Abstract:. glumaepatula were phylogenetically close to each other and carried low genetic diversity. They were separated from independent lineages, suggesting that they had diverged from a single ancestral maternal lineage, but diverged later to keep gene flow within respective species, as SSR compositions suggested. Genetic relationships among AA genome species indicate how these species have evolved and become distributed across four continents.
“…In the current study, we found six groups of African rice and that the group membership of the O. barthii samples generally agrees with their country of origin but not ecology. However, nearly 40% of the O. barthii accessions were clustered together with African rice accessions, which differed between the current study and other studies (Orjuela et al 2014 ; Wang et al 2014 ), which may be due to differences in the genetic background of the germplasm and sample size (Iwamoto et al 1999 ; Lu et al 2000 ; Nagano et al 2000 ; Ishii et al 2001 ; Park et al 2003 ; Ren et al 2003 ; Zhu and Ge 2005 ; Duan et al 2007 ; Zhang et al 2014 ; Wambugu et al 2015 ; Yin et al 2016 ).…”
Key message
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions.
Abstract
Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (
Oryza glaberrima
Steud.) as compared to its wild progenitor (
O. barthii
A. Chev.) and to Asian rice (
O. sativa
L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and
O. barthii
(115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of
O. barthii
, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1–32.1 and 16.3–37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10
−4
, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (
π
= 1.6 × 10
−2
), but also accounted for just 4.1%, 0.9% and 2.1% of that of
O. barthii
, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
Electronic supplementary material
The online version of this article (10.1007/s00122-018-3268-2) contains supplementary material, which is available to authorized users.
“…In the current study, we found six groups of African rice and that the group membership of the O. barthii samples generally agrees with their country of origin but not ecology. However, nearly 40% of the O. barthii accessions were clustered together with African rice accessions, which differed between the current study and other studies (Orjuela et al 2014 ; Wang et al 2014 ), which may be due to differences in the genetic background of the germplasm and sample size (Iwamoto et al 1999 ; Lu et al 2000 ; Nagano et al 2000 ; Ishii et al 2001 ; Park et al 2003 ; Ren et al 2003 ; Zhu and Ge 2005 ; Duan et al 2007 ; Zhang et al 2014 ; Wambugu et al 2015 ; Yin et al 2016 ).…”
Key message
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions.
Abstract
Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (
Oryza glaberrima
Steud.) as compared to its wild progenitor (
O. barthii
A. Chev.) and to Asian rice (
O. sativa
L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and
O. barthii
(115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of
O. barthii
, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1–32.1 and 16.3–37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10
−4
, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (
π
= 1.6 × 10
−2
), but also accounted for just 4.1%, 0.9% and 2.1% of that of
O. barthii
, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
Electronic supplementary material
The online version of this article (10.1007/s00122-018-3268-2) contains supplementary material, which is available to authorized users.
“…Thus, the evolutionary lineage depicted by the phylogenetic tree based on mitochondrial DNA might not precisely mirror the actual evolutionary ties. Given its semi-autonomous genetic framework, mitochondria may display divergent evolutionary trajectories compared to the nuclear or chloroplast genomes [ 55 – 57 ]. Fig.…”
Brasenia schreberi, a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this species has been published, its mitochondrial genome (mitogenome) has not been extensively explored, with a notable absence of thorough comparative analyses of its organellar genomes. In our study, we had assembled the entire mitogenome of B. schreberi utilizing the sequencing data derived from both Illumina platform and Oxford Nanopore. The B. schreberi mitogenome mostly exists as six circular DNA molecules, with the largest being 628,257 base pairs (bp) and the smallest 110,220 bp, amounting to 1.49 megabases (Mb). Then we annotated the mitogenome of B. schreberi. The mitogenome encompasses a total of 71 genes: 40 of these are coding proteins genes (PCGs), 28 are genes for transfer RNA (tRNA), and the remaining 3 are genes for ribosomal RNA (rRNA). In the analysis of codon usage, we noted a unique codon preference specific to each amino acid. The most commonly used codons exhibited an average RSCU of 1.36, indicating a noticeable bias in codon selection. In the repeat sequence analysis, a total of 553 simple sequence repeats (SSRs) were identified, 1,822 dispersed repeats (comprising 1,015 forward and 807 palindromic repeats), and 608 long terminal repeats (LTRs). Additionally, in the analysis of homologous sequences between organelle genomes, we detected 38 homologous sequences derived from the plastid genome, each exceeding 500 bp, within the B. schreberi mitochondrial genome. Notably, ten tRNA genes (trnC-GCA, trnM-CAU, trnI-CAU, trnQ-UUG, trnN-GUU, trnT-GGU, trnW-CCA, trnA-UGC, trnI-GAU, and trnV-GAC) appear to have been completely transferred from the chloroplast to the mitogenome. Utilizing the Deepred-mt to predict the RNA editing sites in the mitogenome, we have identified 675 high-quality RNA editing sites in the 40 mitochondrial PCGs. In the final stage of our study, we performed an analysis of colinearity and inferred the phylogenetic relationship of B. schreberi with other angiosperms, utilizing the mitochondrial PCGs as a basis. The results showed that the non-coding regions of the B. schreberi mitogenome are characterized by an abundance of repetitive sequences and exogenous sequences, and B. schreberi is more closely related with Euryale ferox.
“…Based on whole genome sequencing of 3,024 accessions of O. sativa (IRRI 3K SNP project) and 446 accessions of O. rufipogon (Oryza base, NIG), O. rufipogon and O. sativa shared the same one base T-deletion in the S-type intron 20 sequences (Fig. 3A), because there was no SNP in the intron 20 between columns BF and BG in Supplemental 3A), it might be originated with relation to O. rufipogon (Vaughan et al 2005, Yin et al 2015. Two cultivated species, O. sativa and O. glaberrima, were independently originated from O. rufipogon in South-east Asia and O. barthii in West Africa, respectively.…”
Oryza AA-genome complex comprises five wild species, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1, a single-copy nuclear gene, was short (S-type: 141-142 bp) in O. rufipogon, O. barthii, and O. glumaepatula, while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis. Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata. As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AAgenome species.
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