Unexpected dynamic gene family evolution in algal actins

Marginal distribution and high heterozygosity of asexual Caloglossa vieillardii (Delesseriaceae, Rhodophyta) along the Australian coasts

In animals and land plants, many asexual species originate through inter- or intraspecific crosses, and such heterozygous asexuals frequently are more abundant than their sexual relatives in marginal habitats. Although asexual species have been reported in various macroalgal taxa, detailed information regarding their distribution, heterozygosity, and origin is limited. Because many asexual tetrasporophyte strains of Caloglossa vieillardii have been isolated from South Australia, far from their core tropical habitats, we re-examined the distribution range of asexual C. vieillardii and genotyped these and other western Pacific strains using an actin gene marker. We confirmed the marginal distribution of the asexuals; however, a small patch of sexual thalli was newly discovered 450 km further west from asexual populations in South Australia. Three heterozygous genotypes and one homozygous genotypes were detected from nine asexual populations; 21 heterozygous strains were obligately asexual, but one homozygous strain suddenly produced sexual gametophytes after several years of culture. We hypothesized that the most abundant heterozygous genotype (defined as type 3/4) in asexual populations occurred by a cross between type 3 and type 4 allele gametophytes, both of which were isolated from the Australian coasts. In the crossing experiments, certain combinations between type 3 females and type 4 males produced tetrasporophytes, which recycled successive tetrasporophytes. In the culture experiments, whereas both sexual and asexual strains successfully produced tetraspores at 12°C, no sexual strains released carpospores below 14°C. However, it is uncertain whether this slight difference of maturation temperature was related to the marginal distribution of asexual C. vieillardii.

Dynamic actin gene family evolution in primates

Actin is one of the most highly conserved proteins and plays crucial roles in many vital cellular functions. In most eukaryotes, it is encoded by a multigene family. Although the actin gene family has been studied a lot, few investigators focus on the comparison of actin gene family in relative species. Here, the purpose of our study is to systematically investigate characteristics and evolutionary pattern of actin gene family in primates. We identified 233 actin genes in human, chimpanzee, gorilla, orangutan, gibbon, rhesus monkey, and marmoset genomes. Phylogenetic analysis showed that actin genes in the seven species could be divided into two major types of clades: orthologous group versus complex group. Codon usages and gene expression patterns of actin gene copies were highly consistent among the groups because of basic functions needed by the organisms, but much diverged within species due to functional diversification. Besides, many great potential pseudogenes were found with incomplete open reading frames due to frameshifts or early stop codons. These results implied that actin gene family in primates went through “birth and death” model of evolution process. Under this model, actin genes experienced strong negative selection and increased the functional complexity by reproducing themselves.

INDUCTION OF APOMIXIS BY OUTCROSSING BETWEEN GENETICALLY DIVERGENT ENTITIES OF CALOGLOSSA LEPRIEURII (CERAMIALES, RHODOPHYTA) AND EVIDENCE OF HYBRID APOMICTS IN NATURE(1)

Our previous study revealed that apomixis, recycling of tetrasporophytes, can be generated through outcrossing between genetically divergent entities of Caloglossa monosticha M. Kamiya, though such apomicts have never been found in nature. In the case of C. leprieurii (Mont.) G. Martens, the most widespread species in this genus, many apomictic strains have been isolated worldwide, but it is unknown whether these apomicts evolved through an outcrossing process similar to that in C. monosticha. In this study, heterogeneity of the apomicts and their sexual relatives as well as their evolutionary relationships was examined using the nuclear-encoded actin gene and plastid-encoded RUBISCO spacer region. Thirteen out of 18 apomictic strains were heterogeneous and contained divergent actin alleles, whereas only two out of 23 sexual strains were heterogeneous. The five homogeneous apomicts were genetically identical, or quite similar, to the sexual strains isolated from adjacent sites. Furthermore, three of the five homogeneous apomicts frequently produced tetraspores that grew into gametophytes, while all the heterogeneous apomicts never generated gametophytes. Apomictic strains from Florida were allotriploid, and each of the three actin sequences was closely related to those of sexual strains from Florida, Peru, and Mexico/Guatemala. In crossing tests, obligate apomixis was generated through the outcrossing between the male from Madagascar and the female from the northwestern Atlantic. These results suggest that outcrossing between genetically divergent sexual entities is one factor that induces apomixis in C. leprieurii.

Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions

The evolution of actin gene families is characterized by independent expansions and contractions across the eukaryotic tree of life. Here, we assess diversity of actin gene sequences within three lineages of the genus Arcella, a free-living testate (shelled) amoeba in the Arcellinida. We established four clonal lines of two morphospecies, Arcella hemisphaerica and A. vulgaris, and assessed their phylogenetic relationship within the "Amoebozoa" using small subunit ribosomal DNA (SSU-rDNA) genealogy. We determined that the two lines of A. hemisphaerica are identical in SSU-rDNA, while the two A. vulgaris are independent genetic lineages. Furthermore, we characterized multiple actin gene copies from all lineages. Analyses of the resulting sequences reveal numerous diverse actin genes, which differ mostly by synonymous substitutions. We estimate that the actin gene family contains 40-50 paralogous members in each lineage. None of the three independent lineages share the same paralog with another, and divergence between actins reaches 29% in contrast to just 2% in SSU-rDNA. Analyses of effective number of codons (ENC), compositional bias, recombination signatures, and genetic diversity in the context of a gene tree indicate that there are two groups of actins evolving with distinct patterns of molecular evolution. Within these groups, there have been multiple independent expansions of actin genes within each lineage. Together, these data suggest that the two groups are located in different regions of the Arcella genome. Furthermore, we compare the Arcella actin gene family with the relatively well-described gene family in the slime mold Dictyostelium discoideum and other members of the Amoebozoa clade. Overall patterns of molecular evolution are similar in Arcella and Dictyostelium. However, the separation of genes in two distinct groups coupled with recent expansion is characteristic of Arcella and might reflect an unusual pattern of gene family evolution in the lobose testate amoebae. We provide a model to account for both the existence of two distinct groups and the pattern of recent independent expansion leading to a large number of actins in each lineage.