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Discovery of microsatellites and gene functional annotation based on the transcriptome of Oulastrea crispata
Lin Liuqing, Yang Zhao, Zhang Han, Zhang Die, Shi Tuo, Mao Shuoqian, Ding Peng, Zheng Xinqing, Zhou Xijie, He Congying
Journal of Marine Sciences ›› 2026, Vol. 44 ›› Issue (3) : 66-75.
PDF(2354 KB)
PDF(2354 KB)
Discovery of microsatellites and gene functional annotation based on the transcriptome of Oulastrea crispata
Oulastrea crispata is a widely distributed reef-building coral with strong adaptability to various environmental stressors. However, existing studies lack systematic genetic background analysis of this species as a host organism to elucidate its underlying adaptive mechanisms. In this study, coral bleaching was induced by high-temperature treatment to obtain coral tissues with low symbiotic algal background. Transcriptome sequencing and bioinformatics analysis were then performed based on the Illumina HiSeqTM high-throughput sequencing platform. Following data quality assessment, EST-SSR loci were systematically identified, and EST-SSR molecular markers were developed. The results showed that the percentage of bases with Q30 scores (96.32%) of all samples met the high-quality sequencing standard. A total of 594 447 unigenes were assembled, with a transcript N50 length of 1 699 bp, indicating good transcriptome data quality. A total of 101 034 EST-SSR loci were identified from 87 979 unigenes, among which mono- and tri-nucleotide repeats were the dominant motif types, and the EST-SSR repeat number showed a decreasing trend with increasing motif length. Multi-database joint functional annotation revealed significant enrichment of EST-SSR loci in functional genes involved in environmental information processing, suggesting that EST-SSR marker-associated genes were closely linked to the core physiological mechanisms underlying coral environmental stress response. The EST-SSR marker system constructed in this study can serve as a high-quality candidate genetic marker library, provide not only important molecular tools for deciphering the environmental adaptation potential and evolutionary mechanisms of Oulastrea crispata populations, but also scientific references for coral population genetic analysis, cross-latitude adaptability research, and coral reef resource conservation and restoration.
Oulastrea crispata / EST-SSR / adaptation / genetic connectivity / coral reef restoration / functional annotation / transcriptome
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Mining for microsatellites (also called simple sequence repeats [SSRs]) in public sequence databases of a common Indo-Pacific coral Acropora millepora identified 191 SSRs from 10 258 expressed sequence tag (EST) and 618 SSRs from 14 625 whole-genome shotgun (WGS) sequences. In contrast to other animals, trinucleotide repeats, rather than dinucleotide repeats, are dominant in the WGS-SSRs, and AAT is the most frequent trinucleotide motif in EST-SSRs. We successfully developed 40 polymorphic markers from EST-SSRs and WGS-SSRs. Both EST- and WGS-SSRs show high levels of polymorphism within corals from the same reef patch. Interestingly, markers WGS079 and WGS227 revealed SSR duplications in a few individuals, suggesting recent duplication events. Genotypic linkage disequilibrium was identified in 5 pairs of SSR markers, which will be invaluable for high-resolution studies of genetic admixture in natural populations of A. millepora. Transferability analysis showed that 25 of these markers can be successfully amplified in one of the most ubiquitous Indo-Pacific corals Acropora hyacinthus. The marker collection reported here is the largest ever developed for any reef-building coral. It holds great potential for addressing coral reef connectivity across the Indo-Pacific with an unprecedented precision, especially taking into account the cross-species transferability of a substantial number of markers.
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Improved bread wheat (Triticum aestivum L.) cultivars for diverse agroecological environments are important for success in the effort to increase food production. In the 1980s, CIMMYT introduced the megaenvironment (ME) concept to breed wheats specifically adapted to different areas. Our objective was to analyze the genetic diversity among 68 advanced CIMMYT wheat lines targeted to different MEs by using 99 simple sequence repeats (SSRs) and the coefficient of parentage (COP). The average number of alleles detected was higher for the 47 genomic SSRs (5.4) than for the 52 SSRs derived from expressed sequence tags (EST) (3.3), but gene diversity between MEs was similar for both types of markers. No significant differences among the five MEs were observed for the means of SSR‐based genetic similarities (GS), calculated as 1 − Rogers' distance, and COP values. Both measures showed a low correlation (r = 0.43). High levels of genetic diversity were found within the germplasm targeted to each ME. However, principle coordinate analysis based on modified Rogers' distances did not separate the genotypes according to their targeted MEs. We conclude that presence of a single core germplasm can reflect large phenotypic differences. A sufficient number of diverse breeding lines for each ME is required because MEs generally combine various production areas. SSRs represent a powerful tool to quantify genetic diversity in wheat, but genotypic differentiation for adaptation to specific MEs in the CIMMYT program could not be proven.
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