Chloroplast derived SSRs reveals genetic relationships in domesticated alliums and wild relatives

Jayaswall, Kuldip; Sharma, Himanshu; Bhandawat, Abhishek; Sagar, R.; Jayaswal, Deepanshu; Kumar, Akash; Chaturvedi, Pratibha; Mahajan, Vijay; Kumar, Sanjay; Singh, Major

doi:10.1007/s10722-021-01235-z

Cited by 9 publications

(3 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…7). Most cp SSRs are located in intergenic spacer of LSC and SSC regions, with 61% in non-coding regions and only a small amount in protein-coding genes (25%) and introns (14%) (Table S6), which is consistent with other plants [92,93,139]. It is revealed that non-coding regions are more variable to screen valuable polymorphic SSRs.…”

Section: Potential Molecular Markers Selectionsupporting

confidence: 80%

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Niu

Lin

Tong

et al. 2023

Preprint

View full text Add to dashboard Cite

Background Justicia is the largest genus in Acanthaceae and widely distributed in Asia, Africa, Australia and South America. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp) genomes of twelve Asian plants and combined with the previously published cp genome of J. leptostachya for further comparative genomics and phylogenetic analyses.Results All the cp genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434–83,676 bp), a small single copy (SSC, 16,833–17,507 bp) and two inverted repeats (IR, 24,947–25,549 bp). GC contents range from 38.1–38.4%. All the plastomes contain 114 genes, containing 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for Justicia phylogeny. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with morphology evolution of inflorescence position from terminal to axillary and spikes gradually shorten into cymes.Conclusion Our study not only elucidates basic features of Justicia whole plastomes, but also first sheds light on interspecific relationships of Asian Justicia plants.

show abstract

Section: Potential Molecular Markers Selectionsupporting

confidence: 80%

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Niu

Lin

Tong

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Cp microsatellites (cpSSRs) exist widely in cp genomes and have the advantages of codominant inheritance, high polymorphism, and abundance ( Huang et al., 2018 ). Therefore, cpSSR markers were widely used for species authentication, evolutionary studies, population genetics, and so on ( Dzialuk et al., 2009 ; Jayaswall et al., 2015 ; Singha et al., 2017 ; Mahajan et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes

Shi,

Yang,

Miao

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

BackgroundPolygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products’ quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum.MethodsNine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed.ResultsThe total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production.ConclusionThis study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.

show abstract

“…However, the past few decades have witnessed constant breakthroughs in molecular biology, particularly genetics, presenting a new array of tools suitable for unravelling their relationships and elucidating the unique chemical pro les of associated cultivars (Gounaris et al 2002;Labra et al 2004). Discrete markers like RAPDs, AFLPs, and hypervariable DNA regions (such as SSRs) have commonly been employed as molecular methodologies for such investigations (Friesen and Klaas 1998;Labra et al 2004;Trindade 2007;Jayaswall et al 2022). Stilldespite their demonstrated effectiveness -these markers face limitations in discriminating between diverse species or cultivars (Trindade 2007;Azizi et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Genomic profiling reveals intraspecific divergence and interspecific diversity in Allium cepa L.

Packia Lekshmi,

Brindha,

Mahamuni

et al. 2024

Genet Resour Crop Evol

View full text Add to dashboard Cite

Evolution of genus is accompanied by ecological diversi cation. The majority of species grow in open, sunny, rather dry sites in arid and moderately humid climates. However, Allium species have adapted for many other ecological niches. Classical approaches for the identi cation of Allium cultivars are based on morphological traits. The assessment of these traits is di cult and their evaluation can be subjective considering that most of these cultivars are closely related. Hence, this study of Internal Transcribed Spacer (ITS) sequencing and four barcoding regions, matK, rbcL, trnH-psbA, trnL and Inter Simple Sequence Repeats (ISSR) were researched in onion, Allium cepa L. (Alliaceae) collected from three different cultivation sites. The results established noticeable hereditary divergence among the three cultivars. In ITS and matK, BDUT 1453, BDUT 1454 and BDUT 1455 were independent of each other and formed three clusters. In rbcL, BDUT 1453 formed an independent cluster from the cluster of BDUT 1454 and BDUT 1455. But in trnH-psbA, BDUT 1454 formed an independent cluster and BDUT 1453 and BDUT 1455 were closely placed whereas trnL showed all the three forming a cluster wherein BDUT 1453 and BDUT 1454 were placed closely in a sub-cluster. In ISSR, BDUT 1454 and BDUT 1455 formed a single cluster and BDUT 1453 diverged from it. Even though the tested cultivars belong to the same species they showed genetic divergence among themselves.

show abstract

Chloroplast derived SSRs reveals genetic relationships in domesticated alliums and wild relatives

Cited by 9 publications

References 33 publications

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes

Genomic profiling reveals intraspecific divergence and interspecific diversity in Allium cepa L.

Contact Info

Product

Resources

About