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卷曲黑星珊瑚转录组微卫星发掘与基因功能注释
林柳青, 杨钊, 张涵, 张碟, 石拓, 毛硕乾, 丁鹏, 郑新庆, 周曦杰, 何丛颖
海洋学研究 ›› 2026, Vol. 44 ›› Issue (3) : 66-75.
PDF(2354 KB)
PDF(2354 KB)
卷曲黑星珊瑚转录组微卫星发掘与基因功能注释
Discovery of microsatellites and gene functional annotation based on the transcriptome of Oulastrea crispata
卷曲黑星珊瑚(Oulastrea crispata)为广布型造礁石珊瑚,对多种环境胁迫具有较强的适应能力,但现有研究中对该适应性机制的认知仍较匮乏,尤其缺乏其作为宿主的遗传背景系统性分析。本研究采用高温诱导珊瑚白化的方法,获得低共生藻背景的珊瑚组织,基于Illumina HiSeqTM高通量测序平台开展珊瑚转录组测序与生物信息学分析,在数据质量评估的基础上,系统鉴定EST-SSR位点,开发EST-SSR分子标记。结果显示,所有样本的碱基Q30占比(96.32%)满足高质量测序标准,组装共得到594 447条非冗余基因序列(unigenes),转录本N50长度达1 699 bp,表明转录组数据质量良好;从87 979条unigenes中鉴定获得101 034个EST-SSR位点,其中单核苷酸与三核苷酸重复为优势基序类型,且EST-SSR重复次数随基序长度的增加呈递减趋势;多数据库联合功能注释显示,EST-SSR位点显著富集于涉及环境信息处理的相关功能基因中,提示EST-SSR标记关联基因与珊瑚环境胁迫响应的核心生理机制密切相关。本研究构建的EST-SSR标记体系可作为优质候选遗传标记库,不仅为解析卷曲黑星珊瑚种群的环境适应潜力与进化机制提供重要分子工具,也为珊瑚种群遗传学分析、跨纬度适应性研究及珊瑚礁资源保护修复提供科学参考。
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.
卷曲黑星珊瑚 / 微卫星标记 / 适应性 / 遗传连通性 / 珊瑚礁修复 / 功能注释 / 转录组
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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