Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales)

Kuo, Li‐Yaung; Tang, Te‐Yen; Li, Fay‐Wei; Su, Hong‐Ji; Chiou, Wen‐Liang; Huang, Yao‐Moan; Wang, Chun‐Neng

doi:10.3389/fpls.2018.00486

Cited by 29 publications

(22 citation statements)

References 51 publications

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“…The chloroplast genome contains two large 6–76 Kb inverted repeats (IRs) that are divided into a large single copy (LSC) and small single copy region (SSC) [24–26]. The chloroplast genome is non-recombinant and inherited uniparentally through maternal inheritance [27, 28]. Therefore, the chloroplast genome is an excellent tool for genomic and evolutionary studies.…”

Section: Introductionmentioning

confidence: 99%

Genomic and evolutionary aspects of chloroplast tRNA in monocot plants

et al. 2019

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BackgroundChloroplasts are one of the most indispensable organelles that make life forms on the earth possible by their capacity to photosynthesize. These organelles possess a circular genome with a number of coding genes responsible for self-regulation. tRNAs are an important evolutionary-conserved gene family that are responsible for protein translation. However, within the chloroplast genome, tRNA machinery are poorly understood.ResultsIn the present study, the chloroplast genome of six monocot plants, Oryza nivara (NC_005973), Oryza sativa (NC_001320), Sachharum officinarum (NC_006084), Sorghum bicolor (NC_008602), Triticum aestivum (NC_002762), and Zea mays (NC_001666) were downloaded and analyzed to identify tRNA sequences. Further analysis of the tRNA sequences in the chloroplast genomes of the monocot plants resulted in the identification of several novel features. The length of tRNAs in the chloroplast genome of the monocot plants ranged from 59 to 155 nucleotides. Pair-wise sequence alignment revealed the presence of a conserved A-C-x-U-A-x-U-A-x-U-x5-U-A-A nucleotide consensus sequence. In addition, the tRNAs in chloroplast genomes of the monocot plants also contain 21–28 anti-codons against 61 sense codons in the genome. They also contain a group I intron and a C-A-U anti-codon for tRNAIle, which is a common anti-codon of tRNAMet. Evolutionary analysis indicates that tRNAs in the chloroplast genome have evolved from multiple common ancestors, and tRNAMet appears to be the ancestral tRNA that underwent duplication and diversification to give rise to other tRNAs.ConclusionThe results obtained from the study of chloroplast tRNA will greatly help to increase our understanding of tRNA biology at a new level. Functional studies of the reported novel aspects of the chloroplast tRNA of the monocot plants will greatly help to decipher their roles in diverse cellular processes.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1625-6) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genomic and evolutionary aspects of chloroplast tRNA in monocot plants

et al. 2019

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“…sp1, whereas C. angustifolium is a sexual diploid (2n = 72) with oblong spores [67]. The chloroplast is generally maternally inherited in ferns [68][69][70]. Therefore, it is likely that each of these taxa is a hybrid between the species with which they share rbcL as the mother and another unknown species as the father.…”

Section: Plos Onementioning

confidence: 99%

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

2020

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Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.

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“…Compared with the nuclear genome, the cp genome is more conserved in terms of gene structure and composition, which is advantageous for the study of taxa at higher taxonomic levels [1,2]. Moreover, the cp genome does not recombine and is uniparentally inherited [3,4], which can elucidate the history and evolution of plant populations [5]. Complete cp genome sequences were first reported for tobacco [6] and liverwort [7] in 1986.…”

Section: Introductionmentioning

confidence: 99%

Complete chloroplast genomes of wild and cultivated Cryptomeria japonica var. sinensis

Yan

Wang

et al. 2021

Biotechnology & Biotechnological Equipment

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The tree Cryptomeria japonica var. sinensis is native to China and is an important forest species widely used for wood production. Here, we sequenced the complete chloroplast (cp) genomes of six wild and six cultivated accessions of this tree. The 12 cp genomes ranged from 131,379 to 131,528 bp. The GC content was 35.4%, similar to other gymnosperm species. The cp genomes lacked typical inverted repeat (IR) regions and encoded 118 genes. Most genes appeared in one copy and 17 genes contained introns. Two multi-copy genes (trnM-CAU × 3, trnQ-UUG × 2) were identified. And 59-61 simple sequence repeats (SSRs) were identified in the whole cp genomes, and most SSR loci consisted of A or T bases. Phylogenetic analysis indicated that wild and cultivated accessions were not clearly differentiated. Our results will provide useful information for the conservation and utilization of this variety.

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Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales)

Cited by 29 publications

References 51 publications

Genomic and evolutionary aspects of chloroplast tRNA in monocot plants

Genomic and evolutionary aspects of chloroplast tRNA in monocot plants

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

Complete chloroplast genomes of wild and cultivated Cryptomeria japonica var. sinensis

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