Complete chloroplast DNA sequences of Zanduri wheat (Triticum spp.)

Gogniashvili, M.; Naskidashvili, P. P.; Bedoshvili, D.; Kotorashvili, Adam; Kotaria, Nato; Beridze, Tengiz

doi:10.1007/s10722-015-0230-x

Cited by 27 publications

(25 citation statements)

References 18 publications

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“…Triticum lineage, recovery of major subclades in the lineage is congruent with other studies (Petersen et al, 2006;Gornicki et al, 2014;Bernhardt et al, 2017). The Aegilops speltoides + Triticum timopheevii sublineage has been found in other studies (Golovnina et al, 2007;Gornicki et al, 2014;Gogniashvili et al, 2015) plastome (Gornicki et al, 2014) and nuclear (Petersen et al, 2006;Nasernakhaei et al, 2015) trees, but none of those studies sampled the Georgian endemic Triticum macha. Golovnina et al Aegilops clade is congruent with other plastid trees with similar sampling (Petersen et al, 2006; PeerJ reviewing PDF | (2017:08:19682:2:0:NEW 4 Jan 2018)…”

Section: Triticeaesupporting

confidence: 86%

“…Our sampling includes plastomes from additional species of Aegilops and Triticum (Gornicki et al, 2014;Gogniashvili et al, 2015) compared to an earlier study (Saarela et al, 2015 (Petersen et al, 2006). Despite our incomplete genus-level sampling of the Aegilops and…”

Section: Triticeaementioning

confidence: 99%

“…Manuscript to be reviewed Golovnina et al, 2007;Gornicki et al, 2014;Middleton et al, 2014;Gogniashvili et al, 2015).…”

Section: Triticeaementioning

confidence: 99%

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Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"

2018

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The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (180 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including 1) complete plastomes; 2) protein coding regions; 3) noncoding regions; and 4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce false signal. Resolution of

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Section: Triticeaesupporting

confidence: 86%

Section: Triticeaementioning

confidence: 99%

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Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"

2018

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“…Next, we performed BLASTs between trimmed reads and reference sequences ( Artemisia frigida ) to extract cp-like reads [ 55 ]. Finally, the cp-like reads were used for sequence assembly with SOAPdenovo [ 56 ]. Sequence extension was executed using SSPACE [ 57 ], and gaps were filled using GapCloser [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua

et al. 2017

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The complete chloroplast genome of Artemisia annua (Asteraceae), the primary source of artemisinin, was sequenced and analyzed. The A. annua cp genome is 150,995 bp, and harbors a pair of inverted repeat regions (IRa and IRb), of 24,850 bp each that separate large (LSC, 82,988 bp) and small (SSC, 18,267 bp) single-copy regions. Our annotation revealed that the A. annua cp genome contains 113 genes and 18 duplicated genes. The gene order in the SSC region of A. annua is inverted; this fact is consistent with the sequences of chloroplast genomes from three other Artemisia species. Fifteen (15) forward and seventeen (17) inverted repeats were detected in the genome. The existence of rich SSR loci in the genome suggests opportunities for future population genetics work on this anti-malarial medicinal plant. In A. annua cpDNA, the rps19 gene was found in the LSC region rather than the IR region, and the rps19 pseudogene was absent in the IR region. Sequence divergence analysis of five Asteraceae species indicated that the most highly divergent regions were found in the intergenic spacers, and that the differences between A. annua and A. fukudo were very slight. A phylogenetic analysis revealed a sister relationship between A. annua and A. fukudo. This study identified the unique characteristics of the A. annua cp genome. These results offer valuable information for future research on Artemisia species identification and for the selective breeding of A. annua with high pharmaceutical efficacy.

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“…Chloroplast-like reads were predicted from clean-reads by BLAST [32] searches using the sequences of the reference Rosa chinensis. Then, the cp reads was used to assemble sequences by SOAPdenovo-2.04 [33]. Finally, sequences were extended and gaps filled with SSPACE-3.0 and Gap-Closer-1.12 [34,35].…”

Section: Dna Sequencing Assembly and Validation Of The Cp Genomementioning

confidence: 99%

The chloroplasts genomic analyses of Rosa laevigata, R. rugosa and R. canina

et al. 2020

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Background: Many species of the genus Rosa have been used as ornamental plants and traditional medicines. However, industrial development of roses is hampered due to highly divergent characteristics. Methods: We analyzed the chloroplast (cp) genomes of Rosa laevigata, R. rugosa and R. canina, including the repeat sequences, inverted-repeat (IR) contractions and expansions, and mutation sites. Results: The size of the cp genome of R. laevigata, R. rugosa and R. canina was between 156 333 bp and 156 533 bp, and contained 113 genes (30 tRNA genes, 4 rRNA genes and 79 protein-coding genes). The regions with a higher degree of variation were screened out (trnH-GUU, trnS-GCU , trnG-GCC , psbA-trnH, trnC-GCA,petN, trnT-GGU , psbD, petA, psbJ, ndhF, rpl32,psaC and ndhE). Such higher-resolution loci lay the foundation of barcode-based identification of cp genomes in Rosa genus. A phylogenetic tree of the genus Rosa was reconstructed using the full sequences of the cp genome. These results were largely in accordance with the current taxonomic status of Rosa. Conclusions: Our data: (i) reveal that cp genomes can be used for the identification and classification of Rosa species; (ii) can aid studies on molecular identification, genetic transformation, expression of secondary metabolic pathways and resistant proteins; (iii) can lay a theoretical foundation for the discovery of disease-resistance genes and cultivation of Rosa species.

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Complete chloroplast DNA sequences of Zanduri wheat (Triticum spp.)

Cited by 27 publications

References 18 publications

Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"

Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua

The chloroplasts genomic analyses of Rosa laevigata, R. rugosa and R. canina

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