[1]

Wanda GJMK, Gamo FZ, Njamen D. 2015. Medicinal plants of the family of Fabaceae used to treat various ailments. In Fabaceae: Fabaceae classification, nutrient composition and health benefits, ed. Garza W. New York, US: Nova Science Publishers. pp. 1–20

[2]

Ogwu MC, Ahana CM, Osawaru ME. 2018. Sustainable food production in Nigeria: a case study for Bambara Groundnut (Vigna subterranea (L.) Verdc. Fabaceae). Journal of Energy and Natural Resource Management 1:68−77

[3]

Gulewicz P, Martinez-Villaluenga C, Kasprowicz-Potocka M, Frias J. 2014. Non-nutritive compounds in Fabaceae family seeds and the improvement of their nutritional quality by traditional processing–a review. Polish Journal of Food and Nutrition Sciences 64:75−89

doi: 10.2478/v10222-012-0098-9
[4]

Shavanov M. 2021. The role of food crops within the Poaceae and Fabaceae families as nutritional plants. IOP Conference Series: Earth and Environmental Science 624:012111

doi: 10.1088/1755-1315/624/1/012111
[5]

Maria ZDaH. 2000. Domestication of plants in the old world. 3rd Edition. pp. 105–7

[6]

Flores-Félix JD, Carro L, Cerda-Castillo E, Squartini A, Rivas R, et al. 2020. Analysis of the interaction between Pisum sativum L. and Rhizobium laguerreae strains nodulating this Legume in Northwest Spain. Plants 9:1755

doi: 10.3390/plants9121755
[7]

Magris G, Jurman I, Fornasiero A, Paparelli E, Schwope R, et al. 2021. The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes. Nature Communications 12:7240

doi: 10.1038/s41467-021-27487-y
[8]

Wu DT, Li WX, Wan JJ, Hu YC, Gan RY, et al. 2023. A comprehensive review of pea (Pisum sativum L.): chemical composition, processing, health benefits, and food applications. Foods 12:2527

doi: 10.3390/foods12132527
[9]

Tulbek MC, Wang YL, Hounjet M. 2024. Pea—a sustainable vegetable protein crop. In Sustainable protein sources, eds. Nadathur S, Wanasundara JPD, Scanlin L. 2nd Edition. Amsterdam, Netherlands: Academic Press. pp. 143−62. doi: 10.1016/B978-0-323-91652-3.00027-7

[10]

Kumar S, Pandey G. 2020. Biofortification of pulses and legumes to enhance nutrition. Heliyon 6:e03682

doi: 10.1016/j.heliyon.2020.e03682
[11]

Sinjushin A, Semenova E, Vishnyakova M. 2022. Usage of morphological mutations for improvement of a garden pea (Pisum sativum): The experience of breeding in Russia. Agronomy 12:544

doi: 10.3390/agronomy12030544
[12]

Abbo S, Rachamim E, Zehavi Y, Zezak I, Lev-Yadun S, et al. 2011. Experimental growing of wild pea in Israel and its bearing on Near Eastern plant domestication. Annals of Botany 107:1399−404

doi: 10.1093/aob/mcr081
[13]

Weeden NF. 2007. Genetic changes accompanying the domestication of Pisum sativum: is there a common genetic basis to the 'domestication syndrome' for legumes? Annals of Botany 100:1017−25

doi: 10.1093/aob/mcm122
[14]

Irwin ME. 2020. Agricultural Plants in the Ancient Mediterranean. A companion to ancient agriculture pp 83-102

[15]

Kosterin OE. 2023. Natural range, habitats and populations of wild peas (Pisum L.). Genetic Resources and Crop Evolution 70:1051−83

doi: 10.1007/s10722-023-01544-5
[16]

Hanci F, Cebeci E. 2019. Determination of morphological variability of different pisum genotypes using principal component analysis. Legume Research-An International Journal 42:162−67

doi: 10.18805/lr-438
[17]

Liu R, Huang YN, Yang T, Hu JG, Zhang HY, et al. 2022. Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers. Journal of Systematics and Evolution 60:85−100

doi: 10.1111/jse.12710
[18]

Ladizinsky G, Abbo S, Ladizinsky G, Abbo S. 2015. The Pisum genus. The search for wild relatives of cool season legumes: pp 55−69

[19]

Barilli E, Cobos MJ, Carrillo E, Kilian A, Carling J, et al. 2018. A high-density integrated DArTseq SNP-based genetic map of Pisum fulvum and identification of QTLs controlling rust resistance. Frontiers in Plant Science 9:167

doi: 10.3389/fpls.2018.00167
[20]

Yan XL, Kan SL, Wang MX, Li YY, Tembrock LR, et al. 2024. Genetic diversity and evolution of the plastome in allotetraploid cotton (Gossypium spp.). Journal of Systematics and Evolution 62:1118−36

doi: 10.1111/jse.13070
[21]

