Identification Of Simple Sequence Repeats Research Articles

Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution

BackgroundPleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species.ResultsOur analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices.ConclusionsThis study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations.

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae.

The present study provides a detailed analysis of the chloroplast genome of Microula sikkimensis. The genome consisted of a total of 149,428 bp and four distinct regions, including a large single-copy region (81,329 bp), a small single-copy region (17,261 bp), and an inverted repeat region (25,419 bp). The genome contained 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, and some exhibited duplication in the inverted repeat region. The chloroplast genome displayed different GC content across regions, with the inverted repeat region exhibiting the highest. Codon usage analysis and the identification of simple sequence repeats (SSRs) offer valuable genetic markers. Comparative analysis with other Boraginaceae species highlighted conservation and diversity in coding and noncoding regions. Phylogenetic analysis placed M. sikkimensis within the Boraginaceae family, revealing its distinct relationship with specific species.

Species identification through deep learning and geometrical morphology in oaks (Quercus spp.): Pros and cons.

Plant phenotypic characteristics, especially leaf morphology of leaves, are an important indicator for species identification. However, leaf shape can be extraordinarily complex in some species, such as oaks. The great variation in leaf morphology and difficulty of species identification in oaks have attracted the attention of scientists since Charles Darwin. Recent advances in discrimination technology have provided opportunities to understand leaf morphology variation in oaks. Here, we aimed to compare the accuracy and efficiency of species identification in two closely related deciduous oaks by geometric morphometric method (GMM) and deep learning using preliminary identification of simple sequence repeats (nSSRs) as a prior. A total of 538 Asian deciduous oak trees, 16 Q. aliena and 23 Q. dentata populations, were firstly assigned by nSSRs Bayesian clustering analysis to one of the two species or admixture and this grouping served as a priori identification of these trees. Then we analyzed the shapes of 2328 leaves from the 538 trees in terms of 13 characters (landmarks) by GMM. Finally, we trained and classified 2221 leaf-scanned images with Xception architecture using deep learning. The two species can be identified by GMM and deep learning using genetic analysis as a priori. Deep learning is the most cost-efficient method in terms of time-consuming, while GMM can confirm the admixture individuals' leaf shape. These various methods provide high classification accuracy, highlight the application in plant classification research, and are ready to be applied to other morphology analysis.

Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in brown trout (Salmo trutta)

Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in brown trout (Salmo trutta)

Investigating the patterns of simple sequence repeats (SSRs) inferred from the whole genome of a critically endangered species Cassine koordersii kosterm

Cassine koordersii Kosterm. (Celastraceae) is a critically endangered species indigenous to Jember, East Java. Programs for genetic conservation and plant breeding have recently implemented next-generation sequencing (NGS) techniques based on genomic data. This research aims to explore and distinguish between perfect and imperfect SSR patterns in the assembled genome. The Abyss assembler produced 3,060,362 scaffolds with 35.63 % GC content for the assembled genome. The investigation and identification of SSRs using the Krait tool found 139,236 and 582,360 sequences for including perfect and imperfect SSRs, respectively. There were six motif repeats of perfect and imperfect SSRs consisting of 73,175 and 202,438 sequences of mononucleotide (the most motif was A); 17,179 and 65,705 sequences of dinucleotide (the most motif was AT); 5,175 and 51,948 sequences of trinucleotide (the most motif was AAT); 3,824 and 14,010 sequences of tetranucleotide (the most motif was AAAT); 659 and 3,082 sequences of pentanucleotide (the most motif is AAAAT); 118 and 757 sequences of hexanucleotide (the most motif is AAAAAT). The depicted perfect and imperfect SSRs markers can be employed in future genetic studies of Cassine and related genera for either recommendation effort or improvement in conservation genetic concerns.

