H.Y. Liu

• PhD
• Professor (Associate) at Nanjing Forestry University

Introduction Migratory birds exhibit unique annual cycles that complicate their gut microbiota. However, the annual dynamics of gut microbiota in migratory birds remain unclear, hindering our understanding of their environmental adaptation. Methods Here, we collected fecal samples from black-necked cranes (Grus nigricollis) across four seasons at...

Scorpions, a diverse group of arachnids consisting of over 2,000 valid species, have received limited research attention in terms of their complete mitochondrial genomes (mitogenomes). To increase the taxonomic sampling frequency of species available for study based on mitogenomes, we reconstructed the complete mitogenomes of five scorpions, Androc...

Understanding how animals coexist within an ecosystem is essential for the conservation of biodiversity. In China, large populations of a non-native snail Rumina decollata (a highly invasive species reported by various other countries) coexist with two native snail species (Acusta ravida and Euphaedusa aculus). However, the potential mechanisms tha...

Aims: Urbanization, the rapid expansion of urban areas and the transformation of natural landscapes into manmade environments, has significantly altered the habitat of many organisms. This process has not only reshaped landscapes but has also impacted ecological balance. Soil fauna are integral components of the food chain and play a crucial role i...

To better understand the evolution of mitochondrial genomes (mitogenomes) within the family Theraphosidae, we characterized mitogenomes of four tarantulas (Grammostola pulchripes, Phormictopus atrichomatus, Pterinochilus murinus and Pterinopelma sazimai) for the first time. The mitogenomes were all classical circular structures, with lengths rangin...

Invertebrates greatly support the growth, development, and reproduction of insectivorous birds. However, the influence of human activity (e.g., pesticide use, deforestation, and urbanization) inevitably leads to a decrease in global arthropods. The diversity and variation in invertebrate diet influence the food composition of birds, especially spec...

Channidae (snakehead fish) is a family of medium-to-large freshwater carnivorous fish and contain the genus, Channa. Here, the complete mitogenomes of two Channa fish were determined and comparatively analyzed with the mitogenomes of 16 other Channidae fish species. The two newly sequenced complete mitogenomes were circular DNA molecules with sizes...

Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in this study, we characterized mitochondrial...

There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patr...

This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized...

The ruminants, as the main group of livestock, have been extensively studied in terms of their physiology, endocrinology, biochemistry, genetics, and nutrition. Despite the wide geographic distribution and habitat diversity of animals in this group, their ecology and evolution remain poorly understood. In this study, we analyzed the gene copy numbe...

Understanding the diet of threatened wildlife is vital for species-specific conservation and habitat managementmeasures. The Red-crowned Crane (Grus japonensis) is a vulnerable bird distributed in Northeast Asia. Previousdietary studies of this bird focused mainly on its plant food composition based on field observations andmicrohistological identi...

In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprolo-gus kungweensis, L. meleagris, L. ornatipinnis, Neolamprologus brevis, N. caudopunctatus, N. leleupi, and N. similis) are characterized for the first time. The newly sequenced mi-togenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal R...

All jawed vertebrates have four T cell receptor (TCR) chains expressed by thymus-derived lymphocytes that play a significant role in animal immune defense. However, avian TCR studies have been limited to a few species, although their co-functional major histocompatibility complexes (MHCs) have been studied for decades, showing various copy numbers...

Soil invertebrates are a major element of soil biodiversity, which play critical roles in soil ecosystems. However, the impacts of urban landscapes on the genetic diversity and gene flows of soil arthropods remain unclear. Here, we studied the genetic diversity and gene flow of Scolopendra mutilans in an urban area using mitochondrial Cytb genes an...

The migratory and omnivorous common crane ( Grus grus ) uses a nature reserve with crucial ecological value that provides supplementary food resources, although the extent of their use by these cranes is unknown. In this study, we used DNA metabarcoding of plants through the chloroplast rbcL gene to investigate the diets of 25 common crane fecal sa...

Background Exploring the association of diet and indoor and outdoor environments on the gut microbiome of red-crowned cranes. We investigated the microbiome profile of the 24 fecal samples collected from nine cranes from day 1 to 35. Differences in the gut microbiome composition were compared across diet and environments. Results A total of 2,883...

Mitochondrial genome (mitogenome) sequencing is one of the most effective methods for studying spider phylogeny. In this study, the mitogenomes of wolf spiders (Lycosa grahami and Lycosa sp.) were sequenced and compared with those of other spiders to study their evolutionary trends. The mitogenomes of L. grahami and Lycosa sp. were 14,240 and 14,58...

