in the genus Eospalax, which are endemic to northern and western China, are subterranean rodents that inhabit various niches, including grasslands, high-altitude meadows, forests, and farmlands. Six species in Eospalax were described a century ago but their taxonomy and phylogeny remain controversial. In this study, we performed high-depth whole-genome sequencing of 47 zokor samples, comprising all six previously described species. Genomic analyses revealed a reliable and robust phylogeny of Eospalax and supported the validity of the six named species. According to the inferred phylogenetic relationships, Eospalax first divergent into two clades in the early Pliocene (ca. 4.68 million years ago (Ma)), one inhabiting the high-altitude Qinghai-Xizang (Tibet) Plateau (QTP) and adjacent regions, and the another inhabiting the low-altitude Loess Plateau and Qinling-Daba Mountains. The most recent divergences occurred between E. baileyi and E. smithii and between E. rufescens and E. rothschildi in the late Pliocene (ca. 2.09 and 2.19 Ma, respectively). We also collected specimens of zokors in the southern Hengduan Mountains (Muli County, Sichuan Province), far from the known distributions of all other zokors. Morphological and molecular analyses strongly suggested that the specimens represent a new species, formally described here as Eospalax muliensis sp. nov . The new species belongs to the high-altitude clade and diverged from closely related species (ca. 4.22 Ma) shortly after the first divergence in Eospalax. Interestingly, Eospalax muliensis sp. nov . possesses more supposedly plesiomorphic characters, suggesting a possible origin of the genus in the Hengduan Mountains.
MonkeyTrail: A scalable video-based method for tracking macaque movement trajectory in daily living cages
2022, 43(3): 343-351. doi: 10.24272/j.issn.2095-8137.2021.353
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Behavioral analysis of macaques provides important experimental evidence in the field of neuroscience. In recent years, video-based automatic animal behavior analysis has received widespread attention. However, methods capable of extracting and analyzing daily movement trajectories of macaques in their daily living cages remain underdeveloped, with previous approaches usually requiring specific environments to reduce interference from occlusion or environmental change. Here, we introduce a novel method, called MonkeyTrail, which satisfies the above requirements by frequently generating virtual empty backgrounds and using background subtraction to accurately obtain the foreground of moving animals. The empty background is generated by combining the frame difference method (FDM) and deep learning-based model (YOLOv5). The entire setup can be operated with low-cost hardware and can be applied to the daily living environments of individually caged macaques. To test MonkeyTrail performance, we labeled a dataset containing >8 000 video frames with the bounding boxes of macaques under various conditions as ground-truth. Results showed that the tracking accuracy and stability of MonkeyTrail exceeded that of two deep learning-based methods (YOLOv5 and Single-Shot MultiBox Detector), traditional frame difference method, and naïve background subtraction method. Using MonkeyTrail to analyze long-term surveillance video recordings, we successfully assessed changes in animal behavior in terms of movement amount and spatial preference. Thus, these findings demonstrate that MonkeyTrail enables low-cost, large-scale daily behavioral analysis of macaques.
2022, 43(3): 352-355. doi: 10.24272/j.issn.2095-8137.2022.055
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Three new genera and 46 new species of phrurolithid spiders (Araneae, Phrurolithidae) are described from Jiangxi Province, southern China. These results support our hypothesis that a large percentage of China’s species remain unknown (Li, 2020).
A new gobionine species, Microphysogobio oujiangensis sp. nov. , was collected from the Oujiang River Basin during field work in Lishui City, Zhejiang Province in 2021. The new species can be well distinguished from its congeners by the combination of the following characteristics: mouth shallow arc-shaped, width of cutting edge on upper jaw equal to half mouth width, central portion of anterior papillae arranged in one row with 6–10 well-developed papillae of equal size, medial pad on lower lip bisected into two squircle-shaped pads, and grooved; midventral region completely scaled and thorax scaleless, lateral line scales 36–38, pre-dorsal scales 8–10; barbel length 26.7%–31.4% of head length; eye diameter 30.9%–36.9% of head length, interorbital width 21.3%–27.6% of head length; posterior chamber of air-bladder weak, length smaller than half eye diameter. Bayesian inference and maximum-likelihood phylogenetic analyses based on the cyt b gene sequence and species delineation also supported the specimens as a distinct species, sister to M. brevirostris (Günther, 1868).
