Progress in Fishery Sciences (Jun 2024)
Screening and Characteristics Analysis of Microsatellites in the Whole Genome of Five Groupers
Abstract
Grouper, a species of coral reef fish, exhibits a wide geographical distribution within the warm waters of the tropical and subtropical regions across the globe, primarily inhabiting the middle and lower layers of water. Characterized as a substantial marine economic fish, grouper possesses considerable nutritional value, boasts a high market worth, and garners significant consumer demand. Its popularity among consumers is attributed to its inherent attributes, and it holds immense potential for further cultivation and breeding endeavors. This study utilized micro-satellite (MISA) software to investigate the distribution characteristics of microsatellites in the genomes of five grouper species (Epinephelus akaara, E.coioides, E.fuscoguttatus, E.lanceolatus, and E.moara). A custom script was developed to analyze the screening results, and statistical analyses were conducted on the microsatellite repeat types, duplicate copy types, and core copy numbers in the genomes of the five grouper species. Over 280 000 microsatellite sites were identified from the entire genomes of the five grouper species. The relative abundance of microsatellites ranged from 271–296, with a total length ranging from 6.30–7.06 Mb. The average length of the microsatellites was approximately 22 bp, and their proportion in the genomes ranged from 0.59%–0.67%. These results provide insights into the distribution characteristics of microsatellites in the genomes of these five grouper species and can inform future studies on their genomic architecture and evolution. The repetitive types of microsatellites were analyzed in terms of number, proportion, and relative abundance. The number, proportion, and relative abundance of repetitive types followed a consistent pattern, with the highest number of double base repeats, followed by single base repeats. This pattern decreased as the number of repeat units increased. A, AC, AAT, AAG, AGC, AATC, AAAT, AGAT, AATG, AGAGG, AAAAT, AAGAT, ACAGAG, AAANNN, and AANNNN (N represents any of the three bases except A) were the most dominant types of each duplicate copy type. Type A accounted for 90.00% of single base repeats, while type AC was the most dominant in double base repeats, accounting for nearly 80.00%. Interestingly, the content of the CG duplication category was the least, accounting for only 0.04%–0.10% in the five grouper species. This may be owing to the fact that the composition content of the four bases in the different species' genomes is different, and there may be structural problems with different bases. The results of this study provide insight into the distribution characteristics of microsatellites in the genomes of these five grouper species. The high frequency distribution of AGG and AGC in the dominant types of triple base repeats may play a crucial role in regulating genes involved in immunity, disease, and other genes in groupers. Previous studies show that AGG is a well-known binding site for numerous transcription factors involved in early growth and development of various species. Additionally, the change of base repeat polymorphism of the AGC category is directly linked to genetic diseases and holds significant evolutionary and medical research value. AAAN, AAAAN, and AAAAAN are dominant repeat types that are widely distributed in mammals among the four, five, and six base repeat types, respectively. Different types of microsatellites show significant variability in the number of core copy numbers. Nevertheless, the number of duplicate copies of each type of microsatellite exhibit a consistent trend in the five groupers, and the number of microsatellites decrease with an increase in the number of duplicate copies. The analysis of microsatellite distribution revealed several key findings. First, over 95% of single base repeat copies were concentrated in a range of 12 to 25 times. The main number of copies for two base repeats ranged from 6 to 32 times, with a small peak between 11 and 14 copies, and decreasing numbers with increasing copies. The number of copies for four and five base repeats was mainly concentrated in the ranges of 5–16 and 5–17, and 5–14, respectively. Notably, AGAT, AAAG, AAGAG, AATAT, and AGAGG repeats exhibited a large number of copies, even when the number of copies was high. The increase in copy number may represent changes in polymorphism at these loci that may lead to disease or changes in corresponding functions. Overall, these findings provide important insights into the distribution and potential functional significance of microsatellites in the genome of the studied species. The distribution characteristics of microsatellites in the genomes of the five groupers provide a valuable basis to understand the evolutionary mechanisms and functional expression of these species. The distribution of duplicate copy numbers of each type of duplication displays two peaks at 6 and 12 repetitions, with the number of microsatellites decreasing with increasing numbers of core copies. Some duplication types show particularly prominent numbers in specific species, such as T, TA, and AGACAG in E.lanceolatus, copied 502, 803, and 48 times respectively; GAG, CACT, and CCACA in E.moara, copied 205, 652, and 111 times respectively. These variations highlight the importance of exploring the role of microsatellite loci to develop a better understanding of the genetic distance and kinship among the five groupers. This analysis lays the groundwork to develop high-quality microsatellite molecular markers, and facilitates the selection of favorable varieties and the development of new varieties. In general, these research results provide important data to understand the genomic characteristics of the five groupers and helps to conduct advanced genetic research on these species.
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