Summary
The Closterium peracerosum–strigosum–littorale complex (Closterium, Zygnematophyceae) has an isogamous mating system. Members of the Zygnematophyceae are the closest relatives to extant land ...plants and are distantly related to chlorophytic models, for which a genetic basis of mating type (MT) determination has been reported. We thus investigated MT determination in Closterium.
We sequenced genomes representing the two MTs, mt+ and mt−, in Closterium and identified CpMinus1, a gene linked to the mt− phenotype. We analyzed its function using reverse genetics methods.
CpMinus1 encodes a divergent RWP‐RK domain‐containing‐like transcription factor and is specifically expressed during gamete differentiation. Introduction of CpMinus1 into an mt+ strain was sufficient to convert it to a phenotypically mt− strain, while CpMinus1‐knockout mt− strains were phenotypically mt+.
We propose that CpMinus1 is the major MT determinant that acts by evoking the mt− phenotype and suppressing the mt+ phenotype in heterothallic Closterium. CpMinus1 likely evolved independently in the Zygnematophyceae lineage, which lost an egg–sperm anisogamous mating system. mt− specific regions possibly constitute an MT locus flanked by common sequences that undergo some recombination.
Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies ...belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an important role in the divergence of the two subspecies and the evolution of selfing in subsp. littorale. These results shed new light on the relationship between mating system evolution and past demographic change in fern species.
Plant leaves occur in diverse shapes. Divarication patterns that develop during early growths are one of key factors that determine leaf shapes. We utilized leaves of Microsorum pteropus, a ...semi-aquatic fern, and closely related varieties to analyze a variation in the divarication patterns. The leaves exhibited three major types of divarication: no lobes, bifurcation, and trifurcation (i.e., monopodial branching). Our investigation of their developmental processes, using time-lapse imaging, revealed localized growths and dissections of blades near each leaf apex. Restricted cell divisions responsible for the apical growths were confirmed using a pulse-chase strategy for EdU labeling assays.
Liagora japonica is a red algal species distributed in temperate regions of Japan. This species has not been collected from its type locality on the Pacific coast of Japan since 1927 and seems to ...have become extinct in this area. For molecular characterization of L. japonica, we extracted DNA from the topotype material of L. japonica collected in 1927, analyzed seven genes using Illumina next-generation sequencing, and compared these data with sequences from modern samples of similar red algae collected from the Japan Sea coast of Japan. Both morphological and molecular data from modern samples and historical specimens (including the lectotype and topotype) suggest that the specimens from the Pacific and Japan Sea coasts of Japan should be treated as a single species, and that L. japonica is phylogenetically separated from the genus Liagora. Based on the phylogenetic results and examination of reproductive structures, we propose Otohimella japonica gen. et comb. nov., characterized morphologically by diffuse carposporophytes, undivided carposporangia, and involucral filaments initiated only from the cortical cell on the supporting cell.
The coexistence of three sexual phenotypes (male, female and bisexual) in a single species, 'trioecy', is rarely found in diploid organisms such as flowering plants and invertebrates. However, ...trioecy in haploid organisms has only recently been reported in a green algal species, Pleodorina starrii. Here, we generated whole-genome data of the three sex phenotypes of P. starrii to reveal a reorganization of the ancestral sex-determining regions (SDRs) in the sex chromosomes: the male and bisexual phenotypes had the same "male SDR" with paralogous gene expansions of the male-determining gene MID, whereas the female phenotype had a "female SDR" with transposition of the female-specific gene FUS1 to autosomal regions. Although the male and bisexual sex phenotypes had the identical male SDR and harbored autosomal FUS1, MID and FUS1 expression during sexual reproduction differed between them. Thus, the coexistence of three sex phenotypes in P. starrii is possible.
In apogamous ferns, all offspring from a parent are expected to be clonal. However, apogamous ‘species’ frequently demonstrate a large amount of morphological and genetic variations.
