Chromosomal-level genome assembly data from the pale chub, Zacco platypus (Jordan & Evermann, 1902).

The pale chub, Zacco platypus (Cypriniformes; Xenocyprididae; homotypic synonym: Opsariichthys platypus; Jordan & Evermann, 1902), is widely distributed in the freshwater ecosystems throughout East Asia, including South Korea. In this study, we constructed a de novo genome assembly of Z. platypus to serve as a reference for fundamental and applied research. The assembly was generated using a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. The draft genome of Z. platypus consisted of 16,422,113 reads from the HiFi library, 702,143,130 reads from the Illumina TruSeq library, and 250,789,660 reads from the Hi-C library. Assembly with Hifiasm resulted in 336 contigs, with an N50 length of 31.9 Mb. The final assembled genome size was 838.6 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis indicated that 3,572 (98.1 %) of the expected genes were found in the assembly, with 3,521 (96.7 %) being single-copy and 51 (1.4 %) duplicated after searching against the Actinopterygii database. Of the 319 Hi-C scaffolds, 24 exceeded 10 Mb were thus classified as chromosome-level scaffolds. The assembled genome comprises 41.45 % repeat sequences. Gene annotation was performed using Illumina RNA-Seq and PacBio Iso-Seq data, based on repeat-masked genome sequences. The final annotation resulted in 34,036 protein-coding genes. This chromosomal-level genome assembly is expected to be a valuable resource for future health assessments in aquatic ecosystems, providing insights into the developmental, environmental, and ecological aspects of Z. platypus.

The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses.

Hemiculterella wui is an endemic small freshwater fish, distributed in the Pearl River system and Qiantang River, China. In this study, we identified and annotated the complete mitochondrial genome sequence of H. wui. The mitochondrial genome was 16,619 bp in length and contained 13 protein coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The nucleotide composition of the mitochondrial genome was 29.9% A, 25.3% T, 27.4% C, and 17.5% G, respectively. Most PCGs used the ATG start codon, except COI and ATPase 8 started with the GTG start codon. Five PCGs used the TAA termination codon and ATPase 8 ended with the TAG stop codon, and the remaining seven genes used two incomplete stop codons (T and TA). Most of the tRNA genes showed classical cloverleaf secondary structures, except that tRNASer(AGY) lacked the dihydrouracil loop. The average Ka/Ks value of the ATPase 8 gene was the highest, while the average Ka/Ks value of the COI gene was the lowest. Phylogenetic analyses showed that H. wui has a very close relationship with Pseudohemiculter dispar and H. sauvagei. This study will provide a valuable basis for further studies of taxonomy and phylogenetic analyses in H. wui and Xenocyprididae.

Non-linear effects on the population performance of Bighead Carp under different maturation schedules.

Bighead Carp currently threatens to invade the Laurentian Great Lakes from the Mississippi River, but the novel climatic conditions it will encounter by expanding northwards could affect its population performance. Bighead Carp in colder climates exhibits slower growth and matures later, with later maturation typically leading to larger adult size and increased fecundity and survival. Accordingly, the life-history strategies of Bighead Carp at its northern range limits could differ from those observed in its current invaded range. To explore how population performance could differ across changing environmental conditions, we used a stage- and age-based matrix population model parameterized with values reported for Bighead Carp populations around the world. The model was used to evaluate how different ages of maturity and their resulting impacts to body size, survival, and fecundity could impact rates of population growth and establishment. Age of maturity had a non-linear effect on population growth, with maturation at intermediate ages (4-6 years) resulting in better performance. However, performance differed less between maturation ages when fecundity was allowed to increase disproportionately with body size. Greater population growth at younger ages of maturity suggest that invasion at lower latitudes could enable establishment in fewer years due to faster rates of development in warmer temperatures. Across all maturation schedules, population growth was most sensitive to the recruitment of age-1 individuals and least sensitive to adult survival, and vital rates overall varied more in their contribution to population growth at younger ages of maturity. Thus, understanding the factors that control age-1 recruitment would inform projections of population performance for Bighead Carp in the Laurentian Great Lakes. Supplementary Information: The online version contains supplementary material available at 10.1007/s10530-023-03126-z.

Monsoon boosted radiation of the endemic East Asian carps.

Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.

Characterization of the complete mitochondrial genome of Aphyocypris chinensis (Cypriniformes, Xenocyprididae), and its phylogenetic position in Cypriniformes.

Aphyocypris chinensis Günther, 1868 is a small freshwater fish of the family Xenocyprididae (Cypriniformes). In this study, we determined its complete mitochondrial genome and phylogenetic position in Cypriniformes. The complete mitochondrial genome is 16,608 bp in size, containing 13 protein-coding genes, two RNAs, 22 tRNAs, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Our mitogenomic phylogeny revealed that A. chinensis belongs to Xenocyprididae, rather than Danionidae. This mitogenome information could play an essential role in resolving the conflict over its current taxonomic status in Cypriniformes.