Genome-wide identification of microsatellites for mapping, genetic diversity and cross-transferability in wheat (Triticum spp)

Wheat (Triticum aestivum L.) is a crucial global staple crop, and is consistently being improved to enhance yield, disease resistance, and quality traits. However, the development of molecular markers is a challenging task due to its hexaploid genome. Molecular marker system such as simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) are helpful for breeding, but SNP has limitations due to its development cost and its conversion to breeder markers. The study proposed an in-silico approach, by utilizing the low-cost transcriptome sequencing of two parental lines, ‘TAC 75′ and ‘WH 1105′, to identify polymorphic SSRs for mapping in a recombinant inbred line (RIL) population. This study introduces a new approach to bridge wheat genetics intricacies and next-generation sequencing potential. It presents a comprehensive genome-wide SSR distribution using IWGSC CS RefSeq v2.1 genome assembly and to identify 189 polymorphic loci through in-silico strategy. Of these, 54.76% showed polymorphism between parents, surpassing the traditional low polymorphic success rate. A RIL population screening validated these markers, demonstrating the fitness of identified markers through chi-square tests. The designed SSRs were also validated for genetic diversity analysis in a subset of 37 Indian wheat genotypes and cross-transferability in the wild/relative wheat species. In diversity analysis, a subset of 38 markers revealed 95 alleles (2.5 allele/locus), indicating substantial genetic variation. Population structure analysis unveiled three distinct groups, supported by phylogenetic and PCoA analyses. Further the polymorphic SSRs were also analyzed for SSR-gene association using gene ontology analysis. By utilizing the developing seed transcriptome data within parental lines, the study has enhanced the polymorphic SSR identification precision and facilitated in the RIL population. The undertaken study pioneers the use of transcriptome sequencing and genetic mapping to overcome challenges posed by the intricate wheat genome. This approach offers a cost-effective, less labour-intensive alternative to conventional methods, providing a platform for advancing wheat breeding research.

Characterization of gill transcriptome, SSR/SNP markers and expression analysis of lysozyme LysC gene from Carassius auratus upon Aeromonas hydrophila infection

The gills are large mucosal surfaces and play primary roles in respiration and immune defences. However, the molecular mechanism for gills of fish needs still to be explored. In the present study, transcriptomic analysis and identification of SSR and SNP markers were performed in the gills of crucian carp Carassius auratus. The results showed a total of 84,259 unigenes were annotated to NCBI NR, KEGG and GO databases for 55,283, 39,303, 33,388, respectively. Enriched KEGG pathway analyses for the identified genes showed the mainly functional modules such as metabolism, cellular processes, environmental adaptation, genetic processing, organismal and immune systems. Moreover, 22,102 SSRs (simple sequence repeats) were potentially identified and 9776 (44.2%) were accounted for the most dinucleotides. Transition and transversion sites of SNPs (single nucleotide polymorphisms) were also observed. Tissue distribution showed that the expression level of lysozyme LysC gene was relatively high in intestine, liver, spleen and kidney tissues and up-regulated in gills, skin and brain after the A. hydrophila infection. We discovered the immune-related pathways through the transcriptome analysis in the gills of crucian carp, some potential SSR/SNP markers were identified, and lysozyme gene predominantly expressed in mucosal immune organs (eg., gills, skin, intestine) responded to A. hydrophila infection. To the best of our knowledge, this was the detailed report on the molecular characteristics in crucian carp gills with transcriptome analysis, which will not only provide a scientific reference for further understanding the local defense mechanism, but also lay a foundation for molecular marker-assisted breeding in fish.

Unveiling the demographic background and genetic diversity of Urochloa mosambicensis (Poaceae) through genome-wide identification of simple sequence repeats and molecular marker development

Unveiling the demographic background and genetic diversity of Urochloa mosambicensis (Poaceae) through genome-wide identification of simple sequence repeats and molecular marker development

Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources.

Jujube (Ziziphus jujuba Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.