The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with t...

The rice-fish system (RFS), a traditional coculture farming model, was selected as a “globally important agricultural heritage system.” Host-associated microbiota play important roles in development, metabolism, physiology, and immune function. However, studies on the gut microbiota of aquatic animals in the RFS are scarce, especially the lack of b...

Although classical morphological classification within the Characidae has long history, this taxonomic perspective is now challenged when using mitochondrial genes to investigate phylogeny of this family. We discovered the problems of classical taxonomic systems from the point of mitochondrial genome of Characidae species. Here, six newly sequenced...

Soil macrofauna, such as Spirobolus bungii, are an important component of ecosystems. However, systematic studies of the genetic diversity, population genetic structure, and the potential factors affecting the genetic differentiation of S. bungii are lacking. We performed a population genetic study of 166 individuals from the mountains to the south...

Millipedes (Diplopoda) comprise one of the most important groups of large soil arthropods in terrestrial ecosystems; however, their phylogenetic relationships are poorly understood. Herein, the mitochondrial genome (mitogenome) of Spirobolus bungii was sequenced and annotated, which was 14,879 bp in size and included 37 typical mitochondrial genes...

We determined the complete mitochondrial genome of Thereuopoda clunifera (Chilopoda: Scutigeridae) to clarify the phylogenetic status within Chilopoda. Using Sanger sequencing and next-generation sequencing technologies, the entire mitogenome of T. clunifera was assembled and annotated, with 14,898 bp in length and 37 genes (13 protein-coding genes...

We sequenced the complete mitochondrial genomes of Lycosa shansia, and Lycosa singoriensis by combining Sanger and next-generation sequencing methods and analyzed the sequenced genomes in order to explore the phylogenetic placement and the mitogenome composition and evolution of these species. The mitochondrial genome of L. shansia was 14,638 bp, w...

The red-crowned crane (Grus japonensis) has been demoted to “vulnerable species” because its populations have apparently stabilized in Japan and Korea. Low variation and genetic drift may cause damage to the nascent recovery of the G. japonensis population. The major histocompatibility complex (MHC) is one of the most polymorphic gene families in t...

Gut microbiota homeostasis is important for host health and well-being; however, drugs may affect the composition and function of the gut microbiota. Red-crowned cranes are a vulnerable species. Treatment of red-crowned cranes with avian influenza vaccines and anthelmintics has played pivotal roles in therapeutic management in zoos. To investigate...

Background Centipedes are one of the oldest terrestrial arthropods belonging to the sub phylum Myriapoda. With the expansion of our understanding of the application of the two centipedes Scolopendra morsitans and Scolopendra hainanum, belonging to the order Scolopendromorpha, an exhaustive classification was required. Although consensus has been re...

The red-crowned crane (Grus japonensis) is a critically endangered species. Three-dimensional–printed prosthetic beaks made of titanium alloy and polyether ether ketone (PEEK) were used to repair the beak of a red-crowned crane that had a complete fracture of the anterior maxillary bone and rhinotheca. The physical properties and stability of the p...

The red-crowned crane ( Grus japonensis ) is an endangered species distributed across southeast Russia, northeast China, Korea, and Japan. Here, we sequenced for the first time the full-length unreferenced transcriptome of red-crowned crane mixed samples using a PacBio Sequel platform. A total of 359,136 circular consensus sequences (CCS) were obta...

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendr...

Ducks (Anatidae) are often vectors for the spread of pathogens because of their long-distance migrations. These migrations also expose ducks to a wide variety of pathogens in their wintering and breeding grounds, and, as a consequence, we might expect strong selection on their immune genes. Here, we studied exons 2 and 3 of the MHC class I in four...

To date, the taxonomic status and phylogenetic affinities within Hyphessobrycon, even among other genera in Characidae, remain unclear. Here, we determined five new mitochondrial genomes (mitogenomes) of Hyphessobrycon species (H. elachys, H. flammeus, H. pulchripinnis, H. roseus, and H. sweglesi). The mitogenomes were all classical circular struct...

The earthworm species Metaphire vulgaris (a member of the Clitellata class) is widely distributed across China, and has important ecological functions and medicinal value. However, investigations into its genetic diversity and differentiation are scarce. Consequently, we evaluated the genetic diversity of five populations of M. vulgaris (GM, HD, NY...

