Genome Survey and Evolutionary Analysis of Eight Lamprotula Species: SSR Profiling, Mitochondrial Characterization, and Population Dynamics Inference.

Freshwater bivalves are vital to aquatic ecosystems but face severe global threats. Understanding their genomic traits and evolution is crucial for effective conservation. This study conducted whole-genome sequencing on eight Lamprotula species.

Population Patterns and Dynamics of (Clupeiformes: Pristigasteridae) Revealed by Target Enrichment Data.

The elongate ilisha () is an important commercial species found along the Northwestern Pacific Coast. A sharp decline in the annual catch of over recent decades implies a concerning situation regarding its fishery stocks. Nonetheless, inadequate knowledge of the genetic diversity, population structure, and historical demography of this species has hindered the establishment of sustainable fishery policies and appropriate conservation measures.

Cryptic Diversity and Climatic Niche Divergence of Kieffer (Diptera: Chironomidae): Insights from a Global DNA Barcode Dataset.

Accurate species identification of small aquatic insects remains challenging due to their morphological similarities. This study addresses this issue by developing a DNA barcode reference library for the globally distributed (Diptera: Chironomidae). We analyzed cytochrome oxidase subunit I (COI) sequences of 241 specimens belonging to 13 species from 18 countries, including 56 newly generated and 185 publicly available COI barcodes.

Genomic Evolution of White Spot Syndrome Virus in Shrimp: Insights from Transposon Dynamics.

White spot syndrome virus (WSSV) has emerged as a significant threat to global shrimp aquaculture, causing economic losses because of its rapid spread and high mortality rates. This study aims to elucidate the genetic and evolutionary dynamics of WSSV through a comprehensive genome analysis. Utilizing 27 complete genome sequences sourced from public databases, this study investigates the genetic variability, potential recombination events, and evolutionary patterns of WSSV.

Resolving taxonomic uncertainties in ailiid catfishes (Siluriformes: Ailiidae) using Genome-Scale data.

The Ailiidae family, endemic to South and Southeast Asia, comprises diverse freshwater catfish inhabiting major river basins across the region. Evolutionary relationships and taxonomic classification within Ailiidae family remain contentious. Here, we resolve these uncertainties using phylogenomic data from 29 specimens representing 11 species and six of the seven recognized genera, supplemented by two outgroup taxa(Pachypterus atherinoidesandP.

Stochastic Processes Drive the Assembly of Planktonic Ciliates in A Trellised River Network.

The topology and connectivity of rivers can be modified by the water project operation for agriculture and civilization, as exemplified by the trellised river system in Chongming Island. Ciliates, as an exceptional indicator, are often employed for monitoring the health of aquatic ecosystems. However, the assembly and structure of planktonic microeukaryote (e.

A chromosome-level genome assembly of the Chinese herring (Ilisha elongata) uncovered its population dynamics and genes related to lipid metabolism.

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 assembly of the Chinese herring, generated using a combination of Nanopore sequencing, Illumina sequencing, and high-throughput chromatin conformation capture (Hi-C) technologies.

Comparative Mitogenomic Analyses of (Diptera: Chironomidae).

, a genus within the species-rich subfamily Orthocladiinae (Diptera: Chironomidae), remains poorly resolved in molecular phylogenetics due to limited available molecular data. Here, we sequenced and analyzed the complete mitogenomes of five species, using two species as outgroups. Our results reveal that the mitogenomes of are structurally conserved and retain a presumed ancestral gene order.

Species Delimitation and Cryptic Diversity in Thienemann & Bause, 1913 (Diptera: Chironomidae) Based on DNA Barcoding.

The genus Thienemann & Bause, 1913 (Diptera: Chironomidae) currently includes more than 120 recognized species worldwide, but precise species-level identification based solely on morphology remains challenging. Pronounced morphological differences among life stages and the time-consuming inefficiency of rearing larvae further complicate life-stage matching in this genus. In this study, we assessed species diversity by integrating morphological examination and DNA barcoding, analyzing 911 DNA barcodes from newly collected samples and a public database.

Chromosome-Level Genome Assembly and Comparative Transcriptome Analyses Identified Energy Conservation as a Key Strategy for Anadromous Adaptation of the Hilsa Shad, (Clupeiformes: Dorosomatidae).

Anadromous migration toward riverine tributaries is often challenged by altered environmental cues, food scarcity, and energy demands, sometimes at the expense of life itself. (Clupeiformes: Dorosomatidae), the national fish of Bangladesh, an anadromous shad, offers a model for understanding the molecular mechanisms of migration. To this end, we present a chromosome-level genome of and compare its transcriptomic imprints from muscle and liver across environments to trace the physiological shifts driving the migration.

Comparative Mitogenomic Analyses of Tanypodinae (Diptera: Chironomidae).

Tanypodinae, a highly diverse subfamily within Chironomidae (Diptera), has been poorly represented in mitochondrial genome (mitogenome) databases, with only a limited number of complete or partial sequences available. To address this gap, we present the first complete mitogenome sequences of 16 Tanypodinae species and 1 Podonominae species. By integrating these novel data with previously published chironomid mitogenomes, we conducted a comprehensive comparative mitogenomic analysis of 21 Tanypodinae species.

Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA).

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 concentration-species abundance relationship.

The complete mitochondrial genomes and phylogenetic analysis of two Chinese endemic cave fishes, and (Cypriniformes: Cyprinidae).

is a group of cyprinid fishes endemic to China distributed in the karst region of southwest China. In this study, the complete mitogenomes of Ji, 1985 and Zhu et al. 2011 are reported and characterized.

