Limits...
The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin.

Leliaert F, Lopez-Bautista JM - BMC Genomics (2015)

Bottom Line: The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region.Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA. frederik.leliaert@ugent.be.

ABSTRACT

Background: Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified).

Results: Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.

Conclusions: The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae.

No MeSH data available.


Related in: MedlinePlus

Gene map of the chloroplast genome ofBryopsis plumosa. The 106,859 bp genome contains 115 unique genes, including three ribosomal RNA genes, 26 transfer RNA genes, and 86 protein coding genes. Genes shown on the outside of the circle are transcribed counterclockwise. Annotated genes are colored according to the functional categories shown in the legend bottom left. The red arcs indicate gene regions of putative bacterial origin.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4487195&req=5

Fig2: Gene map of the chloroplast genome ofBryopsis plumosa. The 106,859 bp genome contains 115 unique genes, including three ribosomal RNA genes, 26 transfer RNA genes, and 86 protein coding genes. Genes shown on the outside of the circle are transcribed counterclockwise. Annotated genes are colored according to the functional categories shown in the legend bottom left. The red arcs indicate gene regions of putative bacterial origin.

Mentions: The circular cpDNAs of B. plumosa (Figure 2) and T. expeditiones (Figure 3) consist of 106,859 bp and 105,200 bp, respectively. This is smaller than most published cpDNAs of free-living species of core Chlorophyta, but similar to those found in Pedinomonas minor (98 kb), Marvania geminata (108 kb), Pseudochloris wilhelmii (110 kb), and Planctonema lauterbornii (114 kb) [9,19,22]. Most prasinophytes have even smaller cpDNAs, ranging between 64-86 kb, with the exception of Nephroselmis, which has larger chloroplast genomes (125 and 201 kb) [3]. Unexpectedly, the cpDNA of B. plumosa is much smaller than the 153,429 bp cpDNA of B. hypnoides. This size difference is mainly a result of large intergenic spacers (up to 20,875 bp in length), totaling 59,842 bp or 38.9% of the cpDNA in B. hypnoides (Additional file 2). Intergenic spacers in B. plumosa and T. expeditiones account for only 20.3% and 16.3% of the total cpDNA. Nevertheless, some long intergenic spacer regions are present in both genomes. In B. plumosa, the largest intergenic spacer was 3,307 bp long. This region contains a few ORFs (>300 bp), none of which showed significant homology to known proteins (blastp E-values > 0.1). In T. expeditiones, a large spacer region (6,583 bp) contains ten ORFs (>300 bp), none with significant homology to known proteins (blastp E-values > 1). GC content of the two genomes falls within the limits of other ulvophycean and green algal cpDNAs (Table 1) [1,2].Figure 2


The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin.

Leliaert F, Lopez-Bautista JM - BMC Genomics (2015)

Gene map of the chloroplast genome ofBryopsis plumosa. The 106,859 bp genome contains 115 unique genes, including three ribosomal RNA genes, 26 transfer RNA genes, and 86 protein coding genes. Genes shown on the outside of the circle are transcribed counterclockwise. Annotated genes are colored according to the functional categories shown in the legend bottom left. The red arcs indicate gene regions of putative bacterial origin.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4487195&req=5

Fig2: Gene map of the chloroplast genome ofBryopsis plumosa. The 106,859 bp genome contains 115 unique genes, including three ribosomal RNA genes, 26 transfer RNA genes, and 86 protein coding genes. Genes shown on the outside of the circle are transcribed counterclockwise. Annotated genes are colored according to the functional categories shown in the legend bottom left. The red arcs indicate gene regions of putative bacterial origin.
Mentions: The circular cpDNAs of B. plumosa (Figure 2) and T. expeditiones (Figure 3) consist of 106,859 bp and 105,200 bp, respectively. This is smaller than most published cpDNAs of free-living species of core Chlorophyta, but similar to those found in Pedinomonas minor (98 kb), Marvania geminata (108 kb), Pseudochloris wilhelmii (110 kb), and Planctonema lauterbornii (114 kb) [9,19,22]. Most prasinophytes have even smaller cpDNAs, ranging between 64-86 kb, with the exception of Nephroselmis, which has larger chloroplast genomes (125 and 201 kb) [3]. Unexpectedly, the cpDNA of B. plumosa is much smaller than the 153,429 bp cpDNA of B. hypnoides. This size difference is mainly a result of large intergenic spacers (up to 20,875 bp in length), totaling 59,842 bp or 38.9% of the cpDNA in B. hypnoides (Additional file 2). Intergenic spacers in B. plumosa and T. expeditiones account for only 20.3% and 16.3% of the total cpDNA. Nevertheless, some long intergenic spacer regions are present in both genomes. In B. plumosa, the largest intergenic spacer was 3,307 bp long. This region contains a few ORFs (>300 bp), none of which showed significant homology to known proteins (blastp E-values > 0.1). In T. expeditiones, a large spacer region (6,583 bp) contains ten ORFs (>300 bp), none with significant homology to known proteins (blastp E-values > 1). GC content of the two genomes falls within the limits of other ulvophycean and green algal cpDNAs (Table 1) [1,2].Figure 2

Bottom Line: The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region.Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA. frederik.leliaert@ugent.be.

ABSTRACT

Background: Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified).

Results: Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.

Conclusions: The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae.

No MeSH data available.


Related in: MedlinePlus