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Functioning as a key regulator of circadian rhythms, the PER2 gene exerts a substantial impact on the reproductive traits of animals. However, the effect of the PER2 gene on ovarian development remains unclear. In order to examine the relationship between bovine reproductive trait and the PER2 gene, a total of 901 ovarian samples were collected, categorized into different oestrus cycles (proestrus, oestrus, post-oestrus, anoestrous), and subjected to analysis for two potential insertion/deletions (InDels) in the PER2 gene. Through agarose gel electrophoresis and DNA sequencing, two polymorphic deletion mutations (P2-D5-bp, P3-D13-bp) were identified. Furthermore, a significant association between mature follicle diameter and P2-D5-bp was found (P < 0.05). Additionally, several significant correlations with ovarian length, width, height, and white body diameter were found for P3-D13-bp (P < 0.05). These findings suggested that the bovine PER2 gene plays an important role in above-mentioned reproductive traits, offering new avenues for improving cow fertility through marker-assisted selection (MAS).

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The Protein Phosphatase 6 Catalytic Subunit (PPP6C) is evolutionarily a conserved gene in eukaryotes known to play a significant role in mammalian reproduction. This study aimed to investigate expression patterns of PPP6C and explore its association with litter size in Shaanbei white cashmere (SBWC) goats. Initially, we determined the mRNA expression levels of PPP6C in both male and female goats across multiple tissues. The results showed that PPP6C mRNA was expressed in multiple tissues, with higher levels in the testis and fallopian tubes, suggesting its involvement in goat reproduction. Additionally, we identified a novel 19 bp InDel within the PPP6C gene in a population of 1030 SBWC goats, which exhibited polymorphism. Statistical analysis revealed a significant association between the19 bp InDel mutation and litter size (P < 0.05). Subsequent, bioinformatics analysis, including linkage disequilibrium (LD) block and selective scanning, highlighted the linkage tendency among most InDel loci did not stand out within B-8 block, there were still some InDel loci linked to the 19 bp within a relatively narrow region. Furthermore, comparative analysis with Bezoars, these selective signals all indicated that this gene was under higher selection pressure, implying that the 19 bp InDel locus within the PPP6C is potentially associated with domesticated traits, particularly in relation to litter size. The results of the present study suggest that the PPP6C is a vital candidate gene affecting prolificacy in goats, with implications for selective breeding programs for goat breeds.

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In recent years, genome-wide association studies (GWAS) have uncovered that the HOXB13 gene is a key regulatory factor for the tail length trait of sheep. Further research has found that there is a functional 168 bp SINE element insertion upstream of the HOXB13 gene, which leads to the occurrence of long tails in sheep. However, the frequency of mutations in the 168 bp SINE element of the HOXB13 gene among different sheep breeds around the world and its relationship with growth traits are still unclear. This study used whole-genome sequencing (WGS) data, including 588 samples from 33 different sheep breeds around the world, to evaluate the frequency of HOXB13 gene mutations in different sheep breeds globally. At the same time, this study also selected 3392 sheep samples from six breeds. The genetic variation in the 168 bp InDel locus in the HOXB13 gene was determined through genotyping, and its association with the growth traits of Luxi black-headed sheep was analyzed. The research results indicate that the polymorphism of the 168 bp InDel locus is significantly correlated with the hip width of adult ewes in the Luxi black-headed sheep breed (p < 0.05) and that the hip width of adult ewes with the DD genotype is significantly larger than that of adult ewes with the ID genotype (p < 0.05). This study indicates that there is consistency between the research results on the sheep tail length trait and growth traits, which may contribute to the promotion of sheep breed improvement.

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The high-mobility group AT-hook 2(HMGA2) gene has been widely studied in the context of cancer and animal growth. However, recently, several studies have uncovered its critical role in cell proliferation. A genome-wide association study (GWAS) further suggests that the HMGA2 gene is a candidate gene in fertility, indicating its connection not only to growth traits but also to reproduction, specifically ovarian traits. Thus, this study aimed to analyze the distribution of the HMGA2 gene in 54 bovine breeds worldwide, identify important short fragment variants (indels), and investigate the relationship between HMGA2 and ovarian development. The dataset included genotypic information from a bovine population of 634 individuals (n = 634). After genotyping and analyzing four selected loci, we found that one out of four loci, rs133750033 (P4-D22-bp), was polymorphic. Our results also reveal that this indel of HMGA2 is significantly associated with certain ovarian traits (p < 0.05). Specifically, it has connection with ovarian length (p = 0.004) and ovarian height (p = 0.026) during diestrus. Additionally, we discovered a higher expression of the HMGA2 gene in Asian cattle breeds. In summary, this study suggests that HMGA2 has the potential to serve as an animal fertility testing marker gene. Moreover, these findings contribute to a more promising outlook for the bovine industry.

