Plastid Genes That Were Lost along the Road to Parasitism

Lockhart, Jennifer A

doi:10.1105/tpc.113.251011

Cited by 2 publications

(3 citation statements)

References 3 publications

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“…This indicated that the chloroplasts maintained relatively low rate of sequence divergence to preserve its primary function. Other parasitic plants that have lost the photosynthetic capability have shown to have lost the functional photosynthetic genes [ 77 , 78 ]. However, it is incorrect to assume that any genes with high level of sequence divergence will soon lose its function, turning into pseudogenes.…”

Section: Resultsmentioning

confidence: 99%

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

Redwan

Saidin²,

Subbiah

2015

BMC Plant Biol

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BackgroundPineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the most important species in the Bromeliaceae family and is largely traded for fresh fruit consumption. Here, we report the complete chloroplast sequence of the MD-2 pineapple that was sequenced using the PacBio sequencing technology.ResultsIn this study, the high error rate of PacBio long sequence reads of A. comosus’s total genomic DNA were improved by leveraging on the high accuracy but short Illumina reads for error-correction via the latest error correction module from Novocraft. Error corrected long PacBio reads were assembled by using a single tool to produce a contig representing the pineapple chloroplast genome. The genome of 159,636 bp in length is featured with the conserved quadripartite structure of chloroplast containing a large single copy region (LSC) with a size of 87,482 bp, a small single copy region (SSC) with a size of 18,622 bp and two inverted repeat regions (IRA and IRB) each with the size of 26,766 bp. Overall, the genome contained 117 unique coding regions and 30 were repeated in the IR region with its genes contents, structure and arrangement similar to its sister taxon, Typha latifolia. A total of 35 repeats structure were detected in both the coding and non-coding regions with a majority being tandem repeats. In addition, 205 SSRs were detected in the genome with six protein-coding genes contained more than two SSRs. Comparative chloroplast genomes from the subclass Commelinidae revealed a conservative protein coding gene albeit located in a highly divergence region. Analysis of selection pressure on protein-coding genes using Ka/Ks ratio showed significant positive selection exerted on the rps7 gene of the pineapple chloroplast with P less than 0.05. Phylogenetic analysis confirmed the recent taxonomical relation among the member of commelinids which support the monophyly relationship between Arecales and Dasypogonaceae and between Zingiberales to the Poales, which includes the A. comosus.ConclusionsThe complete sequence of the chloroplast of pineapple provides insights to the divergence of genic chloroplast sequences from the members of the subclass Commelinidae. The complete pineapple chloroplast will serve as a reference for in-depth taxonomical studies in the Bromeliaceae family when more species under the family are sequenced in the future. The genetic sequence information will also make feasible other molecular applications of the pineapple chloroplast for plant genetic improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0587-1) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

Redwan

Saidin²,

Subbiah

2015

BMC Plant Biol

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“…Diversity 2018, 10, x FOR PEER REVIEW 6 of 18 apparently do not differ substantially, and previous studies showed that gene loss in plastids is associated with an increase in parasitism [31,32]. …”

Section: Figure 1 Blast Ring Image Generator Output Image Of the Chlmentioning

confidence: 86%

“…The mosses share practically the same lack of gene among their representatives; only T. pellucida shows a lack of rps10 and ORF187 in the mtDNA. Seed plants usually have gene contents that apparently do not differ substantially, and previous studies showed that gene loss in plastids is associated with an increase in parasitism [31,32].…”

Section: Figure 1 Blast Ring Image Generator Output Image Of the Chlmentioning

confidence: 99%

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

et al. 2018

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Abstract:In this study, the organelle genomes of Polytrichum juniperinum Hedw. and Polytrichum strictum Menzies ex Brid. (Polytrichaceae, Bryophyta) from Antarctica were sequenced and compared with the plastomes of the model moss species Physcomitrella patens Brid. The sizes of the cpDNA in P. juniperinum and P. strictum were estimated to be 55,168 and 20,183 bp, respectively; the sizes of the mtDNA were 88,021 and 58,896 bp, respectively. The genomes are very similar to each other, with the possible loss of petN in the cpDNA, which also showed some gene inversions when compared with the cpDNAs of P. patens Brid. In the mtDNA, it is possible that rps10 was lost. In contrast, Antarctic Polytrichaceae species have nad7 and orf187, without the occurrence of rearrangement events. Phylogenomic analyses of the plastid and mitochondria revealed that the majority-rule tree suggests some differences in the plastids ancestry, however, P. juniperinum and P. strictum were grouped in the same clade in chloroplast, but in mitochondria P. strictum was grouped with Atrichum angustatum (Brid.) Bruch & Schimp. This study helped us understand the evolution of plastomes and chondriosomes in the family Polytrichaceae, and suggest a hybridization event with relation to the mitochondrial data.

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Plastid Genes That Were Lost along the Road to Parasitism

Cited by 2 publications

References 3 publications

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

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