Chenhong Li

• PhD
• Professor (Full) at Shanghai Ocean University

The Chinese herring (Ilisha elongata) is an economically important clupeiform fish, mostly found along the coast of China and Japan in the western Pacific Ocean. Overfishing and climate change have caused a substantial decline in its annual catch, which may have impacted its population size and structure. Here, we present a chromosome-level genome...

Sex reversal of Hilsa shad, Tenualosa ilisha confirmed by histological data

Anadromous migration toward riverine tributaries is often challenged by altered environmental cues, food scarcity, and energy demands, sometimes at the expense of life itself. Tenualosa ilisha (Clupeiformes: Dorosomatidae), the national fish of Bangladesh, an anadromous shad, offers a model for understanding the molecular mechanisms of migration. T...

The advance of environmental DNA ( eDNA ) has enabled rapid and non‐invasive species detection in aquatic environments. While most studies focus on species detection, recent works explored using eDNA concentration to quantify species abundance. However, the differential individual DNA contribution to eDNA samples could easily obscure the eDNA conce...

Sinocyclocheilus is a group of cyprinid fishes endemic to China distributed in the karst region of southwest China. In this study, the complete mitogenomes of Sinocyclocheilus guilinensis Ji, 1985 and Sinocyclocheilus huangtianensis Zhu et al. 2011 are reported and characterized. Both genomes contain 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and...

Altogether 99 specimens catfishes collected from the Eastern Region of Nepal (ERN), representing 29 species belonging to 21 genera and eight families were successfully barcoded employing mitochondrial COI gene sequence analysis showing 98.5-100% identity with both GeneBank and BOLD databases. Of these, two species i.e. Amblyceps, arunachalense and...

Correlophus ciliatus, or the crested gecko, is widely kept as a pet in many countries around the world due to its ease to care and bred and its high survival rate. However, there is limited number of genomic studies on the crested gecko. In this study, we generated a high-quality chromosome-level genome assembly of the crested gecko by combining Na...

Planktonic ciliates play a vital role in the cycle of matter and energy transfer within the microbial food web. They are usually used to monitor water quality. However, the Utermöhl method, a popular quantitative method for plankton, cannot reveal the ci liature, which usually results in a low taxonomic resolution of ciliates and the underestimatio...

The freshwater bodies of Nepal host a great deal of fish diversity; however, the molecular study of Nepalese fish is still in its early stages. Conservation management tactics require knowledge of the real species composition, often impeded by descriptions of intermittent species based on traditional taxonomy. Catfish, one of the most overfished ta...

Microdous (Gobiiformes: Odontobutidae) is a genus of freshwater sleepers distributed in southern China and Vietnam. There are two described species in this genus, M. chalmersi widely distributed in Hainan Island and Guangxi province of China and M. amblyrhynchos with a very restricted distribution range in Baise, Guangxi. It has been reported that...

The non-native vermiculated sailfin catfish Pterygoplichthys disjunctivus (Weber, 1991) is recorded for the first time in eastern Nepal's aquatic systems. Native to South America, the first reports of P. disjunctivus in Asia were recorded in India, with subsequent reports from Bangladesh, Hongkong, Indonesia, Malaysia, Singapore, Thailand and Vietn...

The Chinese giant salamander (Andrias davidianus), listed as an endangered species under “secondary protection” in China, faces significant threats due to ecological deterioration and the expansion of human activity. Extensive field investigations are crucial to ascertain the current status in the wild and to implement effective habitat protection...

The advance of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. Although most studies focus on assessing the absence or presence of species, some recent studies explored the potential of using eDNA concentration of targeted genes to quantify species abundance. However, eDNA concentration could b...

Study of divergence of freshwater fish populations between island and adjacent mainland areas can shed light on the phylogeographical relationships of these regions. Neodontobutis hainanensis is a freshwater fish species restricted to Hainan Island and in Guangdong and Guangxi provinces in the southern mainland China. We examine the phylogenetic re...

One specimen of tropical shad was caught from the Giang Thanh River, Kien Giang province, Vietnam in a survey on 16 October 2022. We identified the specimen as the hilsa shad, Tenualosa ilisha Hamilton, 1822 using morphological analysis, and further validated by its cytochrome oxidase subunit I (COI) sequence. The specimen was 418 mm long, 1428 g i...

Monitoring and evaluating river ecosystems are of paramount importance in addressing ecological and environmental challenges. While eDNA (environmental deoxyribonucleic acid)-based method has emerged as a valuable tool for understanding these issues, its application in assessing phylogenetic diversity, community stability, and the identification of...

