The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes
Abstract
:1. Introduction
2. Results and Discussion
2.1. U. compressa Genome Assembly, Annotation of Protein-Coding Genes and Comparison with Other Green Algae Genomes
2.2. Classification of Protein-Coding Genes in U. compressa Genome
2.3. U. compressa Encodes Antioxidant Enzymes, Enzymes for ASC and GSH Synthesis, and Metallothioneins
2.4. U. compressa Encodes Signal Transduction Protein Kinases
2.5. Ethylene- and ABA-Responsive Regulatory Transcription Factors and Other Plant-like Transcription Factors
2.6. U. compressa Encodes Enzymes for ACC and ABA-Aldehyde Synthesis but Lacks Enzymes Involved in Ethylene and ABA Synthesis
2.7. U. compressa Genome Encodes Proteins Involved in Cell Cycle Regulation
2.8. U. compressa Genome Encodes Enzymes and Transporters for Cell Wall Synthesis, and Animal Extracellular Matrix Proteins
2.9. U. compressa Genome Encodes Channels for Extracellular Calcium Entry and Intracellular Calcium Release
3. Materials and Methods
3.1. DNA Purification and Sequencing
3.2. Cleaning of the Reads
3.3. Assembly of the Genome and Annotation of Genes
3.4. Functional Classification of Genes
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
ABA | abscisic acid |
ACC | 1-aminocyclopropane carboxylic acid |
AP | ascorbate peroxidase |
AOC | allene oxide cyclase |
AOS | allene oxide synthase |
ASC | ascorbate |
CAT | catalase |
CaMK | calcium/calmodulin-dependent protein kinase |
CBLPK | calcineurin b-like protein kinase |
CDK | cyclin-dependent protein kinase |
CDPK | calcium-dependent protein kinase |
CS | cellulose synthase |
ECM | extracellular matrix |
GCS | glutamyl-cysteinyl synthase |
GluR | glutamate receptor |
GS | glutathione synthase |
GSH | glutathione |
GR | glutathione reductase |
ICS | isochorismate synthase |
L-GLDH | L-gulonolactone dehydrogenase |
L-GDH | L-galactose dehydrogenase |
LOX | lipoxygenase |
MAPK | mitogen-activated protein kinase |
MT | metallothionein |
PAL | phenylalanine ammonia lyase |
PCs | phytochelatins |
PKA | cAMP-dependent protein kinase |
PKG | cGMP-dependent protein kinase |
PRX | peroxiredoxin |
SAM | S-adenosyl methionine |
TRP | transient receptor potential channel |
TRR | NADPH-dependent thioredoxin reductase |
TRX | thioredoxin |
VDCC | voltage-dependent calcium channels |
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Genome | U. compressa | U. mutabilis |
---|---|---|
Genome size | 80.8 Mb | 98.5 Mb |
Number of scaffolds | 2601 | 318 |
Scaffolds N50 | 0.46 Mb | 0.6 Mb |
Scaffolds L50 | 48 | 46 |
Percentage of GC content | 57.3% | 57.2% |
Number of protein coding genes | 19,207 | 12,924 |
Gene density | 238 genes/Mb | 131 genes/Mb |
Average intron per gene | 3.6 | nd |
Average exon length | 322 bp | nd |
Average intron length | 479 bp | nd |
Number of exons in CDS | 88,404 | nd |
Number of introns in CDS | 69,134 | nd |
Percentage of core genes | 80% | 92% |
Repetitive elements (RE) | 18.9% | 35% |
LINE | 1.77% | 15.1% |
LTR | 1.52% | 9.4% |
DNA elements | 0.61% | |
Unknown RE | 15.04% | 10.5% |
Number of rRNAs | 18 | nd |
Number of tRNAs | 109 | nd |
Number of snoRNAs | 27 | nd |
Number of snRNAs | 11 | nd |
Number of primary miRNAs | 87 | nd |
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Osorio, H.; Tapia-Reyes, P.; Espinoza, D.; Laporte, D.; González, A.; Castro-Nallar, E.; Moenne, A. The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes. Int. J. Mol. Sci. 2022, 23, 7279. https://doi.org/10.3390/ijms23137279
Osorio H, Tapia-Reyes P, Espinoza D, Laporte D, González A, Castro-Nallar E, Moenne A. The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes. International Journal of Molecular Sciences. 2022; 23(13):7279. https://doi.org/10.3390/ijms23137279
Chicago/Turabian StyleOsorio, Héctor, Patricio Tapia-Reyes, Daniela Espinoza, Daniel Laporte, Alberto González, Eduardo Castro-Nallar, and Alejandra Moenne. 2022. "The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes" International Journal of Molecular Sciences 23, no. 13: 7279. https://doi.org/10.3390/ijms23137279