Members of the genus Treron (Columbidae) are widely distributed in southern Asia and the Indo-Malayan Region but their relationships are poorly understood. Better knowledge of the systematic status of this genus may help studies of historical biogeography and taxonomy. The complete mitochondrial genome of T. curvirostra was characterized, a first f...

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangements. However, a new type of gene arrangement has been identified in the mitochondrial genomes (mitogenomes) of Moenkhausia. Here, three newly sequenced complete mitogenomes of tetras (Characidae: Moenkhausia) are presented (M. costae, M. pittieri,...

The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenom...

Ornamental feather coloration is usually a reflection of male quality and plays an important role during courtship, whereas the essence of male quality at the genetic level is not well understood. Major histocompatibility complex (MHC)-based mate choice has been observed in various vertebrates. Here, we investigated the relationship between the col...

Diet analysis of potential small mammals pest species is important for understanding feeding ecology and evaluating their impact on crops and stored foods. Chinese mole shrew (Anourosorex squamipes), distributed in Southwest China, has previously been reported as a farmland pest. Effective population management of this species requires a better und...

The earthworm (Drawida gisti) is an ecologically important sentinel species for soils that is widely distributed throughout Eastern Asia; however, the molecular tools required for genetic diversity studies of this earthworm are still rare. The aim of the study was to develop and characterize microsatellite markers in D. gisti and to evaluate their...

Mitochondrial genome sequencing has become widely used in numerous fields, including systematics, phylogeny, and evolutionary genomics. To elucidate phylogenetic relationships among members of the family Characidae, we sequenced the mitogenomes of four species within this family, namely, Aphyocharax rathbuni, Hyphessobrycon herbertaxelrodi, Hyphess...

Background The red-crowned crane (Grus japonensis) is one of the most vulnerable bird species in the world. Mycotoxins are toxic secondary metabolites produced by fungi and considered naturally unavoidable contaminants in animal feed. Our recent survey indicated that the mycotoxins had the potential to contaminate red-crowned crane’s regular diets...

The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii....

Here, the complete mitochondrial genome (mitogenome) of Drawida gisti was sequenced and compared with the mitogenomes of other Metagynophora species. The circular mitogenome was 14,648 bp in length and contained two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The types of constitutive genes and th...

Reintroducing captive giant pandas (Ailuropoda melanoleuca) to the wild is the ultimate goal of their ex situ conservation. Choosing higher fitness candidates to train prior to release is the first step in the giant panda reintroduction program. Disease resistance is one important index of individual fitness and presumed to be related to variation...

The complete mitochondrial genome (mitogenome) of diamond dove (Geopelia cuneata) was first determined in this study. The mitogenome is 17,880 bp in size and composed of 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and a control region. The overall nucleotide composition is 30.11% of A, 13.66% of G, 25.11% of T, and 31.1...

The red-crowned crane (Grus japonensis) is one of the most endangered cranes in the world, and its wild population is still declining. To characterize the genetic resources of East Asian migratory populations, we studied the genetic variation in wild red-crowned cranes at the Yancheng reserve. Based on a partial Cyt b gene sequence, 32 wild red-cro...

New advances in molecular approaches for DNA analysis have enhanced our understanding of the phylogenetic relationship of birds. The Little Owl (Athene noctua) is of great significance for the integrated management of forest diseases and control of regional pests. Here, we sequenced and annotated the 17,772 bp complete mitogenome of A. noctua. The...

The genus Phylloscopus belongs to the order Passeriformes and subfamily Phylloscopinae within the family Sylviidae. Phylloscopus, a small insectivore widely distributed in the old world, includes 66 species and 112 subspecies. We identified five new Phylloscopus mitogenomes: P. tenellipes (16,904 base pairs (bp), MK390475), P. coronatus (16,905 bp,...

The round-tailed paradise fish (Macropodus ocellatus) is important to the local ecosystem and economy. Other species in the genus Macropodus are undergoing population declines, indicating that the M. ocellatus population might also be declining. Therefore, the status of M. ocellatus, related to standing-water ecosystem stability and sustainable uti...

The red-crowned crane (Grus japonensis) is an endangered wading bird distributed in northeast Asia. The population of G. japonensis is continuing to decline owing to the loss and degradation of habitats. In order to protect G. japonensis, we developed 33 single nucleotide polymorphism (SNP) markers for this species using a genotyping-by-sequencing...

We first reported the mitochondrial genome of Lepus yarkandensis. The mitogenome of L. yarkandensis contains 17,011 base pairs. The overall base composition of complete mitogenome is 28.13% A, 27.67% T, 22.02% C, and 22.17% G, with 44.20% of the GC content. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. Ph...

