Gang Li

• PhD
• Professor at Shaanxi Normal University

Genomic rearrangements are primary drivers of evolution, promoting biodiversity. Aphids, an agricultural pest with high species diversity, exhibit rapid chromosomal evolution and diverse karyotypes. These variations have been attributed to their unique holocentric chromosomes and parthenogenesis, though this hypothesis has faced scrutiny. In this s...

Sensory trade-offs between vision and olfaction in the evolution and radiation of primates have long been debated. However, insights have been limited by a lack of sensory gene sequences and accompanying functional predictions. Here we conduct large-scale functional analyses of visual and olfactory receptors and related brain regions across extant...

Horseshoe bats are natural hosts of zoonotic viruses, yet the genetic basis of their antiviral immunity is poorly understood. Here we generated two new chromosomal-level genome assemblies for horseshoe bat species (Rhinolophus) and three close relatives, and show that, during their diversification, horseshoe bats underwent extensive chromosomal rea...

Horseshoe bats (genus Rhinolophus, family Rhinolophidae) represent an important group within chiropteran phylogeny due to their distinctive traits, including constant high-frequency echolocation, rapid karyotype evolution, and unique immune system. Advances in evolutionary biology, supported by high-quality reference genomes and comprehensive whole...

The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as...

Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels of inter-sexual conflict, yet their sex chromosome evolution remains poorly understood. Here, by...

Habitat degradation and loss of genetic diversity are common threats faced by almost all of today’s wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging consi...

Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high‐quality chromosome‐level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of col...

Clouded leopards ( Neofelis spp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comp...

The biological mechanisms that underpin primate social evolution remain poorly understood. Asian colobines display a range of social organizations, which makes them good models for investigating social evolution. By integrating ecological, geological, fossil, behavioral, and genomic analyses, we found that colobine primates that inhabit colder envi...

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, th...

A new flower fly genus (Diptera, Syrphidae), Biema Huo & Zhao gen. nov. from China is described based on two new species: Biema wanglangensis Huo & Zhao gen. et sp. nov. (designated as type-species) and Biema qilianensis Huo & Liu gen. et sp. nov. The new genus can easily be distinguished by the following morphological features: head, mesonotum and...

Insect olfactory receptors (iORs) with atypical 7-transmembrane domains, unlike Chordata olfactory receptors, are not in the GPCR protein family. iORs selectively bind to volatile ligands in the environment and affect essential insect behaviors. In this study, we constructed a new platform (iORbase, https://www.iorbase.com) for the structural and f...

The complete mitochondrial genome of Eristalinus viridis (Coquillett, 1898) was obtained for the first time using Next Generation Sequencing (NGS). The mitogenome assembly of E. viridis is 15,640 bp in length and its annotation confirms the presence of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), a...

In this study, the complete mitochondrial genome (mitogenome) of Melanostoma mellinum (Linnaeus, 1758) was sequenced using the-next generation sequencing technology. The assembled mitogenome of M. mellinum has a total length of 16,055bp and contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). Th...

The genus Psilota Meigen, 1822 is recorded for the first time from China, and the species Psilota bashanensis Huo and Zhao sp. nov. is described and illustrated based on the adult male. The complete cytochrome c oxidase subunit I (COI) gene of this new species has been successfully obtained and compared to that of other congeneric species. An updat...

The genus Archimicrodon Hull, 1945 is recorded for the first time from China. Two new species in the tribe Microdontini are described and illustrated: Archimicrodon (Hovamicrodon) huayangensis sp. nov. and Paramixogaster trifasciatus sp. nov. An updated key to the genus Paramixogaster from China is provided.

Lysozyme enzymes provide classic examples of molecular adaptation and parallel evolution, however, nearly all insights to date come from c-type lysozymes. G-type lysozymes occur in diverse vertebrates, with multiple independent duplications reported. Most mammals possess two g-type lysozyme genes (Lyg1 and Lyg2), the result of an early duplication,...

Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when post-speciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here...

In this study, we present the complete mitogenome of Lathyrophthalmu quinquestriatus (Fabricius, 1794), which has a total length of 16,198 base pairs and includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one putative control region. Most PCGs started with ATN codons except COX1 (CAA), and ended with TAA, TAG (ND3) o...

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary referen...

The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is limited for this species. To empower trait analyses, a new cat genome reference assembly was developed from PacBi...

The complete mitochondrial genome of Ferdinandea cuprea was assembled and annotated applying next generation sequencing, which is the first reported mitogenome reference of species from Rhingiini tribe of Syrphidae family. The mitogenome of F. cuprea has length of 15,907 base pair and comprises of 37 genes (13 protein-coding genes, 22 transfer RNA...

Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We...

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of post-speciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the vali...

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assum...

Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-cop...

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar...

Abstract Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink...

Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo referen...

High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies. Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotyp...

Interspecies hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that conside...

The phenomenon of male sterility in interspecies hybrids has been observed for over a century, however few genes influencing this recurrent phenotype have been identified. Genetic investigations have been primarily limited to a small number of model organisms, thus limiting our understanding of the underlying molecular basis of this well-documented...

