Comparative study of chloroplast genomes across seven Salacca species

##plugins.themes.bootstrap3.article.sidebar##

PDF
Issue
Vol. 25 No. 11 (2024)
Section
Articles
Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

##plugins.themes.bootstrap3.article.main##

ARSLAN ARSHAD
Program of Plant Breeding and Biotechnology, Department of Agronomy and Horticulture, Faculty of Agriculture, Institut Pertanian Bogor. Jl. Meranti, Campus IPB Dramaga, Bogor 16680, West Java, Indonesia
REDI ADITAMA
PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Institut Pertanian Bogor. Jl. Meranti, IPB Dramaga Campus, Bogor 16680, West Java, Indonesia
MEGAYANI SRI RAHAYU
PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Institut Pertanian Bogor. Jl. Meranti, IPB Dramaga Campus, Bogor 16680, West Java, Indonesia
AZIS NATAWIJAYA
Innovation Center, Corporate Development, PT. Bumitama Gunajaya Agro (Bumitama Agri Ltd.). Jl. Melawai Raya No. 10, Jakarta Selatan 12160, Jakarta, Indonesia
DEDEN DERADJAT MATRA
PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Institut Pertanian Bogor. Jl. Meranti, IPB Dramaga Campus, Bogor 16680, West Java, Indonesia
SUDARSONO SUDARSONO ♥
Program of Plant Breeding and Biotechnology, Department of Agronomy and Horticulture, Faculty of Agriculture, Institut Pertanian Bogor. Jl. Meranti, Campus IPB Dramaga, Bogor 16680, West Java, Indonesia

Abstract

Abstract. Arshad A, Aditama R, Rahayu MS, Natawijaya A, Matra DD, Sudarsono S. 2024. Comparative study of chloroplast genomes across seven Salacca species. Biodiversitas 25: 4043-4058. Chloroplast (Cp) genomes play a vital role in comprehending plant evolution, biodiversity, and phylogenetics. Snake fruit is a tropical fruit in the Indo-Malayan region. This work compares seven Salacca species Cp genomes to clarify their genetics and evolutionary connections. Cp genomes were constructed using sequencing data from the BGISeq-500 platform and the GetOrganelle assemblers. The assembled Cp genomes have a standard four-part structure and vary in length from 157,047 to 158,182 kilobase pairs (kbp). Comparative genomics analysis found the ycf1 gene to have the highest number of single nucleotide polymorphisms (SNPs), revealing missing amino acids in Salacca affinis. The Cp genomes showed a high prevalence of mononucleotide SSR motifs. With a few exceptions, especially Salacca wallichiana, most Cp genomes showed stable borders between the large single copy (LSC), inverted repeat (IR), and short single copy (SSC) sections. This research underscores the importance of Cp genome information for identifying species, a crucial tool for evolutionary studies and breeding purposes. Furthermore, it emphasizes the intimate genetic connection between Salacca and Cocos nucifera, which contrasts with Phoenix dactylifera. This thorough research provides vital insights into the genetics of Salacca species and highlights the usefulness of Cp genome data in subsequent analyses.

