Evolutionary divergence in Chenopodium and validation of SNPs in chloroplast rbcL and matk genes by allele-specific PCR for development of Chenopodium quinoa-specific markers

Devi, Rajkumari Jashmi; Chrungoo, Nikhil K.

doi:10.1016/j.cj.2016.06.019

Cited by 8 publications

(10 citation statements)

References 33 publications

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“…In the present study, we identified 10 proteins and 6 tRNAs with introns in cp genes (Table S3 ). Although intron sequence variation such as transversion, transition, and small InDels (3–10 bp) have been reported in proteins (Cho et al, 2016 ; Devi and Chrungoo, 2017 ), the present study is the first report of the variations in TR copy number in tRNA introns. The changes in highly conserved cp genes have been used to resolve phylogenetic relationships in angiosperm families.…”

Section: Discussionmentioning

confidence: 52%

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

et al. 2017

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The Chenopodium genus comprises ~150 species, including Chenopodium quinoa and Chenopodium album, two important crops with high nutritional value. To elucidate the phylogenetic relationship between the two species, the complete chloroplast (cp) genomes of these species were obtained by next generation sequencing. We performed comparative analysis of the sequences and, using InDel markers, inferred phylogeny and genetic diversity of the Chenopodium genus. The cp genome is 152,099 bp (C. quinoa) and 152,167 bp (C. album) long. In total, 119 genes (78 protein-coding, 37 tRNA, and 4 rRNA) were identified. We found 14 (C. quinoa) and 15 (C. album) tandem repeats (TRs); 14 TRs were present in both species and C. album and C. quinoa each had one species-specific TR. The trnI-GAU intron sequences contained one (C. quinoa) or two (C. album) copies of TRs (66 bp); the InDel marker was designed based on the copy number variation in TRs. Using the InDel markers, we detected this variation in the TR copy number in four species, Chenopodium hybridum, Chenopodium pumilio, Chenopodium ficifolium, and Chenopodium koraiense, but not in Chenopodium glaucum. A comparison of coding and non-coding regions between C. quinoa and C. album revealed divergent sites. Nucleotide diversity >0.025 was found in 17 regions—14 were located in the large single copy region (LSC), one in the inverted repeats, and two in the small single copy region (SSC). A phylogenetic analysis based on 59 protein-coding genes from 25 taxa resolved Chenopodioideae monophyletic and sister to Betoideae. The complete plastid genome sequences and molecular markers based on divergence hotspot regions in the two Chenopodium taxa will help to resolve the phylogenetic relationships of Chenopodium.

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Section: Discussionmentioning

confidence: 52%

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

et al. 2017

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“…However, in addition to IGS and introns, we identified a number of coding regions that may prove useful for Salvia phylogenetics. The four protein coding genes with highest π values identified by our study (accD, matK, ndhF, and ycf1) have all been used for phylogenetic inference (Zhang and Li 2004;Chang-Li et al 2012;Cruz et al 2013;Qian et al 2013;Luo et al 2014;Patil et al 2015;Srikulnath et al 2015;Uchoi et al 2016;Devi and Chrungoo 2017;Bengtson and Anderberg 2018;Deng et al 2018;Lei et al 2018;Satoh et al 2018;Veranso-Libalah et al 2018), but only matK and ycf1 Sytsma 2011, 2012;Hu et al 2018) have been utilized in sages.…”

Section: Discussionmentioning

confidence: 97%

Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

et al. 2020

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Sage phylogenies have not resolved many shallow level clades within problematic Salvia subgenus Calosphace, hindered by the difficulty in finding sufficiently variable loci. We assembled fifteen chloroplast genomes and nuclear ribosomal cistrons from non-target reads of a nuclear hybrid enrichment project to assess the phylogenetic utility for a closely related group of mainly Mexican sections. Chloroplast synteny is confirmed with 10 Lamiales chloroplasts, supporting a map to reference assembly. Salvia miltiorrhiza Bunge chloroplast was used as a reference for assemblies, averaging 25,970 reads with mean depth of 20.71 reads; genomes ranged from 141,451 to 150,339 bp. The S. carduacea Benth. nuclear ribosomal cistron (18S, ITS1, 5.8S, ITS2 and 26S) was used as a reference for assembly, averaging 66,387 reads and mean depth of 1508 reads. We evaluated several partitioning schemes for plastid, plastid and nrDNA and reduced sampling, to assess whether these would render the same phylogenetic inferences. Maximum likelihood inferences resulted with high bootstrap support and two main clades with interspersed species from Salvia sect. Scorodoniae: clade A with species from S. sects. Atratae and Mitratae and clade B from S. sects. Sigmoideae and Uricae. Only S. sect. Uricae is monophyletic in every analysis supporting its identity, not merged into S. sect. Scorodoniae; S. sect. Sigmoideae is inferred monophyletic only if the ribosomal DNA sequences are included. Greater resolution and higher branch support are obtained with the entire plastome and nrDNA, rather than subsampling highly variable regions; thus we recommend this approach with expanded taxon sampling, coupled with a morphological review to better solve sectional circumscription in closely related S. subgenus Calosphace species.