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a domestic cat reference genome assembly as well as comparative inferences made with other cat breeds, wildcats, and other mammals. We provide evolutionary assessments of the feline protein-coding genome, population gene...

Significance We present highlights of the first complete domestic cat reference genome, to our knowledge. We provide evolutionary assessments of the feline protein-coding genome, population genetic discoveries surrounding domestication, and a resource of domestic cat genetic variants. These analyses span broadly, from carnivore adaptations for hunt...

Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection a...

Pancreatic ribonuclease gene (RNASE1) was previously shown to have undergone duplication and adaptive evolution related to digestive efficiency in several mammalian groups that have evolved foregut fermentation, including ruminants and some primates. RNASE1 gene duplications thought to be linked to diet have also been recorded in some carnivores. O...

Mature mammalian sperm contain a complex population of RNAs some of which might regulate spermatogenesis while others probably play a role in fertilization and early development. Due to this limited knowledge, the biological functions of sperm RNAs remain enigmatic. Here we report the first characterization of the global transcriptome of the sperm...

Most significant (p<0.001) GO terms for sperm transcripts identified by microarray analysis (count-number of genes associated with this gene set). (DOCX)

Gene Ontology classifications and terms for 165 sperm-enriched transcripts by microarray analysis. This table lists GO analysis statistics for the sperm-enriched genes. The GO categories i) Biological process, ii) Molecular function, and iii) Cellular component are shown on separate spreadsheets; Count-number of genes associated with this gene set;...

Alignment and coverage statistics for RNA-seq reads in the horse genome. (XLSX)

Mapped RNA sequence tags (n = 19,257) from the sperm of the two stallions. The table presents the following information for each mapped sequence tag: i) genomic location, ii) average coverage in sperm 1 (AC1) and sperm 2 (AC2), and iii) log2 ratios between AC1 and AC2. Columns at the left are sorted by AC1 and columns at the right by AC2. Mapped ta...

The ability to uncover the phylogenetic history of recently extinct species and other species known only from archived museum material has rapidly improved due to the reduced cost and increased sequence capacity of next-generation sequencing technologies. One limitation of these approaches is the difficulty of isolating and sequencing large, orthol...

Cauxin is a novel urinary protein recently identified in the domestic cat that regulates the excretion of felinine, a pheromone precursor involved in sociochemical communication and territorial marking of domestic and wild felids. Understanding the evolutionary history of cauxin may therefore illuminate molecular adaptations involved in the evoluti...

The pantherine lineage of cats diverged from the remainder of modern Felidae less than 11 million years ago and consists of the five big cats of the genus Panthera, the lion, tiger, jaguar, leopard, and snow leopard, as well as the closely related clouded leopard. A significant problem exists with respect to the precise phylogeny of these highly th...

The digestive enzyme chitinase degrades chitin, and is found in a wide range of organisms, from prokaryotes to eukaryotes. Although mammals cannot synthesize or assimilate chitin, several proteins of the glycoside hydrolase (GH) chitinase family GH18, including some with enzymatic activity, have recently been identified from mammalian genomes. Cons...

Gap junction protein connexin43 (Cx43), encoded by the GJA1 gene, is the most abundant connexin in the cardiovascular system and was reported as a crucial factor maintaining cardiac electrical conduction, as well as having a very important function in facilitating the recycling of potassium ions from hair cells in the cochlea back into the cochlear...

SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had e...

Table S1. List of 156 sequences of SARS-CoV analyzed in this study.

Figure S1. Detection of recombination with GARD method. (A) putative breakpoints in spike gene; (B) putative breakpoints in replicase domains; (C) putative breakpoints in 3'-end ORFs.

Figure S2. The distribution of positively selected sites identified using the branch-site model A (SARS group as foreground). (A) Positively selected sites among S protein of SARS-CoV; (B) positively selected sites among 3'-end ORFs of SARS-CoV. The most significant peaks (p >95%) were colored in red.

Bats are the only mammals with the capacity for powered flight. When flying, they need abundant energy and oxygen. According to previous works, the hemoglobin (Hb) oxygen loading function of bats is insensitive to variations in body temperature, although different bat species have different heat sensitivity. We cloned Hb alpha-chain sequences from...

Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species' history. Here we pr...

The remarkable high-frequency sensitivity and selectivity of the mammalian auditory system has been attributed to the evolution of mechanical amplification, in which sound waves are amplified by outer hair cells in the cochlea. This process is driven by the recently discovered protein prestin, encoded by the gene Prestin. Echolocating bats use ultr...

Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 2002-2003. We examined the evolutionary relationships between bat CoVs an...

FoxP2 gene (second half) with variable sites shown. For abbreviations, see Table S2. (0.17 MB DOC)

Summary of sequences surveyed in the study. Accession numbers are given for sequences obtained from GenBank. (0.17 MB DOC)

Exon 17 of FoxP2. For abbreviations, see Table S2. (0.10 MB DOC)

Exon 7 of FoxP2. For abbreviations, see Table S2. (0.13 MB DOC)