Deciphering species relationships and evolution in Chenopodium through sequence variations in nuclear internal transcribed spacer region and amplified fragment-length polymorphism in nuclear DNA

Chrungoo, Nikhil K.; Devi, Rajkumari Jashmi; Goel, Shailendra; Das, Kamal

doi:10.1007/s12041-019-1079-0

Cited by 2 publications

(2 citation statements)

References 35 publications

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“…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%

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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Section: Discussionmentioning

confidence: 99%

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

Samuels

Lapointe

Halwas

et al. 2023

Plants

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“…Previous investigations in Chenopodium primarily relied on conventional molecular markers for phylogenetic analysis and species identification. These markers include nuclear DNA amplification fragment length polymorphism, ribosomal DNA (rDNA) internally transcribed spacer sequence (ITS) variation, and chloroplast DNA (cpDNA) fragments [24][25][26][27][28]. However, these research methods have limitations due to the restricted information they provide regarding mutation sites.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera (Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers

Wei,

Chen,

Ding

et al. 2023

Genes

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Species within the genus Chenopodium hold significant research interest due to their nutritional richness and salt tolerance. However, the morphological similarities among closely related species and a dearth of genomic resources have impeded their comprehensive study and utilization. In the present research, we conduct the sequencing and assembly of chloroplast (cp) genomes from six Chenopodium and related species, five of which were sequenced for the first time. These genomes ranged in length from 151,850 to 152,215 base pairs, showcased typical quadripartite structures, and encoded 85 protein-coding genes (PCGs), 1 pseudogene, 37 tRNA genes, and 8 rRNA genes. Compared with the previously published sequences of related species, these cp genomes are relatively conservative, but there are also some interspecific differences, such as inversion and IR region contraction. We discerned 929 simple sequence repeats (SSRs) and a series of highly variable regions across 16 related species, predominantly situated in the intergenic spacer (IGS) region and introns. The phylogenetic evaluations revealed that Chenopodium is more closely related to genera such as Atriplex, Beta, Dysphania, and Oxybase than to other members of the Amaranthaceae family. These lineages shared a common ancestor approximately 60.80 million years ago, after which they diverged into distinct genera. Based on InDels and SNPs between species, we designed 12 pairs of primers for species identification, and experiments confirmed that they could completely distinguish 10 related species.

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Deciphering species relationships and evolution in Chenopodium through sequence variations in nuclear internal transcribed spacer region and amplified fragment-length polymorphism in nuclear DNA

Cited by 2 publications

References 35 publications

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

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

Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera (Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers

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