Construction of a high-density SSR genetic linkage map and identification of QTL for storage-root yield and dry-matter content in sweetpotato

Sweetpotato (Ipomoea batatas (L.) Lam.) is a widely grown food crop especially in developing countries. Increasing storage-root yield and dry-matter content has been the main breeding objective of the crop, and DNA marker-assisted breeding is needed for this purpose. In this study, using a mapping population of 500 F1 individuals from a cross between Xushu 18 (female) and Xu 781 (male), we constructed a high-density genetic linkage map of sweetpotato using 601 simple-sequence repeat (SSR) primer pairs. The Xushu 18 map contained 90 linkage groups with 5547 SSR markers and spanned 18,263.5 cM, and the Xu 781 map contained 90 linkage groups with 4599 SSR markers and spanned 18,043.7 cM, representing the highest genome coverage yet reported for sweetpotato. We identified 33 QTL for storage-root yield and 16 QTL for dry-matter content, explaining respectively 6.5%–47.5% and 3.2%–18.9% of variation. These results provide a foundation for fine-mapping and cloning of QTL and for marker-assisted breeding in sweetpotato.

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes.

Simple sequence repeats (SSRs) are one of the most important molecular markers, which are widespread in plants. Bamboos are important forest resources worldwide. Here, the comprehensive identification and comparative analysis of SSRs were performed in three woody and two herbaceous bamboo species. Altogether 567,175 perfect SSRs and 71,141 compound SSRs were identified from 5737.8 Mb genome sequences of five bamboo species. Di-nucleotide SSRs were the most predominant type, with an average of ~50,152.2 per species. Most SSRs were located in intergenic regions, while those located in genic regions were relatively less. Moreover, the results of annotation distribution indicated that terms with P450, peroxidase and ATP-binding cassette transporter related to lignin biosynthesis might play important roles in woody and herbaceous bamboos under the mediation of SSRs. Furthermore, the peroxidase gene family consisted of a large number of genes containing SSRs was selected for the evolutionary relationship analysis and SSR markers development. Fifteen SSR markers derived from peroxidase family genes of Phyllostachys edulis were identified as polymorphic in 34 accessions belonging to seven genera in Bambusoideae. These results provided a comprehensive insight of SSR markers into bamboo genomes, which would facilitate bamboo research related to comparative genomics, evolution and marker-assisted selection.

Genome-wide mining of simple sequence repeats and development of polymorphic SSR markers in Aquilaria malaccensis

Aquilaria malaccensis is one of the economically important tree species distributed in North-east India which produces oleoresinous heartwood known as Agarwood - the most expensive wood in the world. There are limited genomic resources in this species. Therefore, the publicly available whole-genome sequence of Aquilaria agallocha, which is a synonym of A. malaccensis, was utilized for genome-wide mining of Simple Sequence Repeats (SSR) and to develop polymorphic SSR markers. In total 2,53,155 SSRs were identified from the draft genome. Primers were designed for di-nucleotide and tri-nucleotide repeats and screening of 90 such primers have resulted in the identification of 10 polymorphic markers. The present report is the first one for exhaustive identification of SSRs from the draft genome of the species. The SSR markers identified in the present study may be efficient in genomic analyses and useful in the genetic assessment and conservation of A. malaccensis.

Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

Mungbean is an important pulse crop and it is mainly cultivated in Asia for human consumption. Its small genome and diploid nature make it a well-suited model organism among legume crops. Thus, cost-effective, reliable and highly polymorphic molecular markers distributing the whole genome are needed for diversity, mapping and functional genomics studies in this model species. The whole-genome sequence of mungbean was obtained and used as a source of identification of simple sequence repeats (SSR). The sequence reads were aligned and SSRs detection was performed using the Phobos plugin tandem repeat finder in the Geneious software program. A total of 12 mungbean genotypes were selected to validate the newly developed SSR markers. In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats were identified from the mungbean genome. The tri-repeats were the most abundant (26.10%), followed by hexa (20.82%), penta (20.45%), tetra (17.65%) and di-repeats (14.95%). We designed 1330 SSR primers based on the genomic sequence of flanking perfect SSRs (Di and tri-repeats). Among them, 50 SSR primers uniformly distributed across the 11 mungbean chromosomes were selected and used to validate 12 mungbean genotypes. The newly developed genomic SSR markers generated in the present study are a valuable genomic resource for the mungbean breeding programs.

Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus).

Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes (FIS = 0.155) in one breeding population provide baseline information for future breeding program.

Genome-wide identification of simple sequence repeats and assessment of genetic diversity in Hedychium

Hedychium is an important industrial crop, which is widely cultivated for its medicinal and horticultural significance. However, the development of simple sequence repeat (SSR) for Hedychium has not yet been reported. In this study, 266,825 SSR markers were identified in H. coronarium ‘ZS’ genome. The relationship between the type, repeat times, content, and content of SSR markers and chromosome length was specifically analyzed. The results revealed that the mononucleotides (59.17 %) were the most abundant repeat motifs, followed by dinucleotides (27.97 %) and trinucleotides (10.85 %). To verify the availability of SSR and its polymorphism among different species, 120 primer pairs were randomly selected. Finally, 22 markers were screened to genotype 44 accessions collected from different geographic locations of China, Thailand, Japan, and USA. A number of 224 alleles were identified, with an average of 10.18 alleles and polymorphism information content ranged from 0.17 to 0.96 with a mean of 0.88. Genetic structure analysis indicated that 44 accessions had strong regional characteristics and a clear distinction between cultivated and wild genotypes. Population structure and PCoA analysis revealed that from 44 accessions, 7 cultivated accession were distinctly grouped into cluster A, whilst other wild accessions belong to cluster B. These new SSR markers will provide important references for genetic diversity analysis, identification of germplasm resources, and breeding of Hedychium.

Identification of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) that are associated with the nectariless trait of Gossypium hirsutum L

Cotton (Gossypium hirsutum L.) has nectar containing modified stomates called nectaries that can be located on leaves, bracts or calyces. The nectar attracts some beneficial insects such as bees, but also predatory damaging insects such as heliothines and Lygus species. There is a naturally occurring mutation that eliminates the nectar containing nectaries and makes the cotton plants less attractive to insects. The nectariless (ne) trait is associated with a double recessive mutation of two genes (ne1 and ne2) on homeologous chromosomes 12 and 26. Expression of the trait can be variable and is also affected by environmental conditions. This makes accurately selecting for the trait based on phenotype difficult. This study identified SSR and SNP markers that can be used by breeders for marker assisted selection (MAS) of the nectariless trait. DNA markers associated with the genes conditioning the trait and used for MAS, will allow cotton cultivars to be easily developed that have decreased attractiveness to insects and reduce the need for insecticides, especially those harmful to beneficial insects such as honeybees.

Comprehensive identification and characterization of simple sequence repeats based on the whole-genome sequences of 14 forest and fruit trees.

Simple sequence repeats (SSRs) are popular and important molecular markers that exist widely in plants. Here, we conducted a comprehensive identification and comparative analysis of SSRs in 14 tree species. A total of 16, 298 SSRs were identified from 429, 449 genes, and primers were successfully designed for 99.44% of the identified SSRs. Our analysis indicated that tri-nucleotide SSRs were the most abundant, with an average of ~834 per species. Functional enrichment analysis by combining SSR-containing genes in all species, revealed 50 significantly enriched terms, with most belonging to transcription factor families associated with plant development and abiotic stresses such as Myeloblastosis_DNA-bind_4 (Myb_DNA-bind_4), APETALA2 (AP2), and Fantastic Four meristem regulator (FAF). Further functional enrichment analysis showed that 48 terms related to abiotic stress regulation and floral development were significantly enriched in ten species, whereas no significantly enriched terms were found in four species. Interestingly, the largest number of enriched terms was detected in Citrus sinensis (L.) Osbeck, accounting for 54.17% of all significantly enriched functional terms. Finally, we analyzed AP2 and trihelix gene families (Myb_DNA-bind_4) due to their significant enrichment in SSR-containing genes. The results indicated that whole-genome duplication (WGD) and whole genome triplication (WGT) might have played major roles in the expansion of the AP2 gene family but only slightly affected the expansion of the trihelix gene family during evolution. In conclusion, the identification and comprehensive characterization of SSR markers will greatly facilitate future comparative genomics and functional genomics studies.