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Osteogenesis is a complex multilevel process regulated by multiple genes. The GATA binding protein 4 (GATA4) gene has been extensively studied for its pivotal role in bone genesis and bone differentiation. However, its relationship with the growth traits of Shaanbei white cashmere (SBWC) and Guizhou black (GB) goats remains unclear. This work aims to investigate the potential influence of genetic mutations in the GATA4 gene on the growth traits goats. Thus, two Insertion/deletion (InDel) polymorphisms (8-bp-InDel and 9-bp-InDel) were screened and detected in a total of 1161 goats (including 980 SBWC goats and 181 GB goats) using PCR and agarose gel electrophoresis. The analyses revealed that there were two genotypes (ID and DD) for these two loci. In SBWC goats, 8-bp-InDel and 9-bp-InDel loci were significantly associated with heart girth (HG) and hip width (HW). Notably, individuals with DD genotype of 8-bp-InDel locus were superior while those with DD genotype of 9-bp-InDel locus were inferior. Correlation analyses of the four combined genotypes revealed significant associations with cannon circumference (CC), body height (BH), HG and HW. This work provides a foundation for the application of molecular marker-assisted selection (MAS) in goat breeding programs. Furthermore, the findings highlight the potential of the GATA4 gene and its genetic variations as valuable indicators for selecting goats with desirable growth traits.

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OBJECTIVE: The Janus kinase/signal transducer and transporter activator (JAK/STAT) signaling pathway plays crucial roles in lipid metabolism, glucose metabolism and cell senescence, suggesting that they are potential candidate genes affecting growth traits in animals. The present study aimed to evaluate the association between InDels in the JAK/STAT pathway and growth traits of four Chinese sheep breeds, including Tong sheep, Hu sheep, Small-tailed Han sheep and Lanzhou fat-tailed sheep. RESULTS: Seventy-six indel loci of 11 genes in JAK/STAT were detected, and three genotypes were selected at four loci by PCR amplification, electrophoresis and sequencing, including one locus in STAT3, one locus in STAT5A, and two loci in JAK1. The Correlation analysis indicated that there was no significant correlation between STAT3 and growth traits in four sheep breeds (P > 0.05); STAT5A was significantly associated with body height, rump width and tube circumference in Hu sheep and body length in Tong sheep (P < 0.05); JAK1 was significantly correlated with body height, body oblique length, cross height and tube circumference in Hu sheep (P < 0.05) and body oblique length, cross height and tube circumference in small-tailed Han sheep (P < 0.05). CONCLUSION: Overall, our results indicated a potential association between the growth traits of sheep and the InDels of JAK1 and STAT5A.

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In this study, the relationship between RORA 23bp indel genotype and allele frequency with twin pregnancy, fertility, live weight and milk yield in 106 female Akkaraman ewes raised in Elazig province was investigated. In the study conducted in Elâzig province, 10ml milk was collected from 106 Akkaraman sheep and DNA was extracted from these milk. In RORA 23bp indel genotype frequency, DD genotype was found more than ID and II genotypes and RORA 23bp indel in allele frequency, the D allele was found to be higher than the I allele. In both the first and second parity, the twinning rate was found to be lower. In both the first and second parity, the twinning rate was higher in the DD genotype, and it was observed that this genotype prominated middle livestock weight and milk yield. According to the results of our study, mutations in the RORA gene, which is a gene affecting reproductive efficiency in sheep, do not have a positive effect on fertility and twinning rate in Akkaraman sheep. To sum, this study provided theoretical references for the comprehensively research of the function of RORA gene and the breeding of Akkaraman Sheep. The 23-bp indel variants can be considered as molecular markers for litter size of sheep for marker-assisted selection breeding.

