De Novo Transcriptome Assembly, Gene Annotation, and EST-SSR Marker Development of an Important Medicinal and Edible Crop, Amomum Tsaoko (Zingiberaceae)

Overview

Journal BMC Plant Biol

Publisher Biomed Central

Specialty Biology

Date 2022 Sep 28

PMID 36171538

Authors

Mengli Ma

Hengling Meng

En Lei

Tiantao Wang

Wei Zhang

Bingyue Lu

Affiliations

Soon will be listed here.

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.

Citing Articles

Transcriptomic and metabolomic study of the biosynthetic pathways of bioactive components in Amomum tsaoko fruits.

Luo D, Zhang Y, Jin L, Wu X, Yang C, Zhang T BMC Plant Biol. 2025; 25(1):212.

PMID: 39966750 PMC: 11834249. DOI: 10.1186/s12870-025-06239-w.

Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS).

An K, Zhou C, Tong B, Liu D, Shan X, Zhang X BMC Plant Biol. 2024; 24(1):995.

PMID: 39438785 PMC: 11515793. DOI: 10.1186/s12870-024-05705-1.

Widely targeted volatilomics and transcriptome analyses reveal the differences in volatile organic components in differently shaped Amomum tsao-ko fruits.

Ma M, Fu H, Wang T, Xiong L, Feng P, Lu B BMC Plant Biol. 2024; 24(1):915.

PMID: 39350013 PMC: 11443856. DOI: 10.1186/s12870-024-05594-4.

Development of SSR markers for genetic diversity analysis and species identification in Polygonatum odoratum (Mill.) Druce based on transcriptome sequences.

Pan G, Xie J, Qin Y, Zhang S PLoS One. 2024; 19(9):e0308316.

PMID: 39312515 PMC: 11419394. DOI: 10.1371/journal.pone.0308316.

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province.

Ma M, Lei E, Wang T, Meng H, Zhang W, Lu B Plants (Basel). 2023; 12(8).

PMID: 37111901 PMC: 10146266. DOI: 10.3390/plants12081678.

References

Botstein D, White R, Skolnick M, Davis R . Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980; 32(3):314-31. PMC: 1686077. View

Wu Q, Zang F, Xie X, Ma Y, Zheng Y, Zang D . Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis. Sci Rep. 2020; 10(1):16249. PMC: 7530656. DOI: 10.1038/s41598-020-73289-5. View

Bazzo B, de Carvalho L, Carazzolle M, Guimaraes Pereira G, Colombo C . Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species. BMC Plant Biol. 2018; 18(1):276. PMC: 6233587. DOI: 10.1186/s12870-018-1509-9. View

Zhang X, Tang Y, Guan X, Lu X, Li J, Chen X . Flavonoid constituents of Crevost et Lemarie and their antioxidant and antidiabetic effects in diabetic rats - and studies. Food Funct. 2021; 13(1):437-450. DOI: 10.1039/d1fo02974f. View

Li X, Wen Z, Si M, Jia Y, Liu H, Zheng Y . Exploration of Hanshi Zufei prescription for treatment of COVID-19 based on network pharmacology. Chin Herb Med. 2022; 14(2):294-302. PMC: 8969322. DOI: 10.1016/j.chmed.2021.06.006. View

Jarem D, Huckaby L, Delaney S . AGG interruptions in (CGG)(n) DNA repeat tracts modulate the structure and thermodynamics of non-B conformations in vitro. Biochemistry. 2010; 49(32):6826-37. PMC: 3650493. DOI: 10.1021/bi1007782. View

Guo J, Huang Z, Sun J, Cui X, Liu Y . Research Progress and Future Development Trends in Medicinal Plant Transcriptomics. Front Plant Sci. 2021; 12:691838. PMC: 8355584. DOI: 10.3389/fpls.2021.691838. View

Qian X, Wang C, Tian M . Genetic diversity and population differentiation of Calanthe tsoongiana, a rare and endemic orchid in China. Int J Mol Sci. 2013; 14(10):20399-413. PMC: 3821621. DOI: 10.3390/ijms141020399. View

Morgante M, Hanafey M, Powell W . Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002; 30(2):194-200. DOI: 10.1038/ng822. View

10.

Shi X, Sun H, Chen Y, Pan H, Wang S . Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating . Front Plant Sci. 2016; 7:1577. PMC: 5083712. DOI: 10.3389/fpls.2016.01577. View

11.

Li S, Ji F, Hou F, Cui H, Shi Q, Xing G . Characterization of Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Collection. Front Plant Sci. 2020; 11:686. PMC: 7300269. DOI: 10.3389/fpls.2020.00686. View

12.

Peakall R, Smouse P . GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics. 2012; 28(19):2537-9. PMC: 3463245. DOI: 10.1093/bioinformatics/bts460. View

13.

Liu K, Muse S . PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 2005; 21(9):2128-9. DOI: 10.1093/bioinformatics/bti282. View

14.

Wang K, Liu Y, Shi Y, Yan M, Rengarajan T, Feng X . fruit extract exerts anticonvulsant effects through suppression of oxidative stress and neuroinflammation in a pentylenetetrazol kindling model of epilepsy in mice. Saudi J Biol Sci. 2021; 28(8):4247-4254. PMC: 8325006. DOI: 10.1016/j.sjbs.2021.06.007. View

15.

Martienssen R, Colot V . DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science. 2001; 293(5532):1070-4. DOI: 10.1126/science.293.5532.1070. View

16.

Zhu Y, Yan X, Ye T, Hu J, Wang X, Qiu F . Analyzing the potential therapeutic mechanism of Huashi Baidu Decoction on severe COVID-19 through integrating network pharmacological methods. J Tradit Complement Med. 2021; 11(2):180-187. PMC: 7834580. DOI: 10.1016/j.jtcme.2021.01.004. View

17.

Lu J, Zhang Y, Diao X, Yu K, Dai X, Qu P . Evaluation of genetic diversity and population structure of Fragaria nilgerrensis using EST-SSR markers. Gene. 2021; 796-797:145791. DOI: 10.1016/j.gene.2021.145791. View

18.

Madritsch S, Burg A, Sehr E . Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species. BMC Bioinformatics. 2021; 22(1):146. PMC: 7986043. DOI: 10.1186/s12859-021-04078-8. View

19.

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

20.

Zalapa J, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E . Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot. 2011; 99(2):193-208. DOI: 10.3732/ajb.1100394. View