2022, 43(3): 362-366. doi: 10.24272/j.issn.2095-8137.2021.399
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Using Oxford Nanopore and Hi-C sequencing technology, we successfully assembled a chromosome-level genome of the Tibetan fox (Vulpes ferrilata), with a total size of 2.38 Gb and N50 length of 133 960 477 bp. The 157 contigs were further assembled into 18 chromosomes with a sequence length of 2 378.42 Mb, accounting for 99.95% of the total length. A total of <number>21715</number> protein-coding genes were predicted in the assembled genome, 86.47% of which were functionally annotated. Phylogenetic analysis showed that V. ferrilata and the red fox (V. vulpes) formed a clade, with an estimated divergence time of 3.27 million years ago (Ma). Significantly enriched pathways and Gene Ontology terms associated with the expanded gene families in the V. ferrilata genome were mainly related to hypoxia response and energy metabolism, indicating the mechanistic strategy of V. ferrilata for high-altitude adaptation. Furthermore, selection signature analysis identified genes associated with DNA damage repair and angiogenesis in V. ferrilata. Construction of the V. ferrilata genome provides valuable information for further genetic analysis of important biological processes, which will facilitate the study of genetic changes during evolution.
High-quality reference genomes of swallowtail butterflies provide insights into their coloration evolution
2022, 43(3): 367-379. doi: 10.24272/j.issn.2095-8137.2021.303
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Swallowtail butterflies (Papilionidae) are a historically significant butterfly group due to their colorful wing patterns, extensive morphological diversity, and phylogenetically important position as a sister group to all other butterflies and have been widely studied regarding ecological adaption, phylogeny, genetics, and evolution. Notably, they contain a unique class of pigments, i.e., papiliochromes, which contribute to their color diversity and various biological functions such as predator avoidance and mate preference. To date, however, the genomic and genetic basis of their color diversity and papiliochrome origin in a phylogenetic and evolutionary context remain largely unknown. Here, we obtained high-quality reference genomes of 11 swallowtail butterfly species covering all tribes of Papilioninae and Parnassiinae using long-read sequencing technology. Combined with previously published butterfly genomes, we obtained robust phylogenetic relationships among tribes, overcoming the challenges of incomplete lineage sorting (ILS) and gene flow. Comprehensive genomic analyses indicated that the evolution of Papilionidae-specific conserved non-exonic elements (PSCNEs) and transcription factor binding sites (TFBSs) of patterning and transporter/cofactor genes, together with the rapid evolution of transporters/cofactors, likely promoted the origin and evolution of papiliochromes. These findings not only provide novel insights into the genomic basis of color diversity, especially papiliochrome origin in swallowtail butterflies, but also provide important data resources for exploring the evolution, ecology, and conservation of butterflies.
2022, 43(3): 380-390. doi: 10.24272/j.issn.2095-8137.2022.023
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Maternal sleep deprivation (MSD) is a global public health problem that affects the physical and mental development of pregnant women and their newborns. The latest research suggests that sleep deprivation (SD) disrupts the gut microbiota, leading to neuroinflammation and psychological disturbances. However, it is unclear whether MSD affects the establishment of gut microbiota and neuroinflammation in the newborns. In the present study, MSD was performed on pregnant Sprague-Dawley rats in the third trimester of pregnancy (gestational days 15–21), after which intestinal contents and brain tissues were collected from offspring at different postnatal days (P1, P7, P14, and P56). Based on microbial profiling, microbial diversity and richness increased in pregnant rats subjected to MSD, as reflected by the significant increase in the phylum Firmicutes. In addition, microbial dysbiosis marked by abundant Firmicutes bacteria was observed in the MSD offspring. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA) showed that the expression levels of proinflammatory cytokines interleukin 1β (IL-1β) and tumor necrosis factor α (TNF-α) were significantly higher in the MSD offspring at adulthood (P56) than in the control group. Through Spearman correlation analysis, IL-1β and TNF-α were also shown to be positively correlated with Ruminococcus_1 and Ruminococcaceae_UCG-005 at P56, which may determine the microbiota-host interactions in MSD-related neuroinflammation. Collectively, these results indicate that MSD changes maternal gut microbiota and affects the establishment of neonatal gut microbiota, leading to neuroinflammation in MSD offspring. Therefore, understanding the role of gut microbiota during physiological development may provide potential interventions for cognitive dysfunction in MSD-impacted offspring.
