The complete chloroplast genome of critically endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and phylogenetic analysis

Liu, Yanjiang; Zhu, Xiao Jun; Wu, Mingli; Xue, Xiangxin; Dai, Zhaoxia; Gou, Guangqian

doi:10.1038/s41598-022-13204-2

Cited by 4 publications

(1 citation statement)

References 49 publications

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“…Specifically, whether and how HiFi reads could be used to generate high-quality chloroplast genomes is untested. GetOrganelle is an efficient and accurate toolkit for de novo assembly of organelle genomes ( Freudenthal et al., 2020 ; Jin et al., 2020 ; Odago et al., 2021 ; Ruang-Areerate et al., 2021 ; Singh et al., 2021 ; Drown et al., 2022 ; Liu et al., 2022 ; Zhao et al., 2022 ). It can assemble better plastomes using low coverage WGS data compared with NOVOplasty.…”

Section: Introductionmentioning

confidence: 99%

The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria

Song

Li²,

Liu³

et al. 2023

Front. Plant Sci.

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The genus Fragaria consists of a rich diversity of ploidy levels with diploid (2x), tetraploid (4x), pentaploid (5x), hexaploidy (6x), octoploid (8x) and decaploid (10x) species. Only a few studies have explored the origin of diploid and octoploid strawberry, and little is known about the roles of tetraploidy and hexaploidy during the evolution of octoploid strawberry. The chloroplast genome is usually a stable circular genome and is widely used in investigating the evolution and matrilineal identification. Here, we assembled the chloroplast genomes of F. x ananassa cv. ‘Benihoppe’ (8x) using Illumina and HiFi data seperately. The genome alignment results showed that more InDels were located in the chloroplast genomes based on the PacBio HiFi data than Illumina data. We obtain highly accurate chloroplast genomes assembled through GetOrganelle using Illumina reads. We assembled 200 chloroplast genomes including 198 Fragaria (21 species) and 2 Potentilla samples. Analyses of sequence variation, phylogenetic and PCA analyses showed that Fragaria was divided into five groups. F. iinumae, F. nilgerrensis and all octoploid accessions formed Group A, C and E separately. Species native to western China were clustered into Group B. Group D consisted of F. virdis, F. orientalis, F. moschata, and F. vesca. STRUCTURE and haplotype network confirmed that the diploid F. vesca subsp. bracteata was the last maternal donator of octoploid strawberry. The dN/dS ratio estimated for the protein-coding genes revealed that genes involved in ATP synthase and photosystem function were under positive selection. These findings demonstrate the phylogeny of totally 21 Fragaria species and the origin of octoploid species. F. vesca was the last female donator of octoploid, which confirms the hypothesis that the hexaploid species F. moschata may be an evolutionary intermediate between the diploids and wild octoploid species.

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Section: Introductionmentioning

confidence: 99%

The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria

Song

Li²,

Liu³

et al. 2023

Front. Plant Sci.

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The complete sequence of Lens tomentosus chloroplast genome

Bozkurt,

Kaymaz,

Ateş

et al. 2023

Acta Physiol Plant

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Chloroplast genome skimming of a potential agroforestry species Melia dubia. Cav and its comparative phylogenetic analysis with major Meliaceae members

et al. 2022

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Background: Melia dubia Cav. is a fast-growing plywood species gaining popularity due to high economic returns. This study aimed to assemble and annotate the chloroplast (cp) genome of M.dubia and compare it with previously published cp genomes within the Meliaceae family.Methods and Results: The chloroplast genome was constructed by the de novo and reference-based assembly of paired-end reads generated by long-read sequencing of genomic DNA. The cp genome, sized 171,956 bp, comprised a typical angiosperm quadripartite structure. The large single-copy (LSC) region of 76,055 bp and a small single-copy (SSC) region of 18,693 bp, covers 55% of the genome. The pair of inverted repeats (IRA and IRB) of 38,604 bp each (covering 45% of the genome). We identi ed unique genes (112), including protein-coding genes (79), tRNA (29) and 4 rRNA genes. Phylogenetic analysis using complete cp genomes of 11 species from Meliaceae revealed that M. dubia and M. azedarach hared a sister clade. Comparative analysis using cp genome of M.dubia , M.azedarach and Azadirachta indica revealed a high sequence similarity ( >70%). Five intergenic regions were highly conserved among the three cp genomes. The gene trnG-UCC at LSC region was found to be more divergent in M.dubia and M.azedarach while it shows complete conservation within M.dubia and A.indica.Conclusions: The available levels of taxonomic expertise and clarity in species delineation within the Melia genus is low. The information generated provides scope for identifying new barcodes which increases the discriminatory power of the species within the genus beyond morphological identi cation. Key MessageThis is the rst report on chloroplast genome sequencing and annotation of Melia dubia. There are many confusions related to the taxonomy of the species, especially with M. azedarach, of the same genus. Phylogenetic analysis and comparative cp genomic analysis reveal species-speci c markers that could be used to delineate the species. Analysis of the whole chloroplast genome also provides opportunities for tree improvement, skimming the genetic variability in the natural populations of this species.

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The complete chloroplast genome of critically endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and phylogenetic analysis

Cited by 4 publications

References 49 publications

The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria

The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria

The complete sequence of Lens tomentosus chloroplast genome

Chloroplast genome skimming of a potential agroforestry species Melia dubia. Cav and its comparative phylogenetic analysis with major Meliaceae members

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