Phylogeny and divergence time estimation of cheilostome bryozoans based on mitochodrial 16S rRNA sequences

Transcriptome Analysis Reveals the Molecular Regularity Mechanism Underlying Stem Bulblet Formation in Oriental Lily 'Siberia'; Functional Characterization of the LoLOB18 Gene

The formation of underground stem bulblets in lilies is a complex biological process which is key in their micropropagation. Generally, it involves a stem-to-bulblet transition; however, the underlying mechanism remains elusive. It is important to understand the regulatory mechanism of bulblet formation for the reproductive efficiency of Lilium. In this study, we investigated the regulatory mechanism of underground stem bulblet formation under different conditions regarding the gravity point angle of the stem, i.e., vertical (control), horizontal, and slanting. The horizontal and slanting group displayed better formation of bulblets in terms of quality and quantity compared with the control group. A transcriptome analysis revealed that sucrose and starch were key energy sources for bulblet formation, auxin and cytokinin likely promoted bulblet formation, and gibberellin inhibited bulblet formation. Based on transcriptome analysis, we identified the LoLOB18 gene, a homolog to AtLOB18, which has been proven to be related to embryogenic development. We established the stem bud growth tissue culture system of Lilium and silenced the LoLOb18 gene using the VIGS system. The results showed that the bulblet induction was reduced with down-regulation of LoLOb18, indicating the involvement of LoLOb18 in stem bulblet formation in lilies. Our research lays a solid foundation for further molecular studies on stem bulblet formation of lilies.

Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny

Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.

The Primary Complete Mitochondrial Genome of the Lappet Moth Brahmophthalma hearseyi (Lepidoptera: Brahmaeidae) and Related Phylogenetic Analysis

Simple Summary

In this paper, the complete mitochondrial genome (mitogenome) of B. hearseyi was sequenced using long-PCR and primer-walking methods. The results indicated that the mitogenome is a typical circular molecule that is composed of 15,442 bp. Phylogenetic analysis showed that B. hearseyi is clustered into Brahmaeidae, and the phylogenetic relationships are (Brahmaeidae + Lasiocampidae) + (Bombycidae + (Sphingidae + Saturniidae)). This study provides the first mitogenomic resources for the Brahmaeidae.

Abstract

Background: Brahmophthalma hearseyi (Lepidoptera: Brahmaeidae) is widely distributed across China. Its larvae damage the leaves of many plants such as those belonging to the Oleaceae family, causing significant economic losses and seriously affecting the survival and reproduction of Cervus nippon; however, genetic data for this species are scarce. Methods: The complete mitochondrial genome (mitogenome) of B. hearseyi was sequenced using long-PCR and primer-walking methods. Phylogenetic analysis that was based on 13 PCGs and two rRNAs was carried out using the neighbor-joining and Bayesian interference methods. Results: The mitogenome is a typical circular molecule that is made up of 15,442 bp, which includes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and an A + T-rich region (456 bp). All of the PCGs, except for COX1 and COX2, start with ATN codons. COX2 and ND5 use the incomplete termination codon T, and 11 other PCGs use the typical stop codon TAA. All tRNA genes, except for trnS1 and trnS2, display a typical cloverleaf structure; trnS1 lacks the “DHU” arm, whereas trnS2 exhibits two mismatched base pairs in the anticodon stem. Phylogenetic analysis showed that B. hearseyi is clustered into Brahmaeidae, and the phylogenetic relationships are (Brahmaeidae + Lasiocampidae) + (Bombycidae + (Sphingidae + Saturniidae)). Conclusions: This study provides the first mitogenomic resources for the Brahmaeidae.

Cryptic species and host specificity in the bryozoan-associated hydrozoan Zanclea divergens (Hydrozoa, Zancleidae)

Zanclea divergens is a tropical hydrozoan living in symbiotic association with bryozoans and currently reported from Papua New Guinea, Indonesia, and Maldives. Here, we used an integrative approach to assess the morpho-molecular diversity of the species across the Indo-Pacific. Phylogenetic and species delimitation analyses based on seven mitochondrial and nuclear loci revealed four well-supported molecular lineages corresponding to cryptic species, and representing a Pacific clade, an Indian clade, and two Red Sea clades. Since the general polyp morphology was almost identical in all samples, the nematocyst capsules were measured and analysed to search for possible fine-scale differences, and their statistical treatment revealed a significant difference in terms of length and width among the clades investigated. All Zanclea divergens specimens were specifically associated with cheilostome bryozoans belonging to the genus Celleporaria. The Pacific and Indian clades were associated with Celleporaria sp. and C. vermiformis, respectively, whereas both Red Sea lineages were associated with C. pigmentaria. Nevertheless, the sequencing of host bryozoans revealed that one of the Red Sea hydrozoan clades is associated with two morphologically undistinguishable, but genetically divergent, bryozoan species. Overall, our results show that Z. divergens is a species complex composed of morphologically cryptic lineages showing partially disjunct distributions and host specificity. The presence of two sympatric lineages living on the same host species reveal complex dynamics of diversification, and future research aimed at understanding their diversification process will likely improve our knowledge on the mechanisms of speciation among currently sympatric cryptic species.

