Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India

Plantago ovata (plantaginaceae) is an economically and medicinally important species, however, least is known about its genomics and evolution. Here, we report the first complete plastome genome of P. ovata and comparison with previously published genomes of related species from plantaginaceae. the results revealed that P. ovata plastome size was 162,116 bp and that it had typical quadripartite structure containing a large single copy region of 82,084 bp and small single copy region of 5,272 bp. The genome has a markedly higher inverted repeat (IR) size of 37.4 kb, suggesting large-scale inversion of 13.8 kb within the expanded IR regions. In addition, the P. ovata plastome contains 149 different genes, including 43 tRNA, 8 rRNA, and 98 protein-coding genes. The analysis revealed 139 microsatellites, of which 71 were in the non-coding regions. Approximately 32 forward, 34 tandem, and 17 palindromic repeats were detected. The complete genome sequences, 72 shared genes, matK gene, and rbcL gene from related species generated the same phylogenetic signals, and phylogenetic analysis revealed that P. ovata formed a single clade with P. maritima and P. media. the divergence time estimation as employed in BeASt revealed that P. ovata diverged from P. maritima and P. media about 11.0 million years ago (Mya; 95% highest posterior density, 10.06-12.25 Mya). In conclusion, P. ovata had significant variation in the IR region, suggesting a more stable P. ovata plastome genome than that of other plantaginaceae species.

Section: Discussionmentioning

confidence: 99%

Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata

Asaf

Khan

Lubna

et al. 2020

“…Repetitive sequences have been reported in the chloroplast genome of many plant lineages 49 , 50 . These types of markers are used for a wide range of evolutionary and population genetic studies 51 , 52 . Byrsonima coccolobifolia and B .…”

Section: Discussionmentioning

confidence: 99%

Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences

Menezes

Resende‐Moreira

Buzatti

et al. 2018

130

114

Byrsonima is the third largest genus (about 200 species) in the Malpighiaceae family, and one of the most common in Brazilian savannas. However, there is no molecular phylogeny available for the genus and taxonomic uncertainties at the generic and family level still remain. Herein, we sequenced the complete chloroplast genome of B. coccolobifolia and B. crassifolia, the first ones described for Malpighiaceae, and performed comparative analyses with sequences previously published for other families in the order Malpighiales. The chloroplast genomes assembled had a similar structure, gene content and organization, even when compared with species from other families. Chloroplast genomes ranged between 160,212 bp in B. crassifolia and 160,329 bp in B. coccolobifolia, both containing 115 genes (four ribosomal RNA genes, 28 tRNA genes and 83 protein-coding genes). We also identified sequences with high divergence that might be informative for phylogenetic inferences in the Malpighiales order, Malpighiaceae family and within the genus Byrsonima. The phylogenetic reconstruction of Malpighiales with these regions highlighted their utility for phylogenetic studies. The comparative analyses among species in Malpighiales provided insights into the chloroplast genome evolution in this order, including the presence/absence of three genes (infA, rpl32 and rps16) and two pseudogenes (ycf1 and rps19).

“…One of the basic questions is how to treat O. rufipogon and O. nivara as separate groups on the basis of variation within and between the populations. Rather than analyzing the sub-populations (already identified at K = 2) separately, manually increasing the K value of the previous analysis was preferred 45 . Interestingly, at K = 3, the O. rufipogon accessions collected mostly from North-western regions of Odisha, formed an independent group and at K = 4, the O. nivara accessions from 24 Parganas and its adjacent districts of West Bengal formed a separate group.…”

Section: Discussionmentioning

confidence: 99%

Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation between O. rufipogon and O. nivara populations

Samal

Roy

Sahoo

et al. 2018

Self Cite

The inter relationships between the two progenitors is interesting as both wild relatives are known to be the great untapped gene reservoirs. The debate continues on granting a separate species status to Oryza nivara. The present study was conducted on populations of Oryza rufipogon and Oryza nivara from Eastern India employing morphological and molecular characteristics. The cluster analysis of the data on morphological traits could clearly classify the two wild forms into two separate discrete groups without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Amplification of hyper variable regions of the genome could reveal 144 alleles suggesting high genetic diversity values (average He = 0.566). Moreover, with 42.37% of uncommon alleles between the two wild relatives, the molecular variance analysis (AMOVA) could detect only 21% of total variation (p < 0.001) among them and rest 59% was within them. The population structure analysis clearly classified these two wild populations into two distinct sub-populations (K = 2) without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Clear differentiation into two distinct groups indicates that O. rufipogon and O. nivara could be treated as two different species.