Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes

Gao, Lei; Yi, Xuan; Yang, Yongxia; Su, Yingjuan; Wang, Ting

doi:10.1186/1471-2148-9-130

Cited by 141 publications

(151 citation statements)

References 43 publications

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“…Most of the codons prefer A or T at the third position. The analysis of the composition for the codons showed that A+T content at the third position was 72.6%, similar to what was reported for Alophila (8) and Panax schinseng Nees (1).…”

Section: Gene Content and Codon Usagesupporting

confidence: 63%

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Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

Talat¹,

Wang²

2015

Iran J Biotech

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Section: Gene Content and Codon Usagesupporting

confidence: 63%

“…Therefore and In addition to phylogenetic analysis based on plastidic genomes, it is imperative to understand the chloroplast genome in order to logically design our next generation transplastomics. Accordingly, chloroplast genomes of many species have been sequenced (7)(8)(9)(10)(11)(12)(13)(14).…”

mentioning

confidence: 99%

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

Talat¹,

Wang²

2015

Iran J Biotech

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“…Overall, 44.05, 2.06, and 6.73% of the genome sequence encode proteins, tRNAs, and rRNAs, respectively, whereas the remaining 47.15% of the genome is non-coding and filled with introns and intergenic spacers. Similar to other cp genomes Gao et al, 2009;Yang et al, 2010), the Z. latifolia cp genome is AT-rich (61.02%), and the values vary slightly among defined non-coding, protein-coding, tRNA, and rRNA sequences, with A+T contents of 64.35, 60.52, 47.21, and 45.03%, respectively. The four rRNA genes are all positioned in the IRs.…”

Section: Resultsmentioning

confidence: 89%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

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Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and non-coding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.

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“…Importantly, it has been suggested that other chloroplast introns are targeted by MatK as well: firstly, several chloroplast genomes of parasitic plants and ferns have lost trnK, but have retained a free-standing matK reading frame, suggesting additional tasks for MatK, presumably in splicing other introns (4,5,(11)(12)(13); and secondly, loss of chloroplast translation leads to loss of splicing for some, but not all chloroplast introns, suggesting that a chloroplast reading frame is required for splicing these multiple introns (7,15,16). As there are no other candidates for RNA processing factors in the well-described and small chloroplast genome, it was suggested that matK is responsible for splicing these introns.…”

mentioning

confidence: 99%

An organellar maturase associates with multiple group II introns

Zoschke

Nakamura

Liere

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

157

207

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Bacterial group II introns encode maturase proteins required for splicing. In organelles of photosynthetic land plants, most of the group II introns have lost the reading frames for maturases. Here, we show that the plastidial maturase MatK not only interacts with its encoding intron within trnK-UUU, but also with six additional group II introns, all belonging to intron subclass IIA. Mapping analyses of RNA binding sites revealed MatK to recognize multiple regions within the trnK intron. Organellar group II introns are considered to be the ancestors of nuclear spliceosomal introns. That MatK associates with multiple intron ligands makes it an attractive model for an early trans-acting nuclear splicing activity.roup II introns are highly structured ribozymes, found in bacteria and organellar genomes of plants, fungi, protists, and some animals. They catalyze their own excision from precursor RNAs (1). In addition, bacterial group II introns are mobile genetic elements. These features, as well as structural similarities with nuclear introns, have led to the proposition that ancestors of modern group II introns have crossed kingdoms from prokaryotes to eukaryotes via eubacterial endosymbionts, and eventually evolved into nuclear introns (2). Whereas nuclear introns are removed by a large ribonucleoprotein complex called the spliceosome, each bacterial intron encodes a distinct maturase protein facilitating its splicing. The evolutionary transition from the highly specific, maturase-driven splicing toward the complex transacting spliceosomal machinery is unclear. Without any "living fossils" with a protospliceosome, a key question is how the emerging intron diversification was accompanied by a splicing machinery with the ability to act on multiple targets. At least initially, the already existing splicing factors encoded by the invading group II introns, i.e., modified maturases, may have fulfilled this task.In present day organelles, maturase genes can be found in fungal and plant mitochondria as well as in plant chloroplasts. Although mitochondria are not directly amenable to transgenic studies, there are a number of plant species, foremost tobacco, for which directed mutagenesis of chloroplast genomes is possible (3). All land plant chloroplasts with the exception of some parasitic species in the genus Cuscuta (4, 5) contain a single maturase gene called matK in the intron of the lysine tRNA-K (UUU) gene. matK is expressed at least in green tissue (6-8). Sequence and structural homologies are found to the RNA binding motif (domain X) and the reverse transcriptase domain typically found in bacterial maturases (9, 10). Both domains are involved in splicing. By contrast, domains required for the mobility of group II introns are missing in MatK.The function of matK in chloroplasts is so far unknown, but its position inside the trnK gene suggests a role for splicing the trnK precursor. Importantly, it has been suggested that other chloroplast introns are targeted by MatK as well: firstly, several chloroplast genomes o...

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Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes

Cited by 141 publications

References 43 publications

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

An organellar maturase associates with multiple group II introns

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