A database and comprehensive analysis of the algae genomes

Abstract

Algae characterize their high diversity, taxonomy and morphology for wide-used studying the plant origins and terrestrialization, as well as multicellular evolution. Due to the genome assembly challenge of algae caused by symbionts with microbiome, the published algae genomes are relatively less than the terrestrial plants. Here we comprehensively collected and re-annotated 191 available algae genomes distributed in nine major lineages. We systemically investigated the genome features including genome size, assembly continuity and integrity, GC content, abundance of repetitive sequences and protein-coding gene number. We construct the phylogenetic trees using 193 algae genomes, which is consistent with the well-known evolution path that Glaucophyte is the most ancient, going through eight lineages, and finally evolved to terrestrial plants. We also examined the Horizontal Gene Transfer (HGT) genes distribution in algae genomes and provides a substantial genomic resource for functional gene origins and plant evolution.

The complete mitochondrial genome of Isochrysis galbana harbors a unique repeat structure and a specific trans-spliced cox1 gene

“…The Cercozoa (chlorarachniophytes) was unexpectedly grouped into the clade of Haptophyta (Figure 5) or the clade of stramenopiles (Supplementary Figures S7, S8; both were the red-derived lineages), in contrast to the perception of its green algae-derived origin. The similar trend was also found in recent algal phylogenetic analysis based on conserved BUSCO sequences Fang et al 10.3389/fmicb.2022.966219 Frontiers in Microbiology 19 frontiersin.org (Shi et al, 2021). The cryptophyte lineage was located separately from the SH lineages (Figure 5; Supplementary Figures S7, S8), which is strongly in line with earlier phylogenetic analysis based on a dataset of 16 conserved mtDNA proteins (Kim et al, 2018).…”

A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity

“…In fungi, which are a useful lineage for this comparison as multicellularity has been lost secondarily in multiple clades, taxa with complex multicellularity typically have more than twice as many protein-coding genes as unicellular relatives ( 16 ). Similarly, plants, animals, and macroalgae have substantially larger genomes than their unicellular relatives ( 12 , 13 ), both in terms of the number of protein-coding genes ( 17 , 18 ) and noncoding regions, which serve as a crucial substrate for the evolution of regulatory regions underpinning cellular specialization and morphogenesis ( 19 ).…”

A non-adaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity

“…In fungi, which are a useful lineage for this comparison as multicellularity has been lost secondarily in multiple clades, taxa with complex multicellularity typically have more than twice as many protein coding genes as unicellular relatives (15). Similarly, plants, animals and macroalgae have substantially larger genomes than their unicellular relatives (11, 13), both in terms of the number of protein coding genes (16, 17) and non-coding regions, which serve as a crucial substrate for the evolution of regulatory regions underpinning cellular specialization and morphogenesis (18).…”