Freshwater shrimp is an extremely rich species group with a long and problematic taxonomic history, attributed to its wide distribution, numerous species and similar morphology. Shrimp diversity and species identification is utmost important for fisheries management. However, identification based on morphological characteristics is difficult and complex for a non-specialist to perform. The water system of Henan Province is relatively abundant, but there are few investigations of freshwater shrimps and no description of molecular features. The aim of this study was to uncover the species diversity and phylogenetic of freshwater shrimp in Henan province by combining morphological identification and molecular species delimitation (barcoding gene: COI gene). About 1,200 freshwater shrimp samples from 46 sampling sites were collected for preliminary traditional morphological identification, 222 samples of these were been further microscopic examination and molecular delimitation. Here we used tree based method (NJ, ML) and distance based method (ABGD, bPTP) mainly to define species, detect the cryptic species and assess the validity of the barcoding in molecular. Comprehensive morphological identification and molecular delimitation results, there were 9 effective species and more than one cryptic species of freshwater shrimp in the province and moreover all of them can be identified by DNA barcoding. The results of morphological identification and molecular identification show high consistency, which proves the high efficiency in freshwater shrimp species identification of the DNA barcoding and the presence of cryptic species.

Lake Dali Nur, located in Inner Mongolia, North China, is alkaline, with Triplophysa dalaica one of the three fish species that not only survive, but thrive, in the lake. To investigate the presence of molecular mutations potentially responsible for this adaptation, the whole genome sequence of the species endemic to the lake was sequenced. A total of 126.5 Gb and 106 Gb data, covering nearly 200X of the estimated genome, were generated using long-read sequencing and Hi-C technology, respectively. De novo assembly generated a genome totalled 607.91 Mb, with a contig N50 of 9.27 Mb. Nearly all whole genome sequences were anchored and oriented onto 25 chromosomes, with telomeres for most chromosomes also being recovered. Repeats comprised approximately 35.01% of the whole genome. A total of 23,925 protein-coding genes were predicted, within which, 98.62% could be functionally annotated. Through comparisons of T. dalaica, T. tibetana, and T. siluroides gene models, a total of 898 genes were identified as likely being subjected to positive selection, with several of them potentially associated with alkaline adaptation, such as sodium bicarbonate cotransporter, SLC4A4. Demographic analyses suggested that the Dali population might have diverged from endemic freshwater Hai River populations, approximately 1 million years ago. The high-quality T. dalaica genome, sequenced in this study, not only aids in the analyses of alkaline adaptation, but may also assist in revealing the mysteries of the highly divergent genus Triplophysa.