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“…The literature on the use of DNA barcoding to explore the phylogeny of Chenopodia has preferentially emphasized the maximal breadth of utility across the entire genus [ 17 , 18 , 20 , 21 ]. This does not necessarily lead to the optimization of the markers for the species of interest here.…”

Section: Resultsmentioning

confidence: 99%

“…The various members of the Chenopodium species complex are notoriously challenging to identify in the field [ 41 ]. A variety of barcode markers have been suggested for discriminating all members of the genus with DNA sequencing [ 15 , 17 , 18 , 42 , 43 ]. In some practical situations, however, a universal marker is not required; rather, what is needed is a robust assay for distinguishing the species likely to be encountered in a specific region.…”

Section: Discussionmentioning

confidence: 99%

“…DNA sequence markers to study the overall phylogeny of Chenopodium species have been developed, although these are not optimized to discriminate among the species found in Canada [ 15 , 16 , 17 ]. Devi et al reported sites in the rbcL and matK genes that distinguished C. quinoa from C. album , but they did not report the status of C. berlandieri , and their primers were designed for gel-based, not sequence-based analyses [ 18 ]. However, their success bodes well for the utility of these genes for Chenopodium species identification.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Sequence of Canadian Chenopodium berlandieri: A North American Wild Relative of Quinoa

Samuels

Lapointe

Halwas

et al. 2023

Plants

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Chenopodium berlandieri (pitseed goosefoot) is a widespread native North American plant, which was cultivated and consumed by indigenous peoples prior to the arrival of European colonists. Chenopodium berlandieri is closely related to, and freely hybridizes with the domesticated South American food crop C. quinoa. As such it is a potential source of wild germplasm for breeding with C. quinoa, for improved quinoa production in North America. The C. berlandieri genome sequence could also be a useful source of information for improving quinoa adaptation. To this end, we first optimized barcode markers in two chloroplast genes, rbcL and matK. Together these markers can distinguish C. berlandieri from the morphologically similar Eurasian invasive C. album (lamb’s quarters). Second, we performed whole genome sequencing and preliminary assembly of a C. berlandieri accession collected in Manitoba, Canada. Our assembly, while fragmented, is consistent with the expected allotetraploid structure containing diploid Chenopodium sub-genomes A and B. The genome of our accession is highly homozygous, with only one variant site per 3–4000 bases in non-repetitive sequences. This is consistent with predominant self-fertilization. As previously reported for the genome of a partly domesticated Mexican accession of C. berlandieri, our genome assembly is similar to that of C. quinoa. Somewhat unexpectedly, the genome of our accession had almost as many variant sites when compared to the Mexican C. berlandieri, as compared to C. quinoa. Despite the overall similarity of our genome sequence to that of C. quinoa, there are differences in genes known to be involved in the domestication or genetics of other food crops. In one example, our genome assembly appears to lack one functional copy of the SOS1 (salt overly sensitive 1) gene. SOS1 is involved in soil salinity tolerance, and by extension may be relevant to the adaptation of C. berlandieri to the wet climate of the Canadian region where it was collected. Our genome assembly will be a useful tool for the improved cultivation of quinoa in North America.

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Evolutionary divergence in Chenopodium and validation of SNPs in chloroplast rbcL and matk genes by allele-specific PCR for development of Chenopodium quinoa-specific markers

Cited by 8 publications

References 33 publications

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

Genomic Sequence of Canadian Chenopodium berlandieri: A North American Wild Relative of Quinoa

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