Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell‑eye evolution

Mollusca is the second-largest animal phylum with over 100,000 extant species representing eight classes.Across 1000 extant species in the class Polyplacophora,chitons have a relatively constrained morphology but with some notable deviations.Several genera possess“shell eyes”,i.e.,true eyes with a lens and retina that are embedded within the dorsal shells.The phylogeny of the major chiton clades is mostly well established,in a set of superfamily-level and higher level taxa supported by various approaches,including morphological studies,multiple gene markers,mitogenome-phylogeny,and phylotranscriptomic approaches.However,one critical lineage has remained unclear,namely Schizochiton which was controversially suggested as being the potential independent origin of chiton shell eyes.Here,with the draft genome sequencing of Schizochiton incisus(superfamily Schizochitonoidea)plus assemblies of transcriptome data from other polyplacophorans,we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods.We found that phylogenetic trees from mitogenomic data are inconsistent,reflecting larger scale confounding factors in molluscan mitogenomes.However,a consistent and robust topology was generated with protein-coding genes using different models and methods.Our results support Schizochitonoidea as the sister group to other Chitonoidea in Chitonina,in agreement with the established classification.Combined with evidence from fossils,our phylogenetic results suggest that the earliest origin of shell eyes is in Schizochitonoidea,and that these structures were also gained secondarily in other genera in Chitonoidea.Our results have generated a holistic review of the internal relationship within Polyplacophora,and a better understanding of the evolution of Polyplacophora.

RpL38 modulates germ cell differentiation by controlling Bam expression in Drosophila testis

Switching from mitotic spermatogonia to meiotic spermatocytes is critical to producing haploid sperms during male germ cell differentiation.However,the underlying mechanisms of this switch remain largely unexplored.In Drosophila melanogaster,the gene RpL38 encodes the ribosomal protein L38,one component of the 60S subunit of ribosomes.We found that its depletion in spermatogonia severely diminished the production of mature sperms and thus led to the infertility of male flies.By examining the germ cell differentiation in testes,we found that RpL38-knockdown blocked the transition from spermatogonia to spermatocytes and accumulated spermatogonia in the testis.To understand the intrinsic reason for this blockage,we conducted proteomic analysis for these spermatogonia populations.Differing from the control spermatogonia,the accumulated spermatogonia in RpL38-knockdown testes already expressed many spermatocyte markers but lacked many meiosis-related proteins,suggesting that spermatogonia need to prepare some important proteins for meiosis to complete their switch into spermatocytes.Mechanistically,we found that the expression of bag of marbles(bam),a crucial determinant in the transition from spermatogonia to spermatocytes,was inhibited at both the mRNA and protein levels upon RpL38 depletion.We also confirmed that the bam loss phenocopied RpL38 RNAi in the testis phenotype and transcriptomic profiling.Strikingly,overexpressing bam was able to fully rescue the testis abnormality and infertility of RpL38-knockdown flies,indicating that bam is the key effector downstream of RpL38 to regulate spermatogonia differentiation.Overall,our data suggested that germ cells start to prepare meiosis-related proteins as early as the spermatogonial stage,and RpL38 in spermatogonia is required to regulate their transition toward spermatocytes in a bamdependent manner,providing new knowledge for our understanding of the transition process from spermatogonia to spermatocytes in Drosophila spermatogenesis.

From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

Diversity in freshwater scuticociliates(Alveolata,Ciliophora,Scuticociliatia):Two new species isolated from a wetland in northern China,focusing on their morphology,taxonomy,and molecular phylogeny,with establishment of a new family Glauconematidae fam.nov.

In the aquatic microbial food web,scuticociliates are diverse and predominant in almost all kinds of biotopes while extremely confused regarding their taxonomy and systematic relationships within the subclass Scuticociliatia.Here we provide detailed descriptions of two new and one known species,Glauconema sinica sp.nov.,Pleuronema parasetigerum sp.nov.,and Histiobalantium natans viridis,isolated from a freshwater wetland in northern China,along with their molecular phylogeny based on SSU rRNA gene sequences.Our results show:(1)both molecular and morphological data strongly support that the isolated lineage containing the genera Glauconema,Miamiensis,Paramesanophrys,and Anophryoides should be identified as a new taxon at the family level in the order Philasterida;hence,a new family,Glauconematidae fam.nov.,is established.This new family is mainly characterized by the polymorphic life cycle of its members(macrostome and microstome stages);the trophont(or macrostome)has closely spaced membranelles 1–3,whereas in the tomite(or microstome)membranelle 1 is distant from membranelle 2.(2)Phylogenetic analyses using novel data for these species revealed that all three cluster with their congeners,supporting the validity of the genera to which they belong.Molecular information also supports the monophyly of the two main scuticociliate orders Pleuronematida and Philasterida.