Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica

Qiao, Jiangwei; Zhang, Xiaojun; Huang, Fei; Xu, Kun; Huang, Qian; Huang, Yi; Hu, Qiong; Wu, Xiaoming

doi:10.1186/s12864-020-06889-0

Cited by 18 publications

(9 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The chloroplast genomes in angiosperms usually have a circular structure, ranging from 115 to 165 kb in length, and typical quadripartite structures, which consist of two copies of a large inverted repeat (IR) region separated by a large single-copy (LSC) region and a small single-copy (SSC) region. Phylogenetic analyses based on whole chloroplast genome sequences have been widely used at different taxonomic levels [16][17][18][19][20][21][22][23][24] and have provided effective genetic markers to resolve complex evolutionary histories [25][26][27]. Parasitic plants have partially or entirely lost photosynthetic activity, and are assumed to relax normal constraints on evolution of the chloroplast genome (plastome).…”

Section: Introductionmentioning

confidence: 99%

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Liu

Hong

et al. 2021

Forests

View full text Add to dashboard Cite

Santalum (Santalaceae, sandalwood) is a hemiparasitic genus that includes approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of phylogenetic relationships will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. The Santalum chloroplast genome contains typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 110 unique genes. The whole set of ndh genes and the infA gene were found to lose their functions. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Branch-model-based selection analyses showed that the Santalum species were under widespread purifying selection. Our phylogenomic assessment provides an improved resolution to the phylogenetic relationships of Santalum compared to the past analyses. Our divergence time analysis showed that the crown age of Santalum was 8.46 Mya (million years ago), the first divergence occurred around 6.97 Mya, and diversification was completed approximately 1 Mya. By sequencing the 11 Santalum species chloroplast genomes, we identified the variations in the Santalum chloroplast genomes. Using the chloroplast genome sequences, phylogeny and divergence time analyses discovered that the Santalum species were likely to originate due to radiation evolution, and most speciation events occurred less than 1 Mya.

show abstract

Section: Introductionmentioning

confidence: 99%

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Liu

Hong

et al. 2021

Forests

View full text Add to dashboard Cite

show abstract

“…There were 1,215 cases of nap cytoplasm, 170 cases of cam cytoplasm, 53 cases of pol cytoplasm, and the remaining 18 cases of ole cytoplasm (Table 1 , Supplementary Table S 4 ). The nap -type accessions accounted for 83% of the group, indicating that nap mitotype was predominant in natural B. napus [ 39 ]. Accessions with same cytoplasm type exhibited consistent organelle genome structure supported by Mugsy [ 56 ] alignments.…”

Section: Resultsmentioning

confidence: 99%

A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.

et al. 2022

View full text Add to dashboard Cite

Background Allotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea. Results Based on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus. Conclusions The phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.

show abstract

“…For example, the genus Brassica comprises vegetable crops, such as cabbage (Brassica oleracea L.) or oil crops, such as turnip (B. rapa L.), which also includes vegetable crops such as bok-choy [B. rapa L. subsp. chinensis (L.) Hansel] (Cheng et al, 2016;Lin et al, 2014;Qiao et al, 2020). In this study, we propose that the use of amaranth for different purposes may result from the phenotypic divergence among different species given that amaranth is an ancient crop and has been consumed in various ways in different regions.…”

Section: F I G U R Ementioning

confidence: 99%

De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus

Lin

Chan

et al. 2022

The Plant Genome

View full text Add to dashboard Cite

Amaranth species (Amaranthus spp.) serve as pseudo cereals and also as traditional leafy vegetables worldwide. In addition to high vigor and richness in nutrients, drought and salinity tolerance makes amaranth a promising vegetable to acclimatize to the effects of global climate change. The World Vegetable Center gene bank conserves ∼1,000 amaranth accessions, and various agronomic properties of these accessions were recorded during seed regeneration over decades. In this study, we verified the taxonomic annotation of the germplasm based on a 15K single‐nucleotide polymorphism (SNP) set. Given that the yield components of grain amaranth are different from those of leaf amaranth, we observed that grain amaranth species presented larger inflorescences and earlier flowering than leaf amaranth species. Dual‐purpose amaranth showed larger leaves than leaf amaranth and later flowering than grain amaranth, which seemed reasonable because farmers can harvest more leaves during the prolonged vegetable stage, which also provides recovery time to enrich grain production. Considering frequent interspecific hybridization among species of the grain amaranth complex, we performed an interspecific genome‐wide association study (GWAS) for days to flowering, identifying a AGL20/SOC1 homolog. Another GWAS using only A. tricolor L. accessions revealed six candidate genes homologous to lba1, bri1, sgs1, and fca. These homologous genes were involved in the regulation of flowering time in Arabidopsis thaliana (L.) Heynh. This study revealed the usefulness of genotypic data for species demarcation in the genus Amaranthus and the potential of interspecific GWAS to detect quantitative trait loci (QTL) across different species, opening up the possibility of targeted introduction of specific genetic variants into different Amaranthus species.

show abstract

Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica

Cited by 18 publications

References 62 publications

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.

De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus

Contact Info

Product

Resources

About