Cyrtomium ...fortunei
composed of four varieties (
C. fortunei
var.
fortunei
, var.
clivicola
, var.
intermedium
, and var.
atropunctatum
), is all reported to be apogamous triploids, but demonstrates large and continuous morphological variation. In previous studies, we showed that considerable genetic diversity was observed in many local populations of the apogamous fern ‘species’. We hypothesized that genetic segregation has occurred, because neither sexual type nor intraspecific polyploidy have been observed in
C. fortunei
in Japan. Of 732 progeny examined (250 gametophytes and 482 sporophytes), obtained from a parental sporophyte whose
pgiC
genotype was estimated as
aab
, 11 (4.4%) gametophytes and 8 (1.7%) sporophytes showed a different genotype (
aaa
) from that of the parent sporophyte. We showed that genetic segregation occurs in apogamous
C. fortunei
in relatively high frequency. Moreover, we could first show that the segregation frequency in gametophytes is significantly higher than that in sporophytes of the next generation (
χ
2
= 4.90,
P
= 0.027). It may suggest the existence of deleterious genes, which are expressed during the morphogenesis and growth of sporophytes.
Two types of abnormal sporophytes were observed in a population of diploid
Thelypteris decursive
-
pinnata
. Most sporophytes in this population exhibited regular chromosome pairing, resulting in the ...formation of 30 bivalents in meiosis I; however, they produced abortive spores to various degrees. Some formed large globose spores at low frequencies, most likely to be unreduced diplospores. The other type of abnormal sporophyte underwent synaptic failure to form 60 univalents at meiosis I, but produced fertile spores, mostly large globose ones at low frequencies. The globose spores were considered unreduced diplospores because the gametophytes arising from them produced tetraploid sporophytes by gametophytic selfing. One tetraploid formed only univalents at meiosis I. Allozyme variation was not detected in this population, although neighboring ordinary diploid populations exhibited it to a certain degree. The sympatric occurrence and allozyme uniformity of the two groups suggest that both are offspring of a founder sporophyte, which may have possessed two types of mutated recessive genes responsible for the spore sterility and the synaptic failure in meiosis. Unreduced spores formed by these two types may play an important role in the polyploid speciation of this species.
Abstract
SARS-CoV-2 is the cause of the current worldwide pandemic of severe acute respiratory syndrome. The change of nucleotide composition of the SARS-CoV-2 genome is crucial for understanding the ...spread and transmission dynamics of the virus because viral nucleotide sequences are essential in identifying viral strains. Recent studies have shown that cytosine (C) to uracil (U) substitutions are overrepresented in SARS-CoV-2 genome sequences. These asymmetric substitutions between C and U indicate that traditional time-reversible substitution models cannot be applied to the evolution of SARS-CoV-2 sequences. Thus, we develop a new time-irreversible model of nucleotide substitutions to estimate the substitution rates in SARS-CoV-2 genomes. We investigated the number of nucleotide substitutions among the 7862 genomic sequences of SARS-CoV-2 registered in the Global Initiative on Sharing All Influenza Data (GISAID) that have been sampled from all over the world. Using the new method, the substitution rates in SARS-CoV-2 genomes were estimated. The C-to-U substitution rates of SARS-CoV-2 were estimated to be 1.95 × 10−3 ± 4.88 × 10−4 per site per year, compared with 1.48 × 10−4 ± 7.42 × 10−5 per site per year for all other types of substitutions.
DNA sequencers that can conduct real-time sequencing from a single polymerase molecule are known as third-generation sequencers. Third-generation sequencers enable sequencing of reads that are ...several kilobases long. However, the raw data generated from third-generation sequencers are known to be error-prone. Because of sequencing errors, it is difficult to identify which genes are homologous to the reads obtained using third-generation sequencers. In this study, a new method for homology search algorithm, PAFFT, is developed. This method is the extension of the MAFFT algorithm which was used for multiple alignments. PAFFT detects global homology rather than local homology so that homologous regions can be detected even when the error rate of sequencing is high. PAFFT will boost application of third-generation sequencers.
•Third-generation sequencers can sequence single molecule of DNA.•However, the raw data generated from third-generation sequencers are error-prone.•In this study, a new method for homology search algorithm, PAFFT, is developed.•PAFFT detects homologous regions even when the error rate of sequencing is high.•PAFFT will boost application of third-generation sequencers.
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