Zhang S, Han S, Bi D, Yang J, Ge W, et al. 2024. Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective. Genes 15:444

doi: 10.3390/genes15040444
[22]

Kan J, Zhang S, Wu Z, Bi D. 2024. Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics. Genes 15:441

doi: 10.3390/genes15040441
[23]

Wang J, Liao X, Li Y, Ye Y, Xing G, et al. 2023. Comparative Plastomes of Curcuma alismatifolia (Zingiberaceae) Reveal Diversified Patterns among 56 Different Cut-Flower Cultivars. Genes 14:1743

doi: 10.3390/genes14091743
[24]

Wang J, Kan S, Liao X, Zhou J, Tembrock LR, et al. 2024. Plant organellar genomes: much done, much more to do. Trends in Plant Science 29:754−69

doi: 10.1016/j.tplants.2023.12.014
[25]

Sibbald SJ, Archibald JM. 2020. Genomic insights into plastid evolution. Genome Biology and Evolution 12:978−90

doi: 10.1093/gbe/evaa096
[26]

Choi IS, Jansen R, Ruhlman T. 2019. Lost and found: return of the inverted repeat in the legume clade defined by its absence. Genome Biology and Evolution 11:1321−33

doi: 10.1093/gbe/evz076
[27]

Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, et al. 2016. Variable presence of the inverted repeat and plastome stability in Erodium. Annals of Botany 117:1209−20

doi: 10.1093/aob/mcw065
[28]

Jiao YX, He XF, Song R, Wang XM, Zhang H, et al. 2023. Recent structural variations in the Medicago chloroplast genomes and their horizontal transfer into nuclear chromosomes. Journal of Systematics and Evolution 61:627−42

doi: 10.1111/jse.12900
[29]

Choi IS, Jansen R, Ruhlman T. 2020. Caught in the act: variation in plastid genome inverted repeat expansion within and between populations of Medicago minima. Ecology and Evolution 10:12129−37

doi: 10.1002/ece3.6839
[30]

Kan S, Liao X, Lan L, Kong J, Wang J, et al. 2024. Cytonuclear interactions and subgenome dominance shape the evolution of organelle-targeted genes in the Brassica triangle of U. Molecular Biology and Evolution 41:msae043

doi: 10.1093/molbev/msae043
[31]

Wang J, Kan J, Wang J, Yan X, Li Y, et al. 2024. The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history. Frontiers in Plant Science 15:1404071

doi: 10.3389/fpls.2024.1404071
[32]

Sielemann K, Pucker B, Schmidt N, Viehöver P, Weisshaar B, et al. 2022. Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 23:113

doi: 10.1186/s12864-022-08336-8
[33]

Wang J, Liao X, Gu C, Xiang K, Wang J, et al. 2022. The Asian lotus (Nelumbo nucifera) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics. Ornamental Plant Research 2:2

doi: 10.48130/opr-2022-0002
[34]

Yang T, Liu R, Luo Y, Hu S, Wang D, et al. 2022. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nature Genetics 54:1553−63

doi: 10.1038/s41588-022-01172-2
[35]

Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754−60

doi: 10.1093/bioinformatics/btp324
[36]

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078−79

doi: 10.1093/bioinformatics/btp352
[37]

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using SPAdes de novo assembler. Current protocols in bioinformatics 70:e102

doi: 10.1002/cpbi.102
[38]

Greiner S, Lehwark P, Bock R. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic acids research 47:W59−W64

doi: 10.1093/nar/gkz238
[39]

Wright F. 1990. The 'effective number of codons' used in a gene. Gene 87:23−29

doi: 10.1016/0378-1119(90)90491-9
[40]

Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−85

doi: 10.1093/bioinformatics/btx198
[41]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772−80

doi: 10.1093/molbev/mst010
[42]

Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, et al. 2016. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microbial Genomics 2:e000056

doi: 10.1099/mgen.0.000056
[43]

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, et al. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37:1530−34

doi: 10.1093/molbev/msaa015
[44]

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, et al. 2020. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Molecular Biology and Evolution 37:291−94

doi: 10.1093/molbev/msz189
[45]

Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, et al. 2014. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9:e90346

doi: 10.1371/journal.pone.0090346
[46]

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, et al. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34:3299−302

doi: 10.1093/molbev/msx248
[47]

Leigh JW, Bryant D, Nakagawa S. 2015. POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6(9):1110−16

doi: 10.1111/2041-210X.12410
[48]

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 Molecular Biology 76:273−97

doi: 10.1007/s11103-011-9762-4
[49]

Filiz E, Koc I. 2012. In silico chloroplast SSRs mining of Olea species. Biodiversitas Journal of Biological Diversity 13:3

doi: 10.13057/biodiv/d130302
[50]

Lawson MJ, Zhang L. 2006. Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biology 7:R14

doi: 10.1186/gb-2006-7-2-r14
[51]