2022, 43(3): 391-403. doi: 10.24272/j.issn.2095-8137.2021.291
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In an attempt to generate g.A746G substitution in the BMPR-IB gene, we unexpectedly obtained BMPR-IB homozygous knockout piglets (BMPR-IB-/-) and heterogeneous knockout piglets with one copy of the A746G mutation (BMPR-IB-/746G) via CRISPR/Cas9 editing. Polymerase chain reaction (PCR) and sequencing revealed complex genomic rearrangements in the target region. All BMPR-IB-disrupted piglets showed an inability to stand and walk normally. Both BMPR-IB-/- and BMPR-IB-/746G piglets exhibited severe skeletal dysplasia characterized by distorted and truncated forearms (ulna, radius) and disordered carpal, metacarpal, and phalangeal bones in the forelimbs. The piglets displayed more severe deformities in the hindlimbs by visual inspection, including fibular hemimelia, enlarged tarsal bone, and disordered toe joint bones. Limb deformities were more profound in BMPR-IB-/- piglets than in the BMPR-IB-/746G piglets. Proteomic analysis identified 139 differentially expressed proteins (DEPs) in the hindlimb fibula of BMPR-IB-/746G piglets compared to the wild-type (WT) controls. Most DEPs are involved in skeletal or embryonic development and/or the TGF-β pathway and tumor progression. Gene Ontology (GO) and protein domain enrichment analysis suggested alterations in these processes. Of the top 50 DEPs, a large proportion, e.g., C1QA, MYO1H, SRSF1, P3H1, GJA1, TCOF1, RBM10, SPP2, MMP13, and PHAX, were significantly associated with skeletal development. Our study provides novel findings on the role of BMPR-IB in mammalian limb development.
Anadromous Coilia nasus is a socioeconomically important species from the middle and lower reaches of the Yangtze River. Here, we compared growth and feeding of C. nasus larvae in four reaches along the full migration corridor of the river (640 km) to determine how fitness varies between progenies of short- and long-distance migrants. Results demonstrated that larvae collected in downstream sections grew faster, exhibited higher feeding intensities, and consumed larger zooplankton (a favored food resource). Our results did not support the parent-offspring trade-off theory, which predicts that the costs and benefits of migration increase with migration distance, and higher parental costs with long migration should be offset by increased offspring fitness. We suggest pervasive human impacts along the river are likely driving the observed ecological patterns. Overfishing has resulted in a truncated body size in migrants, which shortens their migration distance; isolation of floodplain lakes from the river restricts fish spawning and nursing to suboptimal lotic river habitats; and higher discharge experienced by larvae born from long-distance migrants in the upstream river reaches during the later flooding season results in declined feeding intensity and slower growth compared to those produced from short-distance migrants in the earlier season. We predict that a fishing ban in the Yangtze River will allow fish to grow larger and older so they can access floodplain lakes further upstream, which will further enhance recruitment of the C. nasus population.
2022, 43(3): 409-412. doi: 10.24272/j.issn.2095-8137.2021.230
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Guigarra cailaoensis sp. nov. , a new genus and species of Labeoninae, was collected from Guangxi Zhuang Autonomous Region, China. It differs from all other genera within Labeoninae by a unique combination of the following characters: (1) rostral cap smooth with posterior margin slightly serrated; (2) upper lip well developed and covering most of upper jaw; (3) gular disc present with crescentic torus, not forming horseshoe shape; (4) boundaries of torus, labrum, and pulvinus on gular disc inconspicuous; (5) posterior edge of labrum free, without notch. Molecular phylogenetic analysis of three gene datasets indicated that the new genus formed a monophyletic clade and was closely related to Discogobio and Discocheilus. Both morphological and molecular phylogenetic analyses indicated that Guigarra cailaoensis sp. nov. differs from all known labeonin genera and is thus described here as a new genus and species.
