Chromosome-level assembly of Triplophysa yarkandensis genome based on the single molecule real-time sequencing.

Triplophysa yarkandensis, a species of freshwater fish endemic to Xinjiang, China, is currently classified as endangered. The objective of this study was to obtain the chromosome-level genome of T. yarkandensis using PacBio and Hi-C techniques. The PacBio sequencing technology resulted in an assembly of 520.64 Mb, with a contig N50 size of 1.30 Mb. Hi-C data was utilized for chromosome mapping, ultimately yielding 25 chromosome sequences. The success rate of chromosome mapping was 93%, with a scaffold N50 of 19.14 Mb, and a BUSCO evaluation integrity of 94.1%. The genome of T. yarkandensis encompasses 25,505 predicted protein-coding genes, with a total of 30,673 proteins predicted. The BUSCO evaluation integrity for predicted protein-coding genes was found to be 91.5%. Additionally, the genome contained a genomic repeat sequence accounting for 27.29% of its total length. Future research employing comparative genomics holds considerable importance in elucidating the molecular mechanisms behind saline-alkali adaptation and ensuring the conservation of biological resources.

Ecology of Saline Watersheds: An Investigation of the Functional Communities and Drivers of Benthic Fauna in Typical Water Bodies of the Irtysh River Basin.

In this study, we investigated how changes in salinity affect biodiversity and function in 11 typical water bodies in the Altai region. The salinity of the freshwater bodies ranged from 0 to 5, the brackish water salinities ranged from 5 to 20, and the hypersaline environments had salinities > 20. We identified 11 orders, 34 families, and 55 genera in 3061 benthic samples and classified them into 10 traits and 32 categories. Subsequently, we conducted Mantel tests and canonical correlation analysis (CCA) and calculated biodiversity and functional diversity indices for each sampling site. The results indicated that biodiversity and the proportion of functional traits were greater in freshwater environments than in saline environments and decreased gradually with increasing salinity. Noticeable shifts in species distribution were observed in high-salinity environments and were accompanied by specific functional traits such as swimming ability, smaller body sizes, and air-breathing adaptations. The diversity indices revealed that the species were more evenly distributed in high-diversity environments under the influence of salinity. In contrast, in high-salinity environments, only a few species dominated. The results suggested that increasing salinity accelerated the evolution of benthic communities, leading to reduced species diversity and functional homogenization. We recommend enhancing the monitoring of saline water resources and implementing sustainable water resource management to mitigate the impact of salinity stress on aquatic communities in response to climate-induced soil and water salinization.

The optimal frozen embryo transfer strategy for the recurrent implantation failure patient without blastocyst freezing: thawing day 3 embryos and culturing to day 5 blastocysts.

This study aimed to investigate the optimal frozen embryo transfer (FET) strategy for recurrent implantation failure (RIF) patients with three consecutive failed cleaved embryo implantations and no blastocyst preservation. This retrospective analysis was divided into three groups based on the FET strategy: thawed day 3 embryo transfer (D3 FET group); and extended culture of frozen-thawed day 3 embryos to day 5 blastocysts transfer (D3-D5 FET group); thawed blastocyst transfer (D5 FET group). Transplant cycle data were compared between the three groups. In total, 43.8% of vitrified-thawed cleavage embryos developed into blastocysts. Analysis of the three transplantation strategies showed that, compared with the D3 FET group, D3-D5 had a significantly better hCG-positivity rate and live-birth rate (P < 0.05). Pregnancy outcomes in the D3-D5 FET group and D5 FET group were similar regarding hCG-positivity rate, implantation rate, clinical pregnancy rate, and live-birth rate. Our findings propose two potentially valuable transfer strategies for patients experiencing repeated implantation failures. The D3-D5 FET approach presents a greater potential for selecting promising embryos in cases without blastocyst preservation; however, this strategy does entail the risk of cycle cancellation. Conversely, in instances where blastocyst preservation is an option, prioritizing consideration of the D5 FET strategy is recommended.

Assessing the Impact of Anthropic Pressures on Aquatic Macroinvertebrates: A Functional Trait Approach in the Irtysh River Watershed.

Little is known about how changes in the biodiversity and functional traits of macroinvertebrates in rivers respond to the responses of anthropic pressures and their driving factors. Macroinvertebrates were sampled at 17 sites in the Irtysh River Basin and classified macroinvertebrates into 10 traits and 38 categories between May and August 2022. Then, we performed R-mode linked to Q-mode (RLQ) analysis and calculated functional richness, evenness, divergence, and Rao's quadratic entropy (RaoQ) for each site and community-weighted means for each trait category. Our results indicated that there were pronounced alterations in species variability in the urban region. Functional divergence indicated fierce competition among species and considerable niche overlap in the urban region. Functional evenness indicated that species abundance distribution and interspecific functional distance were not uniform in the urban region. Functional richness indicated that the urban region was the strongest region in terms of niche occupation, resource utilization, and buffering capacity for environmental fluctuations. Rao's quadratic entropy showed that the trait difference of macroinvertebrates was the largest in all regions, which was caused by the gradient environmental difference. Research has revealed that urbanization significantly influences the evolutionary trajectory of macroinvertebrate fauna, culminating in an upsurge in pollution-tolerant species and a convergence of functional traits. We recommend strengthening the control of urban and industrial pollution and wise planning and management of land and water resources to mitigate the impact of anthropogenic destruction on habitat fragmentation in the Irtysh River Basin.