The genus Odontobutis is a group of freshwater fishes endemic to East Asia. Phylogenetic relationships among the Odontobutis species have never been fully tested due to incomplete taxon sampling and that molecular data have not been collected in many Odontobutis species. In the present study, we sampled 51 specimens from all known eight Odontobutis...

Introduction Rice-fish farming can play an important role in increasing food production in less developed countries. The Lao People’s Democratic Republic (Laos) is one of the least developed countries in the world, and rice is the most important crop in Laos. Methods The present study conducted field surveys in 2022 in order to get a better unders...

Siniperca undulata and S. obscura (Centrarchiformes: Sinipercidae) are small Chinese perches, living in creeks and streams in southern China. While they have sympatric distribution and occupy similar macrohabitat, their body sizes and ecological niches have many differences. Determining the genome sequences of S. undulata and S. obscura would provi...

The Hainan small-toothed sleeper, Microdous chalmersi, is an endemic species disjunctly distributed in Hainan and Guangxi provinces of China. Morphological differences have been previously observed between these populations. We sequenced the mitochondrial genomes of M. chalmersi from Hainan and Guangxi in order to test whether there is a cryptic sp...

In 2016, Amblyceps waikhomi from the Brahmaputra drainage of Arunachal Pradesh, India, was described. Based on morphometric and meristic characteristics, we report the frst-ever sighting of A. waikhomi from the Singhiya River in Morang district. A deeper body depth at the anus sets the A. waikhomi apart from its congeners. Te river systems of Nepal...

Microdous amblyrhynchos , a new species, the second one in the genus, from the family Odontobutidae, is described from the Hongshui River, in the upper reaches of the Xijiang River of the Pearl River drainage, Baise City, Guangxi Zhuang Autonomous Region, southern China. This species is distinguished from its only congener, M. chalmersi , by the bl...

The dynamic climate history that drove sea level fluctuation during past glacial periods mediated the movement of organisms between Asia and North America via the Bering Land Bridge. Investigations of the biogeographic histories of small mammals and their parasites demonstrate facets of a complex history of episodic geographic colonization and refu...

A combination of short-insert paired-ended and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require h...

Simple Summary Mitochondrial genomes (mitogenomes) have been widely used for studying the taxonomy and phylogeny of insects. Chironomids are important bioindicators for monitoring and assessing the health of freshwater ecosystems. However, only a few complete mitogenomes of Chironomus species have been reported till now. In this study, the whole mi...

Cynoglossus senegalensis (Kaup, 1958) is a valuable species in the artisanal fisheries and has been identified as overexploited inmany African countries. The main aim of this study is to determine its basic biological knowledge on the exploitation status in terms oflength-weight relationship (LWR), condition factor, and the depth of information on...

A combination of short-read paired-end and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require high-...

The Laotian shad (Tenualosa thibaudeaui) belongs to the family Clupeidae and is mainly distributed across Lao PRD, Cambodia and northern Thailand. Due to overfishing and dam reconstruction, the Laotian shad is on the verge of extinction and currently listed as vulnerable by the IUCN. Nanopore and Illumina sequencing data were integrated to generate...

The Laotian shad (Tenualosa thibaudeaui) belongs to the family Clupeidae and is mainly distributed across Lao PRD, Cambodia and northern Thailand. Due to overfishing and dam reconstruction, the Laotian shad is on the verge of extinction and currently listed as vulnerable by the IUCN. Nanopore and Illumina sequencing data were integrated to generate...

Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely al...

This study deals with the description of two groupers, Epinephelus bleekeri and E. erythrurus, for the first time from St. Martin’s Island, the only coral island in Bangladesh based on morphology and DNA barcoding by mitochondrial cytochrome oxidase I gene (COI). The morphological identifying character for E. bleekeri was lower two-thirds of the ca...

The tapertail anchovy (Coilia nasus) is an economically important species, mainly distributed along the coast of the northwestern Pacific and associated freshwater bodies, including the Qiantang River, the Yangtze River, the Liaohe River, and the Yalu River of China, and further eastward to Korean Peninsula and Ariake Sound of Japan. There have bee...

The Clupeiformes, including among others herrings, anchovies, shads and menhadens are ecologically and commercially important, yet their phylogenetic relationships are still controversial. Previous classification of Clupeiformes were based on morphological characters or lack of synapomorphic characters. More recent studies based on molecular data a...