A new species of the genus Typhlomys Milne-Edwards, 1877 (Rodentia: Platacanthomyidae) from Chongqing, China
2022, 43(3): 413-417. doi: 10.24272/j.issn.2095-8137.2021.338
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A new species of the genus Typhlomys Milne-Edwards, 1877 (Rodentia: Platacanthomyidae) is described based on 10 specimens collected from Chongqing in southwestern China using integrated taxonomy. Phylogenetic analysis showed that these specimens formed a distinct sister clade to T. daloushanensis Wang and Li, 1996, and differed from all six known Typhlomys species based on Kimura-2-parameter genetic distances of the cytochrome b (cyt b) gene (ranging from 0.122 to 0.215). The new species Typhlomys fengjiensis sp. nov. is most similar to T. daloushanensis in morphology. However, it differs from the latter by the following morphological characters: (1) larger body and skull; (2) deeper incurved zygomatic arch; and (3) mesofossette on first upper molar open on both buccal and lingual sides (vs. inner edge of endoloph closed in T. daloushanensis). The discovery of this new species supports that Typhlomys diversity remains underestimated in southern China.
2022, 43(3): 418-422. doi: 10.24272/j.issn.2095-8137.2021.445
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Mongolian gerbils (Meriones unguiculatus) are small rodents belonging to the family Muridae and widely inhabit typical steppes and desert grasslands across northern China. Yet, few viruses in wild M. unguiculatus have been reported. Using meta-transcriptomic sequencing we identified two novel RNA viruses: an astrovirus, denoted Gerbil astrovirus (GeAstV), and a paramyxovirus – Gerbil paramyxovirus (GePV) in Mongolian gerbils captured during October–November 2018 from one of the plagus zones in Shaanxi Province, China. Phylogenetic analysis based on the amino acid sequences of ORF1a, RdRp and ORF2 revealed that GeAstV clustered with rodent- and porcine-associated astroviruses, sharing the highest amino acid identity of 75.07% with a pig astrovirus in RdRp, while sharing 42.14% and 35.94% amino acid identity with a rodent astrovirus in the deduced ORF1a and ORF2 proteins, respectively, exhibiting apparent recombination and potential cross-species transmission events. For the newly discovered GePV, evolutionary analysis demonstrated that it was closely related to Tailam virus and Beilong virus, and shared 61%–77% identity in the L protein with the seven members of the genus Jeilongvirus. Notably, GeAstV was detected only in lung samples while GePV was positive only in kidney samples. In sum, we demonstrate the presence of two novel gerbil RNA viruses, expanding our understanding of viral diversity in wild Mongolian gerbils.
Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds
2022, 43(3): 423-441. doi: 10.24272/j.issn.2095-8137.2021.379
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In pig-to-human xenotransplantation, the transmission risk of porcine endogenous retroviruses (PERVs) is of great concern. However, the distribution of PERVs in pig genomes, their genetic variation among Eurasian pigs, and their evolutionary history remain unclear. We scanned PERVs in the current pig reference genome (assembly Build 11.1), and identified 36 long complete or near-complete PERVs (lcPERVs) and 23 short incomplete PERVs (siPERVs). Besides three known PERVs (PERV-A, -B, and -C), four novel types (PERV-JX1, -JX2, -JX3, and -JX4) were detected in this study. According to evolutionary analyses, the newly discovered PERVs were more ancient, and PERV-Bs probably experienced a bottleneck ~0.5 million years ago (Ma). By analyzing 63 high-quality porcine whole-genome resequencing data, we found that the PERV copy numbers in Chinese pigs were lower (32.0±4.0) than in Western pigs (49.1±6.5). Additionally, the PERV sequence diversity was lower in Chinese pigs than in Western pigs. Regarding the lcPERV copy numbers, PERV-A and -JX2 in Western pigs were higher than in Chinese pigs. Notably, Bama Xiang (BMX) pigs had the lowest PERV copy number (27.8±5.1), and a BMX individual had no PERV-C and the lowest PERV copy number (23), suggesting that BMX pigs were more suitable for screening and/or modification as xenograft donors. Furthermore, we identified 451 PERV transposon insertion polymorphisms (TIPs), of which 86 were shared by all 10 Chinese and Western pig breeds. Our findings provide systematic insights into the genomic distribution, variation, evolution, and possible biological function of PERVs.