A Comprehensive Analysis of Triplophysa labiata (Kessler, 1874) Mitogenome and Its Phylogenetic Implications within the Triplophysa Genus.

In order to resolve the long-standing controversy surrounding the relationships within the Triplophysa genus, we conducted an extensive analysis of the complete mitogenome of Triplophysa labiata using DNBSEQ short reads. Additionally, we reconstructed the phylogeny of the Nemacheilidae family using mitogenome data. By comparing all available mitogenomes within the Triplophysa genus, we gained valuable insights into its evolutionary history. Our findings revealed that the mitogenome sequence of T. labiata is circular, spanning a length of 16,573 bp. It encompasses 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (D-loop). Among the PCGs, the start codon ATG was commonly observed, except in cox1, while the stop codons TAA/TAG/T were found in all PCGs. Furthermore, purifying selection was evident across all PCGs. Utilizing maximum likelihood (ML) methods, we employed the 13 PCGs and the concatenated nucleotide sequences of 30 Triplophysa mitogenomes to infer the phylogeny. Our results strongly supported the division of the Triplophysa genus into four primary clades. Notably, our study provides the first evidence of the close relationship between T. labiata and T. dorsalis. These findings serve as a significant foundation for future investigations into the mitogenomics and phylogeny of Nemacheilidae fishes, paving the way for further advancements in this field of research.

Complete Mitogenome of the Triplophysa bombifrons: Comparative Analysis and Phylogenetic Relationships among the Members of Triplophysa.

In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of Triplophysa bombifrons via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the Triplophysa genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of T. bombifrons was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for cox1, and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the Triplophysa genus can be divided into 4 main clades and demonstrated that T. bombifrons and T. tenuis are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes.

The mitochondrial genome of Schizothorax argentatus from Northern Xinjiang and its phylogenetic analysis.

In this study, we first sequenced the mitochondrial genome (mitogenome) of Schizothorax argentatus. The circular mitogenome of S. argentatus is 16,587 bp long, containing 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes, and a control region (D-loop region). The base composition is AT biased (63.11%). A phylogenetic tree confirms monophyly at the genus level within Cyprinidae and supports S. argentatus as sister to Schizothorax pseudoaksaiensis.

Population Structure, Genetic Diversity and Differentiation of Triplophysa tenuis in Xinjiang Tarim River.

Triplophysa tenuis is an important indigenous fish in the Xinjiang Tarim River. In this study, we collected 120 T. tenuis individuals from 8 T. tenuis populations in the Tarim River. Through genotyping-by-sequencing (GBS), a total of 582,678,756 clean reads were generated for all the genotypes, and after quality filtering, 595,379 SNPs were obtained for the population genetic analyses. Multiple genetic parameters showed that the 8 T. tenuis populations had high genetic diversity. Phylogenetic tree analysis indicated that all T. tenuis individuals were divided into five branches, the individuals from the north of Tarim River were grouped into cluster 1 (SF and WS) and cluster 3 (DWQ, TKX, and KZE), while the AETS, WLWT and LF individuals from the south of Tarim River were clustered into cluster 2. The result was consistent with the admixture analysis, which supported that the 8 T. tenuis populations were clustered into three subgroups. Furthermore, the pairwise F ST values and genetic distance indicated that there was a large genetic differentiation between WS and other T. tenuis populations. Collectively, this study provides valuable genome-wide data for the conservation of natural T. tenuis populations in the Tarim River.

Comparative transcriptome analysis of Triplophysa yarkandensis in response to salinity and alkalinity stress.

Triplophysa yarkandensis, a fish belonging to the family Nemacheilidae, is distributed in the Tarim River, China, immediately north of the Qinghai-Tibet Plateau. Due to increasing salinity and alkalinity in the Tarim River, the habitats of T. yarkandensis have been seriously altered. To identify the genes and pathways that are important for responding to salinity and alkalinity stress, the gill transcriptomes of fish living under different salinity and alkalinity conditions were obtained using RNA sequencing. A total of 1,123,448,964 clean reads were obtained and assembled into 177,271 unigenes, with an average length of 1703 bp. Around 13,526 unigenes showed differential expression when comparing different salinity concentrations with the controls, 6967 of which were upregulated and 6559 were downregulated. When comparing different alkalinity concentrations with the controls, there were 17,475 unigenes that showed differential expression, of which 10,457 were upregulated and 7018 were downregulated. Only 146 unigenes were both differentially expressed in salinity and alkalinity groups compared to the control. The results of KEGG enrichment showed that there were five upregulated and 12 downregulated pathways in fish subject to salinity treatment. For fish exposed to alkalinity treatment, 15 pathways were upregulated and 13 downregulated. There were four upregulated and four downregulated pathways that were shared by fish subject to salinity and alkalinity treatments. To our knowledge, this is the first study on the T. yarkandensis transcriptome; the information presented here will provide further understanding of the fish's response to salinity and alkalinity stress, as well as further insight into the T. yarkandensis genome.

Complete mitochondrial genome of the Triplophysa (Hedinichthys) yarkandensis (Day).

In this study, we first determined the complete mitochondrial genome of the Triplophysa (Hedinichthys) yarkandensis (Day). The genome was 16,566 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a non-coding region (D-loop region). The overall base composition of T. (H.) yarkandensis (Day) in descending order was T 28.20%, A 27.12%, C 25.61% and G 19.07%, with a slight A + T bias. The complete mitochondrial genome sequence could provide useful information for phylogenetic analysis and studies of population genetics of T. (H.) yarkandensis (Day).