Odontobutis potamophilus is a popular food fish in China, distributed mainly in the middle and lower reaches of the Yangtze River, where it is a famous delicacy and a newly focused species for aquaculture. The wild populations of O. potamophilus are facing the problem of overfishing and habitat degradation. Therefore, it is very necessary to invest...

A new species, Neodontobutis lani (Odontobutidae) is described from the Zuojiang River, a tributary of the Xijiang River of the Pearl River basin, at Longzhou Town, Guangxi Zhuang Autonomous Region, Southern China. This species can be distinguished from other Neodontobutis species by following characters: anterior head flat, with interorbital width...

Library preparation is an essential step for the next-generation sequencing, such as whole-genome sequencing, reduced-representation genome sequencing, exome sequencing and transcriptome sequencing. The library preparation often involves many steps, including DNA fragmentation, end repair, ligation and amplification. Each step involves different en...

The objective of this study was to investigate influence of meso-scale eddies in the western South China Sea on species composition and spatial patterns of fish larvae and juveniles based on the data collected during summer and autumn in 2012. Nintyeight species belonging to 38 families were collected, including 78 species in summer and 41 species...

Objectives American shad ( Alosa sapidissima ) is an important migratory fish under Alosinae and has long been valued for its economic, nutritional and cultural attributes. Overfishing and barriers across the passage made it vulnerable to sustain. To protect this valuable species, aquaculture action plans have been taken though there are no publish...

Among marine species distributed in the Indian Ocean and the Pacific, the Indo–Pacific Barrier (IPB) has been found to be an important barrier of divergence of species distributed on both sides. Among the five species of the genus Pampus, only Pampus chinensis and P. cinereus are distributed across the western Pacific and the Indian Oceans and have...

Background High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.Methods We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep f...

Objectives: American shad (Alosa sapidissima) is an important migratory fish under Alosine and has long been valued for its economic, nutritional and cultural attributes. Overfishing and barriers across the passage made it vulnerable to sustain. To protect this valuable species, aquaculture action plans have been taken though there are no published...

Rhinogobius similis is distributed in East and Southeast Asia. It is an amphidromous species found mostly in freshwater and sometimes brackish waters. We have obtained a high-resolution assembly of the R. similis genome using nanopore sequencing, high throughput chromosome conformation capture (Hi-C) and transcriptomic data. The assembled genome wa...

A combination of next-generation sequencing technologies and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libra...

Nowadays, the promotion of advanced approaches and techniques for collecting data on the fisheries statistics is a key to sound policy-development, better decision-making and responsible fisheries management. In African developing countries, artisanal marine fisheries remain the highest producers of fishery resources and the largest fleet. In devel...

There is an extensive collection of literature on the taxonomy and phylogenetics of flatfishes (Pleuronectiformes) that extends over two centuries, but consensus on many of their evolutionary relationships remains elusive. Phylogenetic uncertainty stems from highly divergent results derived from morphological and genetic characters, and between var...

High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment. We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the d...

A rare specimen of Parmaturus melanobranchus was collected from the South China Sea. The complete mitochondrial genome of the specimen was sequenced using Illumina Hiseq platform and assembled with Geneious and Trinity. The mitogenome is 16,687 bp long with a base composition of 30.4% A, 14.1% G, 23.5% C and 32.1% T, respectively. A total of 37 gen...

Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large dat...

Tenualosa ilisha is a popular anadromous and significant trans-boundary fish. For sustainable management and conservation of this fish, drawing an appropriate picture reflecting population status of this species is very essential based on their all-strategic habitats in Bangladesh. In this study, 139 samples from 18 sites were collected and cross-s...

Siniperca chuatsi and Siniperca kneri are two economically important freshwater fishes endemic to East Asia. Recently, some Siniperca specimens collected from Lake Poyang and Lake Dongting in the middle reaches of the Yangtze River couldn't be clearly identified as they showed intermediate morphological characteristics between S. chuatsi and S. kne...

Investigations of intercontinental dispersal between Asia and North America reveal complex patterns of geographic expansion, retraction and isolation, yet historical reconstructions are largely limited by the depth of the record that is retained in patterns of extant diversity. Parasites offer a tool for recovering deep historical insights about th...

Tenualosa ilisha is a popular anadromous and significant trans-boundary fish. For sustainable management and conservation of this fish, drawing an appropriate picture reflecting population status of this species is very essential based on their all-strategic habitats in Bangladesh. In this study, 139 samples from 18 sites were collected and cross-s...