Mutations in serologically defined colon cancer autoantigen protein 8 (SDCCAG8) were first identified in retinal ciliopathy families a decade ago with unknown function. To investigate the pathogenesis of SDCCAG8-associated retinal ciliopathies in vivo, we employed CRISPR/Cas9-mediated homology-directed recombination (HDR) to generate two knock-in mouse models, Sdccag8Y236X/Y236X and Sdccag8E451GfsX467/E451GfsX467, which carry truncating mutations of the mouse Sdccag8, corresponding to mutations that cause Bardet-Biedl syndrome (BBS) and Senior-Løken syndrome (SLS) (c.696T>G p.Y232X and c.1339–1340insG p.E447GfsX463) in humans, respectively. The two mutant Sdccag8 knock-in mice faithfully recapitulated human SDCCAG8-associated BBS phenotypes such as rod-cone dystrophy, cystic renal disorder, polydactyly, infertility, and growth retardation, with varied age of onset and severity depending on the hypomorphic strength of the Sdccag8 mutations. To the best of our knowledge, these knock-in mouse lines are the first BBS mouse models to present with the polydactyly phenotype. Major phototransduction protein mislocalization was also observed outside the outer segment after initiation of photoreceptor degeneration. Impaired cilia were observed in the mutant photoreceptors, renal epithelial cells, and mouse embryonic fibroblasts derived from the knock-in mouse embryos, suggesting that SDCCAG8 plays an essential role in ciliogenesis, and cilium defects are a primary driving force of SDCCAG8-associated retinal ciliopathies.
COVID-19 is an immune-mediated inflammatory disease caused by SARS-CoV-2 infection, the combination of anti-inflammatory and antiviral therapy is predicted to provide clinical benefits. We recently demonstrated that mast cells (MCs) are an essential mediator of SARS-CoV-2-initiated hyperinflammation. We also showed that spike protein-induced MC degranulation initiates alveolar epithelial inflammation for barrier disruption and suggested an off-label use of antihistamines as MC stabilizers to block degranulation and consequently suppress inflammation and prevent lung injury. In this study, we emphasized the essential role of MCs in SARS-CoV-2-induced lung lesions in vivo, and demonstrated the benefits of co-administration of antihistamines and antiviral drug remdesivir in SARS-CoV-2-infected mice. Specifically, SARS-CoV-2 spike protein-induced MC degranulation resulted in alveolar-capillary injury, while pretreatment of pulmonary microvascular endothelial cells with antihistamines prevented adhesion junction disruption; predictably, the combination of antiviral drug remdesivir with the antihistamine loratadine, a histamine receptor 1 (HR1) antagonist, dampened viral replication and inflammation, thereby greatly reducing lung injury. Our findings emphasize the crucial role of MCs in SARS-CoV-2-induced inflammation and lung injury and provide a feasible combination antiviral and anti-inflammatory therapy for COVID-19 treatment.
Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities
2022, 43(3): 469-480. doi: 10.24272/j.issn.2095-8137.2022.101
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Effective conservation of threatened biota relies on accurate assessments and scientific guidance. As an unfortunate example, Chinese giant salamanders (Andrias, CGS) remain critically endangered in nature. Misguided conservation efforts, e.g., commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids, have further compromised conservation initiatives. Limited information on wild populations of CGS poses a significant conservation challenge. Following 18-month long field monitoring, we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province, China. Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species. Based on morphological and molecular evidences, we describe this CGS as a new species Andrias jiangxiensis sp. nov. This is the only known species of CGS today with a genetically pure, reproducing, in situ population. This discovery emphasizes the important role that closed nature reserves play in protecting species, and the necessity of integrating long-term field monitoring and genetic assessments. It sets a new pathway for discovering and conserving endangered species, especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.
2022, 43(3): 481-496. doi: 10.24272/j.issn.2095-8137.2021.479
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Adult neurogenesis is the creation of new neurons which integrate into the existing neural circuit of the adult brain. Recent evidence suggests that adult hippocampal neurogenesis (AHN) persists throughout life in mammals, including humans. These newborn neurons have been implicated to have a crucial role in brain functions such as learning and memory. Importantly, studies have also found that hippocampal neurogenesis is impaired in neurodegenerative and neuropsychiatric diseases. Alzheimer’s disease (AD) is one of the most common forms of dementia affecting millions of people. Cognitive dysfunction is a common symptom of AD patients and progressive memory loss has been attributed to the degeneration of the hippocampus. Therefore, there has been growing interest in identifying how hippocampal neurogenesis is affected in AD. However, the link between cognitive decline and changes in hippocampal neurogenesis in AD is poorly understood. In this review, we summarized the recent literature on AHN and its impairments in AD.