Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Population genetic diversity and environmental adaptation of Tamarix hispida in the Tarim Basin, arid Northwestern China

Arid ecosystems, characterized by severe water scarcity, play a crucial role in preserving Earth's biodiversity and resources. The Tarim Basin in Northwestern China, a typical arid region isolated by the Tianshan Mountains and expansive deserts, provides a special study area for investigating how plant response and adaptation to such environments. Tamarix hispida, a species well adapted to saline-alkaline and drought conditions, dominates in the saline-alkali lands of the Tarim Basin. This study aims to examine the genetic diversity and environmental adaptation of T. hispida in the Tarim Basin. Genomic SNPs for a total of 160 individuals from 17 populations were generated using dd-RAD sequencing approach. Population genetic structure and genetic diversity were analyzed by methods including ADMIXTURE, PCA, and phylogenetic tree. Environmental association analysis (EAA) was performed using LFMM and RDA analyses. The results revealed two major genetic lineages with geographical substitution patterns from west to east, indicating significant gene flow and hybridization. Environmental factors such as Precipitation Seasonality (bio15) and Topsoil Sand Fraction (T_SAND) significantly shaped allele frequencies, supporting the species' genetic adaptability. Several genes associated with environmental adaptation were identified and annotated, highlighting physiological and metabolic processes crucial for survival in arid conditions. The study highlights the role of geographical isolation and environmental factors in shaping genetic structure and adaptive evolution. The identified adaptive genes related to stress tolerance emphasize the species' resilience and highlight the importance of specific physiological and metabolic pathways.

Germplasm Resources Evaluation of Cultured Largemouth Bass (Micropterus salmoides) in China Based on Whole Genome Resequencing

Background: Largemouth bass (Micropterus salmoides), a valuable freshwater fish species, has experienced significant genetic decline in China due to prolonged domestic breeding and limited introduction of new genetic material. It is necessary to have a comprehensive understanding of the genetic status of largemouth bass populations in China. Method: In this study, we conducted population genetic analyses on nine cultured largemouth bass populations using whole genome resequencing. Results: A total of 3.23 Tb of clean bases were generated, with average Q20 and Q30 values of 98.17% and 94.25%, respectively, and 2,140,534 high-quality SNPs were obtained. Relatively high genetic diversity was observed across all populations. Combined with linkage disequilibrium (LD) patterns, the Wanlu (WL) population possessed the highest genetic diversity, and the Longyou (LY) population possessed the lowest genetic diversity. Additionally, population structure analyses, including pairwise F-statistics, phylogenetic trees, PCA, and admixture analysis, revealed significant genetic differentiation, particularly between the WL, LY, and other 7 populations, while also indicating the occurrence of a common admixture event. Finally, TreeMix inferred migration events from the WL to the Chuanlu (CL) population and from the Taiwan breeding population (TWL) to the Guanglu (GL) population. Conclusions: These findings provide a critical foundation for developing conservation and breeding strategies for largemouth bass in China.

Mitochondrial genome data provide insights into the phylogenetic relationships within Triplophysadalaica (Kessler, 1876) (Cypriniformes, Nemacheilidae)

Due to the detrimental effect of formaldehyde on DNA, ethanol has replaced formalin as the primary preservative for animal specimens. However, short-term formalin fixation of specimens might be applied during field collection. In an increasing number of studies, DNA extraction and sequencing have been successfully conducted from formalin-fixed specimens. Here the DNA from five specimens of Triplophysadalaica (Kessler, 1876) were extracted and performed high-throughput sequencing. Four of the specimens underwent short-term fixation with formalin and were subsequently transferred to ethanol. One was continuously stored in ethanol. No significant difference of DNA quality and amount were observed among these samples. Followed by assembly and annotation, five mitochondrial genomes ranging in length from 16,569 to 16,572 bp were obtained. Additionally, previously published data of other individuals or species were included to perform phylogenetic analyses. In the reconstructed trees, all eight individuals of T.dalaica form a monophyletic group within the Triplophysa branch. The group is divided into three clades: (1) samples from the Yellow River, (2) those from the Yangtze River, and (3) those from the Haihe River, and the Lake Dali Nur. This study sheds initial light on the phylogeographic relationships among different populations of T.dalaica, and will support the research about its evolutionary history in the future.

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.

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2 bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with F_st values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics.

Genetic Diversity and Population Structure of Hemiculter leucisculus (Basilesky, 1855) in Xinjiang Tarim River

Hemiculter leucisculus is an invasive fish and widely distributed in the Xinjiang Tarim River. In this study, RAD-seq was used to explore the genetic diversity and population subgroup structure of H. leucisculus in the Tarim River and develop relevant Simple Sequence Repeat (SSR) markers. The study collected 40 samples distributed at four different sites of the Tarim River. A total of 7,291,260 single nucleotide polymorphisms (SNPs) were obtained. The genetic diversity results showed that the population genetic diversity level of H. leucisculus was low. The population pairwise F_ST values ranged from 0.231 to 0.258, indicating that there was moderate genetic differentiation among these populations. AMOVA showed that the genetic variation within populations accounted for 92.31% of the total variation. The principal component analysis (PCA) and neighbor joining (NJ) tree revealed that the four populations could be separated into two clusters (upper-middle and downstream populations) and the individuals from Taitema Lake (TTMH) showed differences and had a bigger geographic distance than the others. There is the probability that the H. leucisculus from Bosten Lake entered Taitema Lake to breed and then expanded into the Tarim River due to the water diversion projects in location. In addition, 147,705 SSRs loci were detected and 22,651 SSR primer pairs were developed. This study will contribute to providing valuable molecular data for the management of wild populations, marker-assisted selection and resource exploitation of H. leucisculus.

Genetic diversity in natural population of Notopterus notopterus evaluated through mitochondrial DNA marker ATPase 6/8 regions and cytochrome b gene

BACKGROUND

Population structure and genetic diversity of bronze featherback Notopterus notopterus, fish was not studied yet from Pakistan. So, genetic diversity and population structure of N. notopterus was analysed using two mitochondrial DNA genetic markers, ATPase 6/8 and Cytochrome b.

METHODS AND RESULTS

150 specimens were collected from five different rivers of Pakistan, resulting 56 haplotypes were detected for ATPase 6/8, Cytb and concatenated gene. Haplotype and nucleotide diversity for ATPase 6/8, Cytb and concatenated gene was observed below 1% among five natural populations of N. notopterus. ATPase 6/8 and Cytb genetic variance among populations was 6% and among and within individuals was 94%. Concatenated genetic variance among populations was 11%, among individual 5% and within individuals 84%. Fst value among all population was found 0.091 (p-value=0.02, p<0.05). The combined data set mean coefficient of genetic differentiation (F_ST) was 0.5572. The pair-wise F_ST was 0.000 (Chenab) to 0.88911 (Ravi). Maximum likelihood phylogeographic history of concatenated gene haplotypes showed four distinct diversified clusters. AMOVA, PCoA (Principal Coordinate Analysis) and maximum likelihood tree indicated that the natural populations of N. notopterus were comprised of four genetic stocks among five Pakistani rivers (Chenab, Indus, Jehlum, Ravi and Satluj).

CONCLUSIONS

This study provides the higher level of genetic diversity with confirmatory proofs among genetic stocks of five natural populations of N. notopterus. The information of genetic diversity and genetic variation, from this research can be utilised to help conserve and manage the species in the wild.

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.