The complete chloroplast genome of the green algae Hariotina reticulata (Scenedesmaceae, Sphaeropleales, Chlorophyta)

Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata

BACKGROUND

The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additionally, there are currently no reports on the chloroplast genome of Crucigenia.

RESULTS

In this study, we utilize molecular phylogenetics and comparative genomics to show that C. quadrata belongs to Chlorophyceae rather than Trebouxiophyceae. The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. Our study presents the first complete chloroplast genome of C. quadrata, which is 197,184 bp in length and has a GC content of 31%. It has a typical quadripartite structure, and the chloroplast genome codons exhibit usage bias. Nucleotide diversity analysis highlights six genes (ccsA, psbF, chlN, cemA, rps3, rps18) as hotspots for genetic variation. Coding gene sequence divergence analyses indicate that four genes (cemA, clpP, psaA, rps3) are subject to positive selection.

CONCLUSIONS

The determination of the phylogenetic status and the comparative chloroplast genomic analyses of C. quadrata will not only be useful in enhancing our understanding of the intricacy of Crucigenia taxonomy but also provide the important basis for studying the evolution of the incertae sedis taxa within Trebouxiophyceae.

Characterization of the mitochondrial genome of Chlorolobion braunii ITBB-AG6, an azolla-associated green alga isolated from sanitary sewage

Sphaeropleales have the characteristics of rapid growth, high oil content, and efficient removal rates of nitrogen and phosphorus in sewage waters, and is potentially valuable in biodiesel production and environmental remediation. In this study, we isolated a strain of Sphaeropleales, Chlorolobion braunii strain ITBB-AG6 from an azolla community in a sewage pond. Its mitochondrial genome contains 110,124 bp and harbors at least 40 genes, including 15 protein-coding genes, 20 tRNA genes, and three rRNA genes. The protein-coding genes include two for ATP synthases, seven for NAD(P)H-quinone oxidoreductases (nad), three for cytochrome c oxidase subunits (coxs), and one for cytochrome b (cob). Transfer RNA genes for 18 amino acids were identified, in which the tRNA genes for leucine and serine are doubled, but the tRNA genes for threonine and valine are not annotated. Phylogenetic analysis using the mitochondrial genomes of seven families of Sphaeropleales indicated that ITBB-AG6 is closely related to Monoraphidium neglectum, and falls in the family Selenastraceae with 100% bootstrap support. Two species in the family Neochloridaceae are separated by a species in Hydrodictyaceae, indicating a polyphyletic nature. These findings revealed the complicated phylogenetic relationships of the Sphaeropleales and the necessity of genome sequences in the taxonomy of microalgae.

The Draft Genome of Hariotina reticulata (Sphaeropleales, Chlorophyta) Provides Insight into the Evolution of Scenedesmaceae

Hariotina reticulata P. A. Dangeard 1889 (Sphaeropleales, Chlorophyta) is a common member of the summer phytoplankton of meso- to highly eutrophic water bodies with a worldwide distribution. Here, we report the draft whole-genome shotgun sequencing of H. reticulata strain SAG 8.81. The final assembly comprises 107,596,510bp with over 15,219 scaffolds (>100bp). This whole-genome project is publicly available in the CNSA (https://db.cngb.org/cnsa/) of CNGBdb under the accession number CNP0000705.

The Putative Smallest Introns in the Arabidopsis Genome

Most eukaryotic genes contain introns, which are noncoding sequences that are removed during premRNA processing. Introns are usually preserved across evolutionary time. However, the sizes of introns vary greatly. In Arabidopsis, some introns are longer than 10 kilo base pairs (bp) and others are predicted to be shorter than 10 bp. To identify the shortest intron in the genome, we analyzed the predicted introns in annotated version 10 of the Arabidopsis thaliana genome and found 103 predicted introns that are 30 bp or shorter, which make up only 0.08% of all introns in the genome. However, our own bioinformatics and experimental analyses found no evidence for the existence of these predicted introns. The predicted introns of 30–39 bp, 40–49 bp, and 50–59 bp in length are also rare and constitute only 0.07%, 0.2%, and 0.28% of all introns in the genome, respectively. An analysis of 30 predicted introns 31–59 bp long verified two in this range, both of which were 59 bp long. Thus, this study suggests that there is a limit to how small introns in A. thaliana can be, which is useful for the understanding of the evolution and processing of small introns in plants in general.

The internal transcribed spacer 2 of Jenufa (Chlorophyta, Chlorophyceae) is extraordinarily long: A hypothesis

Aided by a host of bioinformatics tools, primary and secondary structural analyses of the internal transcribed spacer 2 (ITS2) from the eukaryotic ribosomal RNA repeat have a long and enviable record of service to diversity studies of fungi, plants and protists. Automation of annotation, secondary structure estimation and sequence alignment have become routine for the vast majority of ITS2 sequences. Challenges to the bioinformatics pipeline for ITS2 analysis generally arise in cases where the sequence length lies well outside the norm. These sequences generally defy protocols for annotation and secondary structure prediction. The long ITS2 sequences (ca. 600 nucleotides) from the green alga, Jenufa, offered an opportunity to explore this problem. Custom BLAST parameters revealed the presence of 4-helix structures (200-250 nucleotides) embedded in the 5' portion of several long ITS2 sequences of Jenufa. Of special note is the ITS2 sequence of J. lobulosa where a 4-helix structure was obtained for both the embedded ITS2 and for the complete sequence. Phylogenetic analysis of these typically-sized sequences resolved Golenkinia longispicula as the sister to Jenufa. Our observations indicate that other long ITS2 sequences should be examined for evidence of expansion or duplication. In addition, if the embedded ITS2 sequences are functional, then ribogenesis is almost certainly more diverse than is already apparent from studies of humans and yeast.