Père David’s deer (Elaphurus davidianus or milu) is a highly endangered species originating from China, and many deer are currently being raised in captivity for gradual re-introduction to the wild. Wild and captive deer currently live in the same region but have vastly different diets. In this study, we used 16S rRNA high-throughput sequencing to...

The complete mitogenome of a lorikeet, Trichoglossus rubritorquis (Psittaciformes, Loriidae), was determined first in the genus Trichoglossus. The assembled mitogenome was 17,915 bp and composed of 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. Nucleotide composition of T. rubritorquis mitogenome was 30.20% A, 33.30% C, 14.04...

The first complete mitogenome of Hong Kong paradise fish (Macropodus hongkongensis) was determined in this study. The assembled mitogenome is 16,494 bp and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition of the complete mitogenome is 30.6% A, 24.8% C, 14.8% G, and 29.8% T, with an A + T bias of...

The complete mitochondrial genome of Lumbricus rubellus was analyzed by next-generation sequencing. The mitogenome was 15,464 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and a non-coding region. The phylogenetic analysis of 13 PCGs within the class Oligochaeta suggested that L. rubellus was placed as...

Gut microbiomes have profound effects on the health of hosts. About 28% of extant parrot species are threatened with extinction. To inform conservation efforts, we characterized and compared the gut microbiomes in nine species of parrots in captivity. The core gut microbiome of parrots was dominated by three bacterial phyla: the Firmicutes, Proteob...

In this paper, we characterized the complete mitogenomes of Aratinga solstitialis, Pionites leucogaster, and Poicephalus senegalus through Sanger sequencing method. The full lengths of the three mitogenomes are 16,986 bp, 18,858 bp, and 18,022 bp, respectively. All genes exhibit original gene arrangement in A. solstitialis mitogenome, but gene rear...

Major histocompatibility complex (MHC) is a highly polymorphic gene family in the vertebrate genome, and its coding products play an important role in the vertebrate immune system. Most of the world's surviving crane (Gruidae) species are threatened due to habitat pollution and destruction. To understand the information of MHC-I sequences of cranes...

Fischer's Lovebird (Agapornis fischeri) is one of the most popular pet birds in the world. Here, we first reported the complete mitochondrial genome of this species. Its mitochondrial genome is a circular molecule of 16,719 bp in size, and all genes exhibit the typical gene arrangement according with most avian consensus. The overall base compositi...

In this paper, we first reported the complete mitogenomes of Psittacula derbiana and Psittacula eupatria. Respectively, P. derbiana and P. eupatria mitogenomes are 16,887 and 17,139 bp base pairs long. The overall base compositions of complete mitogenomes of P. derbiana and P. eupatria are 30.9% A, 22.4% T, 32.8% C, 13.9% G and 31.7% A, 22.0% T, 33...

Gut microbiota plays an important role in animals and are considered microbial organs. Hornbill and toucan are birds of the same ecotypes with high appreciative value. In this study, we characterized and compared the gut microbiota of toco toucan (Ramphastos toco), great hornbill (Buceros bicornis) and wreathed hornbill (Rhyticeros undulatus) using...

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer...

A survey was conducted to determine whether mycotoxins were present in the foods consumed by red-crowned cranes (Grus japonensis) in the Yancheng Biosphere Reserve, China. Collected in the reserve’s core, buffer, and experimental zones during overwintering periods of 2013 to 2015, a total of 113 food samples were analyzed for aflatoxin B1, deoxyniv...

The major histocompatibility complex (MHC) genes play pivotal roles in the immune system of vertebrates against antigens. They are also significant indicators of genetic structure, and are vital to species-level population viability analyses and disease risk assessments. In this study, two DRA and two DQA sequences were isolated from Hainan Eld's d...

Contrary to neutral markers, the major histocompatibility complex (MHC) can reflect the fitness and adaptive potential of a given species due to its association with the immune system. For this reason, the use of MHC in endangered wildlife management has increased greatly in recent years. Here, we isolated complementary DNA (cDNA) and genomic DNA (...

Random amplified polymorphic DNA (RAPD) technique was employed to detect the genetic variations in paradisefishMacropodusopercularispopulations distributed in five geographical colonies. In this study, 11 effective primers out of 40 random primers were selected to amplify genomic DNA, resulting in 139 repeatable RAPD bands. The 5 populations were s...