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General transcription factor IIA subunit 1 (GTF2A1) is required for transcriptional activation from most promoters in eukaryotic transcription. Previous whole-genome association analyses articles have predicted the effect of this gene on lambing in sheep. In the study, a total of nine insertion/deletion (indel) variants named L1 to L9 in the gene were selected to detect in 550 Australian White sheep (AuW) adult ewes. The polymorphisms were detected in four loci (L1, L2, L3 and L8locus) and the polymorphism information content (PIC) values were 0.270, 0.375, 0.372 and 0.314. Further, our study revealed that L1, L2 and L3 loci of GTF2A1 gene were significantly related to the first parity litter size and the polymorphism of L8 was significantly correlated with litter size in the second parity. In details, for the first parity, individuals with the II genotype of the L1 locus had higher little size than that with the ID genotype, individuals with the ID and DD genotype of the L2 locus had higher little size than that with the II genotype, and individuals with the DD genotype of the L3 locus had higher little size than that with the II genotype. All four loci do not follow to Hardy-Weinberg equilibrium, and have no linkage between them. In conclusion, the polymorphisms of GTF2A1 were confirmed and analysis results demonstrated that there are some relevance between difference genotypes and litter size, and these findings may provide new insights for accelerating sheep molecular breeding through molecular marker-assisted selection (MAS).

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In recent years, the insertion/deletion (InDel) polymorphism has become a preferred genetic marker in forensic genetics due to its low mutation rates and small amplicon sizes. In this study, a 36-InDelplex identification panel, consisting of autosomal 34 InDel loci, 1 Y InDel locus, and amelogenin, was developed, and gene frequencies in the Turkish population were determined. The loci of the InDel panel with global minimum allele frequencies (MAF) ≥ 0.4 were selected from the 1000 Genomes Project Phase 3 data. The amplicon sizes of the loci were designed in the range of 69-252 bp. In the validation study of the developed panel, analysis threshold, dynamic range, sensitivity, stochastic threshold, inhibitor tolerance, and reproducibility parameters were studied by following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The sensitivity studies indicated that complete and reliable InDel profiles could be obtained with 0.25 ng of DNA. A population study was evaluated using 250 samples from Turkey. The mean observed heterozygosity ratio (Ho) of all loci was 0.48. The combined discrimination power (CPD) is 0.999999999990867 and the combined exclusion probability (CPE) was 0.9930. The population comparison was also made using Turkish and the five major populations from the 1000 Genomes Phase 3 populations' data (Africa, Europe, East Asia, South Asia, and America). In conclusion, the results showed that the 36-InDelplex panel is a reliable, sensitive, and accurate system that is suitable for human identification and population genetics purposes.

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Platelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations in PDGFD and body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 of PDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation of PDGFD was found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates that PDGFD InDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.

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Background: The hippocampal abundant transcript 1 (HIAT1) gene, also known as major facilitator superfamily domain-containing 14A (MFSD14A), encodes for a transmembrane transporter protein and has been previously shown to be associated with milk production in buffalo and sheep breeds, as well as growth traits in chicken and goats. However, tissue level distribution of the ovine HIAT1 gene, as well as its effect on body morphometric traits in sheep, has yet to be studied. Methods: The HIAT1 mRNA expression profile of Lanzhou fat-tailed (LFT) sheep was determined by quantitative real-time PCR (qPCR). A total of 1498 sheep of three indigenous Chinese sheep breeds were PCR-genotyped for polymorphisms of HIAT1 gene. Student's t-test was used to observe the association between the genotype and sheep morphometric traits. Results: HIAT1 was widely expressed in all examined tissues, and was particularly abundant in the testis of male LFT sheep. Additionally, a 9-bp insertion mutation (rs1089950828) located within the 5'-upstream region of HIAT1 was investigated in Luxi black-headed (LXBH) sheep and Guiqian semi-fine wool (GSFW) sheep. The wildtype allele frequency 'D' was found to be more prevalent than that of the mutant allele 'I'. Furthermore, low genetic diversity was confirmed in all sampled sheep populations. Subsequent association analyses indicated an association between the 9-bp InDel mutation of interest and the morphometric traits of LXBH and GSFW sheep. Furthermore, yearling ewes with a heterozygous genotype (ID) demonstrated smaller body sizes, while yearling rams and adult ewes with the heterozygous genotype were found to have overall better growth performance. Conclusion: These findings imply that functional InDel polymorphism (rs1089950828) has the potential to be utilized for marker-assisted selection (MAS) of growth traits in domestic Chinese sheep populations.

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The insertion/deletion (indel) mutation profiles of SARS-CoV-2 variants, including Omicron, remain unclear. We compared whole-genome sequences from various lineages and used preserved indels to infer the ancestral relationships between different lineages. Thirteen indel patterns from twelve sites were seen in ≥ 2 sequences; six of these sites were located in the N-terminal domain of the viral spike gene. Preserved indels in the coding regions were also identified in the non-structural protein 3 (Nsp3), Nsp6, and nucleocapsid genes. Seven of the thirteen indel patterns were specific to the Omicron variants, four of which were observed in BA.1, making it the most mutated variant. Other preserved indels observed in the Omicron variants were also seen in Alpha and/or Gamma, but not Delta, suggesting that Omicron is phylogenetically more proximal to Alpha. We demonstrated distinct profiles of preserved indels among SARS-CoV-2 variants and sublineages, suggesting the importance of indels in viral evolution.