Morphometric and phylogenetic analysis of a commercial fish (Teleostei, Leiognathidae).

The complete mitochondrial genome and phylogenetic analysis for from the South China Sea was performed using shallow genome skimming. For accurate species identification and redescription, morphometric and meristic characters were examined and compared with previous descriptions. To facilitate the identification of species and to enable comparison with the mitochondrial genome phylogeny, molecular comparisons were conducted using three mitochondrial genes: large ribosomal RNA ( rRNA), cytochrome c oxidase subunit 1 (), and NADH dehydrogenase ().

Revision of the loach genus Claea Kottelat, 2010 (Teleostei: Nemacheilidae) in China, with a description of a new species from the Chang-Jiang basin.

A taxonomic revision of the nemacheilid genus Claea from China is provided based on molecular and morphological data. Three species are identified in this genus: C. dabryi (type species), C.

Microdous hanlini (Gobiiformes: Odontobutidae), a new species of the fine-toothed sleepers from Guangxi, China.

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.

High-quality genome assembly and annotation of the crested gecko (Correlophus ciliatus).

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 Nanopore, Illumina, and Hi-C data.

New insights and investigation: Morphomolecular notes on the infraciliature, taxonomy, and systematics of pleurostomatid ciliates (Protozoa, Ciliophora), with establishment of a new suborder, two new genera, and three new species.

Pleurostomatid ciliates, as a highly diverse and widely distributed unicellular eukaryote group, play a crucial role in the cycling of nutrients and energy in microbial food webs. However, research on pleurostomatids remains insufficient, resulting in a paucity of molecular information and substantial gaps in knowledge of their phylogenetic relationships. In recent years, we investigated pleurostomatid diversity in various Chinese habitats, including their systematic relationships and taxonomic circumscriptions, which were comprehensively analyzed using an integrative morphomolecular approach.

Redescription of (Nichols, 1926) with the description of a new species of the genus (Cypriniformes, Gobionidae) from southern China.

Although (Nichols, 1926) has been treated valid since it was described, its morphology remains vague, especially when comparing it with another similar species, (Yao & Yang, 1977). In this study, the types of both species were examined and also compared with several lots of specimens from a wide geographical range: there is no significant difference in morphology between them. Additionally, molecular evidence supported by mitochondrial gene sequence also showed low genetic distance in between.

A new species of (Teleostei, Cypriniformes, Xenocyprididae) from Southeast China.

is described from the Qiantang and Oujiang rivers in Zhejiang Province and a tributary of the Yangtze River adjacent to the Qiantang River. It is distinguished from congeners by the following combination of morphological features: no obvious anterior notch on the tip of the upper lip; 45-52 lateral-line scales; 18-21 pre-dorsal scales; two rows of pharyngeal teeth; a maxillary extending to or slightly beyond the vertical anterior margin of the orbit in adult males; a pectoral fin extending to the pelvic fin in adult males; nuptial tubercles on the cheeks and lower jaw of males, which are usually united basally to form a plate; uniform narrow pale pink cross-bars on trunk and two widening significantly on caudal peduncle. Its validity was also supported by its distinct Cyt gene sequence divergence from all congeners and its monophyly recovered in a Cyt gene-based phylogenetic analysis.

Characteristics and Comparative Analysis of Six Mitogenomes of Genus Goetghebuer, 1922 (Diptera: Chironomidae).

Chironomidae is a cosmopolitan and species-rich family of insects, with many species serving as useful indicators of aquatic ecosystem health. In this study, we newly sequenced six species of Goetghebuer, 1922 (Chironomidae: Chironominae) by high-throughput sequencing technology. We analyzed characters of the mitochondrial genome, including the sequence length, nucleotide composition, and evolutionary rates of this genus.

Southwestward Expansion of the Pacific Sleeper Shark's () Known Distribution into the South China Sea.

We conducted an experiment of planting a dead cow and a metal-framed cage with cameras on the 1629 m deep sea floor off the southeast coast of Hainan Island in the northwestern South China Sea, using ROV diving and setting up a video camera on the cage to observe animals who came to eat the bait. The deep-sea cameras captured footage of eight Pacific sleeper sharks () swimming and feeding around the dead cow. To our knowledge, this is the first time the occurrence of such a shark species has been reported in the South China Sea.

Coleps shanghaiensis n. sp. challenges the validity of the genus Levicoleps (Ciliophora, Prostomatida).

Coleps is a common genus of pelagic ciliates in freshwater and brackish water habitats. Classification and phylogeny of Coleps species are, however, still full of confusion. In this study, we investigated Coleps shanghaiensis n.

Real-Time Monitoring on the Chinese Giant Salamander Using RPA-LFD.

The Chinese giant salamander (), 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 measures to safeguard this species and support its population development. Traditional survey methods often fall short due to the elusive nature of the , presenting challenges that are time-consuming and generally ineffective.

Divergence of the freshwater sleeper, (Chen, 1985) (Teleostei, Odontobutidae), in the Pearl River basin and on Hainan Island of southern China.

Study of divergence of freshwater fish populations between island and adjacent mainland areas can shed light on the phylogeographical relationships of these regions. is a freshwater fish species restricted to Hainan Island and in Guangdong and Guangxi provinces in the southern mainland China. We examine the phylogenetic relationship and population structure of based on 3,176 nuclear loci using a gene-capture method.