Maximizing Hybrid Seedlings Recovery and Early Identification of Highly Polyembryonic Acid Lime (Citrus aurantifolia Swing.) × Lemon (Citrus limon Burm.) Hybrids using SSR Markers

Abstract Nucellar embryony is the major obstacle in getting hybrid seedlings in interspecific crosses in citrus. Hence, the present study was conducted to standardize embryo age, culture media for maximizing germination, and subsequent identification of simple sequence repeat (SSR) markers to differentiate the hybrids. A factorial experiment was conducted with three embryo ages – 80–90, 110–120, and 130–140 days after pollination (DAP). The germination of the rescued immature embryos of acid lime × lemon crosses was initiated on three different growing media. The fruits harvested at 130–140 and 80–90 DAP had a higher number of functional seeds (90%). Older embryos (130–140 DAP) and middle-aged embryos (110–120 DAP) germinated in 100% on Murashige and Skoog (MS) medium supplemented with 500 mg·l−1 malt extract, 1.5 mg·l−1 gibberellic acid (GA3), and 0.02 mg·l−1 naphthalene acetic acid (NAA). MS medium supplemented with 500 mg·l−1 malt extract proved better for the germination of embryos taken at 80–90 DAP. Plantlet survival was the highest in younger embryos (80–90 DAP) cultured on MS basal medium (84.21%) and the lowest in older embryos cultured on MS medium supplemented with 500 mg·l−1 malt extract plus 1.5 mg·l−1 GA3 and 0.02 mg·l−1 NAA. The seedlings obtained from the culture 80–90 DAP had the highest root length (4.9 mm) and shoot length (5.3 mm) at 60 days after inoculation (DAI) on the above medium. SSR marker analysis revealed that CCSM-4 and CAC-33 markers expressed polymorphism between female and male parents, proving their ability to identify the hybrids of ‘Kagzi’ acid lime × ‘Konkan Seedless’ lemon.

SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects.

PREMISEMany programs can identify simple sequence repeat (SSR) motifs in genomic data. SSRgenotyper extends SSR identification to en masse genotyping from resequencing data for diversity panels and linkage mapping populations.METHODS AND RESULTSSSRgenotyper will find and genotype SSRs from SAM files and an SSR reference FASTA. Several outputs are possible, including a simple table with the SSR marker name, position, and SSR alleles, defined by the repeat number of the repeat motif. Specific output files include a GENEPOP‐formatted file for downstream genetic diversity analyses and a traditional A, H, B mapping file output that is phased to the parents of the population for biparental linkage map construction. Linkage maps produced using SSRgenotyper genotypes were highly collinear with physical maps and correctly inferred known phylogenies.CONCLUSIONSSSRgenotyper provides an easy‐to‐use, accurate, and scalable SSR genotyping platform for whole‐genome resequencing data. SSRgenotyper is freely available at https://github.com/dlewis27/SSRgenotyper.

Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica.

Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in genes, and identified 811 polymorphic SSRs. Of the identified SSRs, 172, 470, and 76 were located in 5′ UTRs, CDSs, and 3′ UTRs in 591 transcripts; and AG/CT, AAC/GTT, and AT/AT were the most abundant repeats in each gene region. Functional annotation showed that many of the identified polymorphic SSRs were in genes that were enriched in several GO terms and KEGG pathways, suggesting the functional significance of these genes in the environmental adaptation process. The identification of polymorphic genic SSRs in our study lays a foundation for future studies investigating the contribution of SSRs to regulation of genes in natural populations of T. mongolica and their importance for adaptive evolution of this species.