Wang XT, Zhang YJ, Qiao L, Chen B. 2019. Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: identification, characterization and distribution (Diptera: Culicidae). Insect Science 26:607−19

doi: 10.1111/1744-7917.12577
[52]

Coenye T, Vandamme P. 2005. Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA research 12:221−33

doi: 10.1093/dnares/dsi009
[53]

Li MY, Tan HW, Wang F, Jiang Q, Xu ZS, et al. 2014. De novo transcriptome sequence assembly and identification of AP2/ERF transcription factor related to abiotic stress in parsley (Petroselinum crispum). PLoS One 9:e108977

doi: 10.1371/journal.pone.0108977
[54]

Gebeyehu A, Hammenhag C, Tesfaye K, Vetukuri RR, Ortiz R, et al. 2022. RNA-Seq provides novel genomic resources for noug (Guizotia abyssinica) and reveals microsatellite frequency and distribution in its transcriptome. Frontiers in Plant Science 13:882136

doi: 10.3389/fpls.2022.882136
[55]

Korkovelos AE, Mavromatis AG, Huang WG, Hagidimitriou M, Giakoundis A, et al. 2008. Effectiveness of SSR molecular markers in evaluating the phylogenetic relationships among eight Actinidia species. Scientia Horticulturae 116:305−10

doi: 10.1016/j.scienta.2008.01.011
[56]

Wu YX, Daud MK, Chen L, Zhu SJ. 2007. Phylogenetic diversity and relationship among Gossypium germplasm using SSRs markers. Plant Systematics and Evolution 268:199−208

doi: 10.1007/s00606-007-0565-7
[57]

Duan H, Zhang Q, Wang C, Li F, Tian F, et al. 2021. Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints. PeerJ 9:e10787

[58]

Zhang Y, Shen Z, Meng X, Zhang L, Liu Z, et al. 2022. Codon usage patterns across seven Rosales species. BMC Plant Biology 22:65

doi: 10.1186/s12870-022-03450-x
[59]

Wang AH-J, Hakoshima T, van der Marel G, van Boom JH, Rich A. 1984. AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d (m5CGTAm5CG). Cell 37:321−31

doi: 10.1016/0092-8674(84)90328-3
[60]

Benisty H, Hernandez-Alias X, Weber M, Anglada-Girotto M, Mantica F, et al. 2023. Genes enriched in A/T-ending codons are co-regulated and conserved across mammals. Cell Systems 14:312−23. e3

[61]

Shao ZQ, Zhang YM, Feng XY, Wang B, Chen JQ. 2012. Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency. PLoS One 7:e33547

doi: 10.1371/journal.pone.0033547
[62]

Khan MF, Patra S. 2018. Deciphering the rationale behind specific codon usage pattern in extremophiles. Scientific Reports 8:15548

doi: 10.1038/s41598-018-33476-x
[63]

Pal A, Saha BK, Saha J. 2019. Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination. Plos One 14:e0219231

doi: 10.1371/journal.pone.0219231
[64]

Baruah VJ, Satapathy SS, Powdel BR, Konwarh R, Buragohain AK, et al. 2016. Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins. Journal of Genetics 95:537−49

doi: 10.1007/s12041-016-0667-5
[65]

Rivera-Jiménez HJ, Rossini BC, Del Carmen Humanez Alvarez A A, Silva SR, Yepes-Escobar J, et al. 2020. DNA barcoding for molecular identification of Gynerium sagittatum (Poales: Poaceae): genetic diversity in savannah genotypes from Córdoba, Colombia. Revista de Biología Tropical 68:1049−61

doi: 10.15517/rbt.v68i4.39350
[66]

Jiang S, Chen F, Qin P, Xie H, Peng G, et al. 2022. The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants. Physiology and Molecular Biology of Plants 28:837−48

doi: 10.1007/s12298-022-01175-7
[67]

Cid J, Grivet D, Olsson S, Fernández M. 2019. Evaluation of the chloroplast regions matK and ycf1 as diagnostic markers for the genus Pinus. Cuadernos de la Sociedad Española de Ciencias Forestales: 215-35

[68]

Dong W, Xu C, Li C, Sun J, Zuo Y, et al. 2015. ycf1, the most promising plastid DNA barcode of land plants. Scientific Reports 5:8348

doi: 10.1038/srep0834
[69]

Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, et al. 2021. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. The Plant Journal 107:861−75

doi: 10.1111/tpj.15351
[70]

Schneider AC, Braukmann T, Banerjee A, Stefanović S. 2018. Convergent plastome evolution and gene loss in holoparasitic Lennoaceae. Genome Biology and Evolution 10:2663−70

doi: 10.1093/gbe/evy190
[71]

Kim YK, Jo S, Cheon SH, Joo MJ, Hong JR, et al. 2020. Plastome evolution and phylogeny of Orchidaceae, with 24 new sequences. Frontiers in Plant Science 11:22

doi: 10.3389/fpls.2020.00022