De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)
Abstract Background Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples fro...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-09-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-022-03827-y |
| _version_ | 1797998173000564736 |
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| author | Mengli Ma Hengling Meng En Lei Tiantao Wang Wei Zhang Bingyue Lu |
| author_facet | Mengli Ma Hengling Meng En Lei Tiantao Wang Wei Zhang Bingyue Lu |
| author_sort | Mengli Ma |
| collection | DOAJ |
| description | Abstract Background Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers. Results A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species. Conclusions Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko. |
| first_indexed | 2024-04-11T10:44:28Z |
| format | Article |
| id | doaj.art-7f1589033d754659b41a4cf26e7cce17 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-11T10:44:28Z |
| publishDate | 2022-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-7f1589033d754659b41a4cf26e7cce172022-12-22T04:29:06ZengBMCBMC Plant Biology1471-22292022-09-0122111810.1186/s12870-022-03827-yDe novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)Mengli Ma0Hengling Meng1En Lei2Tiantao Wang3Wei Zhang4Bingyue Lu5Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe UniversityKey Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe UniversityCollege of Biological and Agricultural Sciences, Honghe UniversityCollege of Biological and Agricultural Sciences, Honghe UniversityKey Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe UniversityKey Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Honghe UniversityAbstract Background Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers. Results A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species. Conclusions Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.https://doi.org/10.1186/s12870-022-03827-yAmomum tsaokoTranscriptome sequencingEST-SSR markersGenetic diversity |
| spellingShingle | Mengli Ma Hengling Meng En Lei Tiantao Wang Wei Zhang Bingyue Lu De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae) BMC Plant Biology Amomum tsaoko Transcriptome sequencing EST-SSR markers Genetic diversity |
| title | De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae) |
| title_full | De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae) |
| title_fullStr | De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae) |
| title_full_unstemmed | De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae) |
| title_short | De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae) |
| title_sort | de novo transcriptome assembly gene annotation and est ssr marker development of an important medicinal and edible crop amomum tsaoko zingiberaceae |
| topic | Amomum tsaoko Transcriptome sequencing EST-SSR markers Genetic diversity |
| url | https://doi.org/10.1186/s12870-022-03827-y |
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