Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Trigonella Foenum-graecum L

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2023 Dec 8

PMID 38066419

Authors

Yanfeng He

Wenya Liu

Jiuli Wang

Affiliations

Soon will be listed here.

Abstract

Background: Trigonella foenum-graecum L. is a Leguminosae plant, and the stems, leaves, and seeds of this plant are rich in chemical components that are of high research value. The chloroplast (cp) genome of T. foenum-graecum has been reported, but the mitochondrial (mt) genome remains unexplored.

Results: In this study, we used second- and third-generation sequencing methods, which have the dual advantage of combining high accuracy and longer read length. The results showed that the mt genome of T. foenum-graecum was 345,604 bp in length and 45.28% in GC content. There were 59 genes, including: 33 protein-coding genes (PCGs), 21 tRNA genes, 4 rRNA genes and 1 pseudo gene. Among them, 11 genes contained introns. The mt genome codons of T. foenum-graecum had a significant A/T preference. A total of 202 dispersed repetitive sequences, 96 simple repetitive sequences (SSRs) and 19 tandem repetitive sequences were detected. Nucleotide diversity (Pi) analysis counted the variation in each gene, with atp6 being the most notable. Both synteny and phylogenetic analyses showed close genetic relationship among Trifolium pratense, Trifolium meduseum, Trifolium grandiflorum, Trifolium aureum, Medicago truncatula and T. foenum-graecum. Notably, in the phylogenetic tree, Medicago truncatula demonstrated the highest level of genetic relatedness to T. foenum-graecum, with a strong support value of 100%. The interspecies non-synonymous substitutions (Ka)/synonymous substitutions (Ks) results showed that 23 PCGs had Ka/Ks < 1, indicating that these genes would continue to evolve under purifying selection pressure. In addition, setting the similarity at 70%, 23 homologous sequences were found in the mt genome of T. foenum-graecum.

Conclusions: This study explores the mt genome sequence information of T. foenum-graecum and complements our knowledge of the phylogenetic diversity of Leguminosae plants.

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References

Beier S, Thiel T, Munch T, Scholz U, Mascher M . MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017; 33(16):2583-2585. PMC: 5870701. DOI: 10.1093/bioinformatics/btx198. View

Yue J, Lu Q, Ni Y, Chen P, Liu C . Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp. Sci Rep. 2022; 12(1):13931. PMC: 9385723. DOI: 10.1038/s41598-022-18387-2. View

Takahashi A, Ohnishi T . The significance of the study about the biological effects of solar ultraviolet radiation using the Exposed Facility on the International Space Station. Biol Sci Space. 2005; 18(4):255-60. DOI: 10.2187/bss.18.255. View

Grantham R, Gautier C, Gouy M . Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980; 8(9):1893-912. PMC: 324046. DOI: 10.1093/nar/8.9.1893. View

Jiang J, Smith H, Ren D, Dissanayaka Mudiyanselage S, Dawe A, Wang L . Potato Spindle Tuber Viroid Modulates Its Replication through a Direct Interaction with a Splicing Regulator. J Virol. 2018; 92(20). PMC: 6158407. DOI: 10.1128/JVI.01004-18. View

Cheng Y, He X, Priyadarshani S, Wang Y, Ye L, Shi C . Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca. BMC Genomics. 2021; 22(1):167. PMC: 7941912. DOI: 10.1186/s12864-021-07490-9. View

Mower J . The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Res. 2009; 37(Web Server issue):W253-9. PMC: 2703948. DOI: 10.1093/nar/gkp337. View

Stothard P, Wishart D . Circular genome visualization and exploration using CGView. Bioinformatics. 2004; 21(4):537-9. DOI: 10.1093/bioinformatics/bti054. View

Li Q, Su X, Ma H, Du K, Yang M, Chen B . Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia. Sci Rep. 2021; 11(1):9919. PMC: 8110538. DOI: 10.1038/s41598-021-89350-w. View

10.

McLean J, COHN G, BRANDT I, Simpson M . Incorporation of labeled amino acids into the protein of muscle and liver mitochondria. J Biol Chem. 1958; 233(3):657-63. View

11.

Verhage L . Targeted editing of the Arabidopsis mitochondrial genome. Plant J. 2020; 104(6):1457-1458. DOI: 10.1111/tpj.15097. View

12.

Straub S, Cronn R, Edwards C, Fishbein M, Liston A . Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae). Genome Biol Evol. 2013; 5(10):1872-85. PMC: 3814198. DOI: 10.1093/gbe/evt140. View

13.

Wang M, Liu H, Ge L, Xing G, Wang M, Weining S . Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L. Genes (Basel). 2017; 8(1). PMC: 5295008. DOI: 10.3390/genes8010013. View

14.

Liao X, Zhao Y, Kong X, Khan A, Zhou B, Liu D . Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants. Sci Rep. 2018; 8(1):12714. PMC: 6109132. DOI: 10.1038/s41598-018-30297-w. View

15.

Paco A, Freitas R, Vieira-da-Silva A . Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene. Genes (Basel). 2019; 10(12). PMC: 6947457. DOI: 10.3390/genes10121014. View

16.

Alon S, Garrett S, Levanon E, Olson S, Graveley B, Rosenthal J . The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. Elife. 2015; 4. PMC: 4384741. DOI: 10.7554/eLife.05198. View

17.

Ma Q, Wang Y, Li S, Wen J, Zhu L, Yan K . Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid. BMC Plant Biol. 2022; 22(1):29. PMC: 8756732. DOI: 10.1186/s12870-021-03416-5. View

18.

Liu F, Fan W, Yang J, Xiang C, Mower J, Li D . Episodic and guanine-cytosine-biased bursts of intragenomic and interspecific synonymous divergence in Ajugoideae (Lamiaceae) mitogenomes. New Phytol. 2020; 228(3):1107-1114. DOI: 10.1111/nph.16753. View

19.

Chan P, Lowe T . tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 2019; 1962:1-14. PMC: 6768409. DOI: 10.1007/978-1-4939-9173-0_1. View

20.

Zheng S, Poczai P, Hyvonen J, Tang J, Amiryousefi A . Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet. 2020; 11:576124. PMC: 7545089. DOI: 10.3389/fgene.2020.576124. View