The Kelee shad (Hilsa kelee) is currently considered as the only representative species in the genus Hilsa (Clupeidae, Clupeiformes) with a wide distribution in almost all coasts of the Indian Ocean. Two marginal marine water bodies of the Indian Ocean, the Bay of Bengal and the Arabian Sea, are important fisheries areas for this fish. In this stud...

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogs that can mislead phylogenetic...

As habitat and distribution, in the study a total of 18 crab species were identified, belonging to 10 families (Calappidae, Epialtidae, Gecarcinidae, Grapsidae, Matutidae, Ocypodidae, Panopeidae, Sesarmidae, Varunidae, and Xanthidae) order Decapoda under subphylum crustacean with relevant distinguish morphological and meristic character and geograp...

Background The flathead grey mullet, Mugil cephalus has a global distribution in tropical, subtropical and temperate seas worldwide. Previous studies proposed that globally distributed M. cephalus comprises at least 14 different lineages, and divided into two or three groups in the northwest Pacific. Therefore, we hypothesized that there may exist...

Most of the closely related fish species are similar in appearance, with slight differences. This study evaluated 35 morphological characteristic parameters and the number, shape, and spatial location of bones in the skull and vertebrae of the mandarin fish Siniperca chuatsi and big-eye mandarin fish Siniperca kneri. We can understand their ecologi...

The aquaculture of yellowtail kingfish (Seriola lalandi) has expanded around the globe, including China. Genetic resource of Chinese S. lalandi urgently needs to be assessed for improving production. Here, we collected wild S. lalandi samples from the Bohai Sea, China and evaluated its genetic diversity based on 17,690 nuclear loci. A population fr...

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogs that can mislead phylogenetic...

Crab diversity in Coastal Bangladesh

The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history...

As habitat and distribution, in the study a total of 18 crab species were identified , belonging to 10 families (Calappidae, Epialtidae, Gecarcinidae, Grapsi-dae, Matutidae, Ocypodidae, Panopeidae, Sesarmidae, Varunidae, and Xan-thidae) order Decapoda under subphylum crustacean with relevant distinguish morphological and meristic character and geog...

Many flatfish species, such as Scophthalmus maximus, Paralichthys olivaceus, Solea senegalensis, are extensively cultured worldwide. In flatfishes, eye migration varies among different species and even within the same species. The genetic mechanism underlying eye migration is still unclear, and it is the key to improve metamorphosis in flatfish aqu...

Abstract Freshwater fish evolved from anadromous ancestors can be found in almost all continents. The roles of paleogeographic events and nature selection in speciation process often are under focus of research. We studied genetic diversity of anadromous and resident tapertail anchovies (Coilia nasus species complex) in the Yangtze River Basin usin...

Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide p...

Highly specialized grade (HSG; genera Gymnocypris, Oxygymnocypris, Schizopygopsis, Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morpholo...

Gene capture coupled with the next‐generation sequencing has become one of the preferred methods of subsampling genomes for phylogenomic studies. Many exon markers have been developed in plants, sharks, frogs, reptiles, fishes, and others, but no universal exon markers have been tested in ray‐finned fishes. Here, we identified a suite of “single‐co...

Piscivory in vespertilionid bat species in the genus Myotis and trawling as typical element of behaviour in the hunting flight above the water surface are widely acknowledged. However, among the European bat fauna, only long-fingered bats {Myotis capaccinii) are known to consume fish. In Daubenton's bat {Myotis daubentonii) as well as the pond bat...

Background Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene capturing and subsequent next generation sequencing of putative ortholog exons of major clupeocephalan lineages. Sequence information for the RNA bait design...

The use of genome-scale data to infer phylogenetic relationships has gained in popularity in recent years due to the progress made in target-gene capture and sequencing techniques. Data filtering, the approach of excluding data inconsistent with the model from analyses, presumably could alleviate problems caused by systematic errors in phylogenetic...

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unpar...

The genus Rhinogobius Gill 1859 is widely distributed in fresh waters along the Western Pacific coast of tropical and temperate Asia. A new species, Rhinogobius maxillivirgatus, is described from Anhui Province in Eastern China. This species can be differentiated from all congeners by a combination of the following characters: up to 6 longitudinal...

The Odontobutidae is a group of freshwater sleepers endemic to East and Southeast Asia. The composition of the Odontobutidae is controversial and the systematics position of some species (e.g. Philypnus chalmersi) remains unknown. Phylogenetic relationship among the odontobutids has never been really tested due to the lack of informative morphologi...

Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or t...