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To explore the efficacy of commonly used forensic identification panels in complex paternity testing of trios that involved close relatives, we wrote a code by R to generate 10,000 pedigrees at 20 CODIS STR, 21 non-CODIS STR and 30 InDel loci in Chinese five ethnic groups based on their allele frequencies. Parentage identification index--cumulative paternity index (CPI) value was set as output and was further analyzed to evaluate the performance of the aforementioned panels in complex paternity testing when the alleged parent is a random individual, biological parent, grandparent, sibling of biological parent, half-sibling of biological parent, etc. The results showed that the false inclusion of parent sibling posed as parent demonstrated no statistically significant difference from that of grandparent posed as parent. The scenarios where both biological parent and alleged parent were consanguineous to the other parent were also simulated. The results revealed that the complexity of paternity testing would raise when biological parents were consanguineous and the alleged parent was a close relative of theirs. Despite the values of non-conformity number could vary in different genetic relationships, populations and panels, 20 CODIS STRs and 21 non-CODIS STRs performed satisfactorily in most simulated scenarios. However, the joint use of 20 CODIS STRs and 21 non-CODIS STRs is more recommendable when resolving the paternity testing of the incest mating case. Overall, the current study could be regarded as a worthwhile reference in complex paternity testing of trios that involved close relatives.

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Insertion/deletion (InDel) markers are second most abundant polymerase chain reaction (PCR)-based molecular markers having enormous applications in genotyping and molecular breeding in different crops. Although standard polymerase chain reaction (PCR) for DNA amplification generally takes ~ 1.5 to 2 h, small amplicons can be effectively generated using dynamic heating and cooling through PCR with "V"-shaped thermal profile (VPCR) in ~ 15 to 20 min. Here, we evaluated the applicability of a partly modified VPCR method for amplifying InDels of tomato genome. Out of the 31 InDel markers tested in 15 diverse tomato genotypes, 29 markers resulted in sharp amplicons, where 26 markers were found to be polymorphic. Using this method, the individual DNA amplification reactions could be completed within ~ 30 min. The method was effective for primers varying in melting temperature (T m) and GC contents. Furthermore, the need for empirically determining suitable annealing temperature could be bypassed using this generalised thermal profile. Through our results, we advocate the use of this method of DNA amplification in other plants to achieve rapid genotyping using standard molecular biology equipments and procedures. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03499-x.

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The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.

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The SMAD family member 2 (SMAD2), a member of the TGF-beta superfamily, executes a significant part in the oogenesis and ovulation process. A genome-wide selective sweep analysis also found SMAD2 was different in the fertility groups of Laoshan dairy goats; whether this gene was linked to litter size was unknown. Therefore, SMAD2 was chosen to study its effects on Shaanbei white cashmere goat reproduction and mRNA expression profile. Herein, the mRNA expression level of SMAD2 was firstly determined in female goat tissues, revealing significant differences in mRNA levels of different tissues (p < 0.05), including ovary tissue, indicating a potential role for SMAD2 in goat prolificacy. Then, using six pairs of primers, only one indel locus (P3-Del-12-bp) was found to be polymorphic in goat SMAD2 (n = 501). ANOVA also revealed that a P3-Del-12-bp deletion was significantly related to first-born litter size (p = 0.037). The Chi-square (χ2) test revealed that the ID genotype was significantly more prevalent in mothers with multiple lambs (p = 0.01), indicating that heterozygous individuals (ID) are more likely to produce multiple lambs. Our findings suggest that the SMAD2 gene's P3-Del-12-bp deletion could be used to improve goat breeds by assisting with litter size selection.

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Calsyntenin-2 (CLSTN2) is involved in cell proliferation, differentiation, cell death, tumorigenesis, and follicular expression. Although CLSTN2 has been identified as a potential candidate gene for sheep prolificacy, no studies have been done on its effect on goat prolificacy. The purpose of this study was to identify mRNA expression and genetic variation within goat CLSTN2, and its association with prolificacy. Herein, we uncovered significant differences in mRNA levels of the CLSTN2 gene in different tissues in female goats (p < 0.01), including ovary tissue. Nine putative indels were designed to investigate their correlation to litter size, but only one 16-bp deletion was discovered in female Shaanbei white cashmere goats (n = 902). We discovered that a 16-bp deletion within the CLSTN2 gene was significantly correlated with first-born litter size (p = 0.0001). As shown by the chi-squared test, the genotypic II of single-lambs and multi-lambs was dramatically higher than with genotype ID (p = 0.005). Our findings suggest that indel within the CLSTN2 gene is a candidate gene affecting prolificacy in goats and may be used for Marker Assisted Selection (MAS) in goats.