##plugins.themes.bootstrap3.article.details##

References
Ahmed I. 2015. Chloroplast genome sequencing: Some reflections. J Next Generat Seq Appl 2: 000119N. DOI: 10.4172/2469-9853.1000119.
Amiryousefi A, Hyvönen J, Poczai P. 2018. IRscope: An online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34 (17): 3030-3031. DOI: 10.1093/bioinformatics/bty220.
Andrade MC, Perek M, Pereira FB, Moro M, Tambarussi EV. 2018. Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence. Crop Breed Appl Biotechnol 18: 97-102. DOI: 10.1590/1984-70332018v18n1a13.
Bi Y, Zhang M, Xue J, Dong R, Du Y, Zhang X. 2018. Chloroplast genomic resources for phylogeny and DNA barcoding: A case study on Fritillaria. Sci Rep 8: 1184. DOI: 10.1038/s41598-018-19591-9.
Bock R, Knoop V. 2012. Genomics of chloroplasts and mitochondria. Springer, Netherlands. DOI: 10.1007/978-94-007-2920-9.
Chen J, Hao Z, Xu H, Yang L, Liu G, Sheng Y, Zheng C, Zheng W, Cheng T, Shi J. 2015. The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng. Front Plant Sci 6: 447. DOI: 10.3389/fpls.2015.00447.
Deng N, Zhou H, Fan H, Yuan Y. 2017. Single nucleotide polymorphisms and cancer susceptibility. Oncotarget 8 (66): 110635-10649. DOI: 10.18632/oncotarget.22372.
Downie SR, Jansen RK. 2015. A comparative analysis of whole plastid genomes from the Apiales: Expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent non-coding regions. Syst Bot 40 (1): 336-351. DOI: 10.1600/036364415X686620.
Gan P, Liu F, Li R, Wang S, Luo J. 2019. Chloroplasts-beyond energy capture and carbon fixation: Tuning of photosynthesis in response to chilling stress. Intl J Mol Sci 20: 5046. DOI: 10.3390/ijms20205046.
Gao X, Zhang X, Meng H, Li J, Zhang D, Liu C. 2018. Comparative chloroplast genomes of Paris Sect. Marmorata: Insights into repeat regions and evolutionary implications. BMC Genomics 19 (10): 878. DOI: 10.1186/s12864-018-5281-x.
Green BR. 2011. Chloroplast genomes of photosynthetic eukaryotes. Plant J 66 (1): 34-44. DOI: 10.1111/j.1365-313X.2011.04541.x.
Gun L, Yumiao R, Haixian P, Liang Z. 2018. Comprehensive analysis and comparison on the codon usage pattern of whole Mycobacterium tuberculosis coding genome from different areas. Biomed Res Intl 2018: 3574976. DOI: 10.1155/2018/3574976.
Harnelly E, Thomy Z, Fathiya N. 2018. Phylogenetic analysis of Dipterocarpaceae in Ketambe Research Station, Gunung Leuser National Park (Sumatra, Indonesia) based on rbcL and matK genes. Biodiversitas 19 (3): 1074-1080. DOI: 10.13057/biodiv/d190340.
Huang Y, Wang J, Yang Y, Fan C, Chen J. 2017. Phylogenomic analysis and dynamic evolution of chloroplast genomes in Salicaceae. Front Plant Sci 8: 1050. DOI: 10.3389/fpls.2017.01050.
Irwani AN, Oskandar YA, Rahmawati DP, Tara PDR. 2022. Process of making Nata de Salacca from honey salak fruit (Salacca edulis Reinw) with the application of biotechnology techniques. J Biosci Nat Resour 1 (2): 73-79. DOI: 10.12928/jbns.v1i2.5306.
Ismail NA, Abu Bakar MF. 2018. Salak-Salacca zalacca. In: Rodrigues S, de Oliveira Silva E, de Brito ES (eds). Exotic Fruits. Elsevier. DOI: 10.1016/B978-0-12-803138-4.00051-4.
Jansen RK, Ruhlman TA. 2012. Plastid Genomes of Seed Plants. In: Bock R, Knoop V (eds). Genomics of Chloroplasts and Mitochondria. Springer, Netherlands. DOI: 10.1007/978-94-007-2920-9_5.
Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z. 2020. GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21 (1): 241. DOI: 10.1186/s13059-020-02154-5.
Kaila T, Chaduvla PK, Rawal HC, Saxena S, Tyagi A, Mithra SVA, Solanke AU, Kalia P, Sharma TR, Singh NK, Gaikwad K. 2017. Chloroplast genome sequence of cluster bean (Cyamopsis tetragonoloba L.): Genome structure and comparative analysis. Genes 8 (9): 212. DOI: 10.3390/genes8090212.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33 (7): 1870-1874. DOI: 10.1093/molbev/msw054.
Lestari R, Ebert G, Juanda H, Obstbau F. 2002. Salak (Salacca zalacca (Gaertner.) Voss.) - The Snakefruit from Indonesia: Preliminary Results of an Ecophysiological Study. https://www.doc-developpement-durable.org/file/Culture/Arbres-Fruitiers/FICHES_ARBRES/salak/Salak %20Salacca%20zalacca%20%E2%80%93%20The%20Snakefruit%20from%20Indonesia.pdf
Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. 2015. Plant DNA barcoding: From gene to genome. Biol Rev 90 (1): 157-166. DOI: 10.1111/brv.12104.
Liu H, Lu Y, Lan B, Xu J. 2020. Codon usage bias in chloroplast genes of Hemiptelea davidii. J Genet 99 (1): 8. DOI: 10.1007/s12041-019-1167-1.
Lowe TM, Chan PP. 2016. tRNAscan-SE Online: Integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44 (W1): W54-W57. DOI: 10.1093/nar/gkw413.
Matra DD, Ritonga AW, Natawijaya A, Poerwanto R, Sobir, Siregar UJ, Widodo WD, Inoue E. 2019. Datasets for genome assembly of six underutilized Indonesian fruits. Data Brief 22: 960-963. DOI: 10.1016/j.dib.2018.12.070.
Menezes APA, Resende-Moreira LC, Buzatti RSO, Nazareno AG, Carlsen M, Lobo FP, Kalapothakis E, Lovato MB. 2018. Chloroplast genomes of Byrsonima species (Malpighiaceae): Comparative analysis and screening of high divergence sequences. Sci Rep 8: 2210. DOI: 10.1038/s41598-018-20189-4.
Niu Z, Pan J, Zhu S, Li L, Xue Q, Liu W, Ding X. 2017. Comparative analysis of the complete plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) reveals different evolutionary dynamics of ir/ssc boundary among photosynthetic orchids. Front Plant Sci 8: 1713. DOI: 10.3389/fpls.2017.01713.
Rahmawati A, Volkaert HA, Dinarti D, Maskromo I, Hatta ANN L, Sudarsono S. 2021. Complete chloroplast genome sequences of coconut cv. kopyor green dwarf and comparative genome analysis to oil palm, date palm, sago palm, and miniature sugar palm. In: Tombuloglu H, Unver T, Tombuloglu G, Hakeem KR (eds). Oil Crop Genomics. Springer International Publishing. DOI: 10.1007/978-3-030-70420-9_10.
Saleh MSM, Siddiqui M, Mediani A, Ismail N, Ahmed Q, So'ad SM, Saidi-Besbes S. 2018. Salacca zalacca: A short review of the palm botany, pharmacological uses and phytochemistry. Asian Pac J Trop Med 11 (12): 645. DOI: 10.4103/1995-7645.248321.
Sehn JK. 2015. Insertions and deletions (Indels). In: Kulkarni S, Pfeifer J. (eds). Clinical Genomics. Elsevier. DOI: 10.1016/B978-0-12-404748-8.00009-5.
Silitonga YW, Lubis RH, Harahap QH. 2019. Utilization of salak sidimpuan (Salacca sumatrana Becc) as a nata de Salacca substrate in Sitaratoit Village South Tapanuli Selatan Sumatera Utara. J Saintech Transfer 1 (2): 175-180. DOI: 10.32734/jst.v1i2.818.
Visendi P, Batley J, Edwards D. 2014. Next-generation sequencing and germplasm resources. In: Tuberosa R, Graner A, Frison E (eds). Genomics of Plant Genetic Resources. Springer Netherlands. DOI: 10.1007/978-94-007-7572-5_15.
Wang Y, Zhan D-F, Jia X, Mei W-L, Dai H-F, Chen X-T, Peng S-Q. 2016. Complete chloroplast genome sequence of Aquilaria sinensis (Lour.) Gilg and evolution analysis within the Malvales order. Front Plant Sci 7: 280. DOI: 10.3389/fpls.2016.00280.
Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. 2011. The evolution of the plastid chromosome in land plants: Gene content, gene order, gene function. Plant Mol Biol 76: 273-297. DOI: 10.1007/s11103-011-9762-4.
Wilson CA. 2004. Phylogeny of Iris based on chloroplast matK gene and trnK intron sequence data. Mol Phylogenet Evol 33 (2): 402-412. DOI: 10.1016/j.ympev.2004.06.013.
Yamada KD, Tomii K, Katoh K. 2016. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics 32 (21): 3246-3251. DOI: 10.1093/bioinformatics/btw412.
Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, Al-Mssallem IS, Yu J. 2010. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5 (9): e12762. DOI: 10.1371/journal.pone.0012762.
Yang J, He J, Wang DB, Shi E, Yang W, Geng Q, Wang Z. 2016. Progress in research and application of InDel markers. Biodiver Sci 24 (2): 237-243. DOI: 10.17520/biods.2015205.
Yu X-Q, Drew BT, Yang J-B, Gao L-M, Li D-Z. 2017. Comparative chloroplast genomes of eleven schima (Theaceae) species: Insights into DNA barcoding and phylogeny. PLoS One 12 (6): e0178026. DOI: 10.1371/journal.pone.0178026.
Zhang Y, Du L, Liu A, Chen J, Wu L, Hu W, Zhang W, Kim K, Lee S-C, Yang T-J, Wang Y. 2016. The complete chloroplast genome sequences of five Epimedium species: Insights into phylogenetic and taxonomic analyses. Front Plant Sci 7: 306. DOI: 10.3389/fpls.2016.00306.
Zumaidar, Miftahuddin. 2018. Species distribution of genus Salacca. J Phys Conf Ser 1116: 052083. DOI: 10.1088/1742-6596/1116/5/052083.

Most read articles by the same author(s)

1 2 3 > >>