Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus
Koki NishitsujiAsuka ArimotoYoshitaka YonashiroKanako HisataManabu FujieMayumi KawamitsuEiichi ShoguchiNoriyuki Satoh
11
Citation
49
Reference
10
Related Paper
Citation Trend
Abstract:
Abstract Background The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is one of the most important edible seaweeds, and it is cultivated for market primarily in Okinawa, Japan. Four strains, denominated S, K, O, and C, with distinctively different morphologies, have been cultivated commercially since the early 2000s. We previously reported a draft genome of the S-strain. To facilitate studies of seaweed biology for future aquaculture, we here decoded and analyzed genomes of the other three strains (K, O, and C). Results Here we improved the genome of the S-strain (ver. 2, 130 Mbp, 12,999 genes), and decoded the K-strain (135 Mbp, 12,511 genes), the O-strain (140 Mbp, 12,548 genes), and the C-strain (143 Mbp, 12,182 genes). Molecular phylogenies, using mitochondrial and nuclear genes, showed that the S-strain diverged first, followed by the K-strain, and most recently the C- and O-strains. Comparisons of genome architecture among the four strains document the frequent occurrence of inversions. In addition to gene acquisitions and losses, the S-, K-, O-, and C-strains possess 457, 344, 367, and 262 gene families unique to each strain, respectively. Comprehensive Blast searches showed that most genes have no sequence similarity to any entries in the non-redundant protein sequence database, although GO annotation suggested that they likely function in relation to molecular and biological processes and cellular components. Conclusions Our study compares the genomes of four strains of C. okamuranus and examines their phylogenetic relationships. Due to global environmental changes, including temperature increases, acidification, and pollution, brown algal aquaculture is facing critical challenges. Genomic and phylogenetic information reported by the present research provides useful tools for isolation of novel strains.Keywords:
Strain (injury)
Comparative Genomics
Gene Annotation
Nuclear gene
A significant challenge in bacterial genomics is to catalogue genes acquired through the evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and sequence composition-based methods have often been invoked to quantify horizontally acquired genes in bacterial genomes. Comparative genomics methods rely on completely sequenced genomes and therefore the confidence in their predictions increases as the databases become more enriched in completely sequenced genomes. Recent developments including in microbial genome sequencing call for reassessment of alien genes based on information-rich resources currently available. We revisited the comparative genomics approach and developed a new algorithm for alien gene detection. Our algorithm compared favourably with the existing comparative genomics-based methods and is capable of detecting both recent and ancient transfers. It can be used as a standalone tool or in concert with other complementary algorithms for comprehensively cataloguing alien genes in bacterial genomes.
Comparative Genomics
Horizontal Gene Transfer
Bacterial genome size
Functional Genomics
Cite
Citations (9)
Comparative Genomics
Synteny
Functional Genomics
Identification
Cite
Citations (22)
As a type of ancient eukaryote,Giardia lamblia has played a very important role in the process of biological evolution.Comparative genomics can reveal the evolutionary relationships of G.lambliaat the genetic level and further clarify the role of G.lambliain the process of biological evolution.This review describes the main research techniques used in comparative genomics and it describes the use of comparative genomics to study the biological evolution of G.lamblia.This review also discusses the prospects for using comparative genomics to study G.lamblia.
Comparative Genomics
Giardia lamblia
Eukaryote
Convergent evolution
Cite
Citations (0)
Abstract Comparative genomics involves the comparison of features of completely sequenced (or nearly so) genomes. Comparative sequence analyses facilitate both the functional annotation of genomes and whole‐genome approaches to evolutionary issues. We present a review of the field of comparative genomics and point out how the comparative approach can be used to help better understand the human genome sequence.
Comparative Genomics
Sequence (biology)
Personal genomics
Functional Genomics
Cite
Citations (0)
Comparative genomics is a science in its infancy. It has been driven by a huge increase in freely available genome-sequence data, and the development of computer techniques to allow whole-genome sequence analyses. Other approaches, which use hybridization as a method for comparing the gene content of related organisms, are rising alongside these more bioinformatic methods. All these approaches have been pioneered using bacterial genomes because of their simplicity and the large number of complete genome sequences available. The aim of bacterial comparative genomics is to determine what genotypic differences are important for the expression of particular traits (e.g., antibiotic resistance, virulence, or host preference). The benefits of such studies will be a deeper understanding of these phenomena; the possibility of exposing novel drug targets, including those for antivirulence drugs; and the development of molecular techniques that reveal patients who are infected with virulent organisms so that health care resources can be allocated appropriately. With more and more genome sequences becoming available, the rise of comparative genomics continues apace.
Comparative Genomics
Functional Genomics
Cite
Citations (3)
Comparative Genomics
Gene Annotation
Structural genomics
Functional Genomics
Computational genomics
Genome Biology
Genomic information
Gene prediction
Cite
Citations (25)
Placing genomes into an evolutionary framework has proved to be usefol for deciphering the genome sequences of organisms.Comparative genomies,as a routine toolkit.has substantially incteased the understanding of the processes by which bacterial genomes evolve and led to a re-evaluation of the history of life.In this review,we present some of the most important recent advances and promising leads in the field of bacterial evolutionary genomics.
Key words:
Comparative genomics; HGT; Phylogeny
Comparative Genomics
Bacterial genome size
Cite
Citations (0)
Wheat is the heterogenous polyploid plant with large chromosomes and high level of repetitive sequences. These characters have limited the progress of wheat genomics studies. Comparative genomics provided a platform for study of wheat genomics by using model plants Functional genomics focused on the expressed portion of the wheat genome. Its aim was determining the expression and function of genes. This paper reviews the application of comparative genomics in wheat genomic studies and the contents and methods of functional genomics of wheat.
Functional Genomics
Comparative Genomics
Polyploid
Structural genomics
Genome Biology
Cite
Citations (12)
Synteny
Comparative Genomics
Functional Genomics
Cite
Citations (1)
Comparative genomics is one of the important research fields in genomics. By comparative genomic studies it was possible to establish a giant genetic system beyond one species which might be significant to tree. Comparative genomics in Salicaceae, Pinaceae, Rosaceae, Fagaceae and Hamamelidaceae had shown that the organization of genomes remained highly conserved over long evolutionary periods and extensive synteny or collinarity or microcollinarity existed in tree genomes. A total of 13,019 pairs of orthologs were identified between genes in Populus and Arabidopsis using the best bidirectional Basic Local Alignment Search Tool (BLAST) hits, with an average mutual coverage of these alignments equal to 93%; 11,654 pairs of orthologs had greater than 90% alignment of gene lengths. The progress of comparative genomics in tree species was reviewed and the prospect of this field was discussed, which might be useful to tree genomics in China.
Comparative Genomics
Synteny
Functional Genomics
Tree (set theory)
Cite
Citations (3)