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GATA binding protein 4 (GATA4) is a typical transcription binding factor, and its main functions include regulating the proliferation, differentiation and apoptosis of ovarian granulosa cells, promoting spermatogenesis and sex differentiation, implying that this gene have possibly roles in animal reproduction. This study aims to detect five potential insertion/deletions (indels) of the GATA4 gene in 606 healthy unrelated Shaanbei white cashmere (SBWC) goats and analyze its association with the litter size. The electrophoresis and DNA sequencing identified two polymorphic indels (e.g., P4-Del-8bp and P5-Ins-9bp indel). Then T-test analysis showed that P4-Del-8bp was significantly correlated with litter size (p = 0.022) because of two different genotypes detected, e.g., insertion-deletion (ID) and deletion-deletion (DD), and the average litter size of individuals with DD genotype goats was higher than that of others. However, there was no correlation between P5-Ins-9bp and lambing of goats. Chi-square (X2) test found that the distribution of and P4-Del-8bp genotypes (X2 = 6.475, p = 0.011) was significantly different between single and multiple-lamb groups, while P5-Ins-9bp (X2 = 0.030, p = 0.862) was not. Therefore, these findings revealed that P4-Del-8bp polymorphism of goat GATA4 gene was a potential molecular marker significantly associated with litter size, which can be used for the marker-assisted selection (MAS) breeding to improve goat industry.

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The biological clock (also known as circadian clock) is closely related to growth and development, metabolism, and diseases in animals. As a part of the circadian clock, the cryptochrome circadian regulator 1 (CRY1) gene is involved in the regulation of biological processes such as osteogenesis, energy metabolism and cell proliferation, however, few studies have been reported on the relationship between this gene and animal carcass traits. Herein, a total of four insertion/deletion (InDel) loci within the CRY1 gene were detected in Shandong Black Cattle Genetic Resource (SDBCGR) population (n = 433). Among them, the P1-6-bp-del locus was polymorphic in population of interest. Moreover, the P1-6-bp-del locus showed two genotypes, with a higher insertion/insertion (II) genotype frequency (0.751) than insertion/deletion (ID) genotype frequency (0.249). Correlation analysis showed that the P1-6-bp-del locus polymorphisms were significantly associated with twenty carcass traits (e.g., slaughter weight, limb weight, and belly meat weight). Individuals with II genotype were significantly better than those with ID genotype for eighteen carcass traits. Therefore, the P1-6-bp-del locus of the CRY1 gene can be used as a molecular marker for beef cattle breeding.

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The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains many insertions/deletions (indels) from the genomes of other SARS-related coronaviruses. Some of the identified indels have recently reported to involve relatively long segments of 10-300 consecutive bases and with diverse RNA sequences around gaps between virus species, both of which are different characteristics from the classical shorter in-frame indels. These non-classical complex indels have been identified in non-structural protein 3 (Nsp3), the S1 domain of the spike (S), and open reading frame 8 (ORF8). To determine whether the occurrence of these non-classical indels in specific genomic regions is ubiquitous among broad species of SARS-related coronaviruses in different animal hosts, the present study compared SARS-related coronaviruses from humans (SARS-CoV and SARS-CoV-2), bats (RaTG13 and Rc-o319), and pangolins (GX-P4L), by performing multiple sequence alignment. As a result, indel hotspots with diverse RNA sequences of different lengths between the viruses were confirmed in the Nsp2 gene (approximately 2500-2600 base positions in the overall 29,900 bases), Nsp3 gene (approximately 3000-3300 and 3800-3900 base positions), N-terminal domain of the spike protein (21,500-22,500 base positions), and ORF8 gene (27,800-28,200 base positions). Abnormally high rate of point mutations and complex indels in these regions suggest that the occurrence of mutations in these hotspots may be selectively neutral or even benefit the survival of the viruses. The presence of such indel hotspots has not been reported in different human SARS-CoV-2 strains in the last 2 years, suggesting a lower rate of indels in human SARS-CoV-2. Future studies to elucidate the mechanisms enabling the frequent development of long and complex indels in specific genomic regions of SARS-related coronaviruses would offer deeper insights into the process of viral evolution.

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