Bryozoans are returning home: recolonization of freshwater ecosystems inferred from phylogenetic relationships

Bryozoans are aquatic invertebrates that inhabit all types of aquatic ecosystems. They are small animals that form large colonies by asexual budding. Colonies can reach the size of several tens of centimeters, while individual units within a colony are the size of a few millimeters. Each individual within a colony works as a separate zooid and is genetically identical to each other individual within the same colony. Most freshwater species of bryozoans belong to the Phylactolaemata class, while several species that tolerate brackish water belong to the Gymnolaemata class. Tissue samples for this study were collected in the rivers of Adriatic and Danube basin and in the wetland areas in the continental part of Croatia (Europe). Freshwater and brackish taxons of bryozoans were genetically analyzed for the purpose of creating phylogenetic relationships between freshwater and brackish taxons of the Phylactolaemata and Gymnolaemata classes and determining the role of brackish species in colonizing freshwater and marine ecosystems. Phylogenetic relationships inferred on the genes for 18S rRNA, 28S rRNA, COI, and ITS2 region confirmed Phylactolaemata bryozoans as radix bryozoan group. Phylogenetic analysis proved Phylactolaemata bryozoan's close relations with taxons from Phoronida phylum as well as the separation of the Lophopodidae family from other families within the Plumatellida genus. Comparative analysis of existing knowledge about the phylogeny of bryozoans and the expansion of known evolutionary hypotheses is proposed with the model of settlement of marine and freshwater ecosystems by the bryozoans group during their evolutionary past. In this case study, brackish bryozoan taxons represent a link for this ecological phylogenetic hypothesis. Comparison of brackish bryozoan species Lophopus crystallinus and Conopeum seurati confirmed a dual colonization of freshwater ecosystems throughout evolution of this group of animals.

Evidence for polyphyly of the genus Scrupocellaria (Bryozoa: Candidae) based on a phylogenetic analysis of morphological characters

The bryozoan genus Scrupocellaria comprises about 80 species in the family Candidae. We propose a hypothesis for the phylogenetic relationships among species assigned to Scrupocellaria to serve as framework for a phylogenetic classification using 35 morphological characters. Our results suggest that the genus Scrupocellaria is polyphyletic. Scrupocellaria s. str. is redefined according to four morphological features: vibracular chamber with a curved setal groove, ooecium with a single ectooecial fenestra, two axillary vibracula, and a membranous operculum with a distinct distal rim. Thus, the genus includes only 11 species: Scrupocellaria aegeensis, Scrupocellaria delilii, Scrupocellaria harmeri, Scrupocellaria incurvata, Scrupocellaria inermis, Scrupocellaria intermedia, Scrupocellaria jullieni, Scrupocellaria minuta, Scrupocellaria puelcha, Scrupocellaria scrupea, and Scrupocellaria scruposa. The monophyly of Cradoscrupocellaria is supported and five new genera are erected: Aquiloniella n. gen., Aspiscellaria n. gen., Paralicornia n. gen., Pomocellaria n. gen. and Scrupocaberea n. gen. Two other new genera, Bathycellaria n. gen. and Sinocellaria n. gen., are erected to accommodate two poorly known species, Scrupocellaria profundis Osburn and Scrupocellaria uniseriata Liu, respectively. Scrupocellaria congesta is tentatively assigned to Tricellaria. Fifteen species are reassigned to Licornia: Licornia cookie n. comb., Licornia micheli n. comb., Licornia milneri n. comb., Licornia curvata n. comb., Licornia diegensis n. comb., Licornia drachi n. comb., Licornia mexicana n. comb., Licornia pugnax n. comb., Licornia raigadensis n. comb., Licornia regularis n. comb., Licornia resseri n. comb., Licornia securifera n. comb., Licornia spinigera n. comb., Licornia tridentata n. comb., and Licornia wasinensis n. comb. Notoplites americanus n. name is proposed as a replacement name for Scrupocellaria clausa Canu & Bassler. Three fossil species are reassigned to Canda: Canda rathbuni n. comb., Canda triangulata n. comb. and Canda williardi n. comb. A species is reassigned to Notoplites, Notoplites elegantissima n. comb. The generic assignment of eleven species of Scrupocellaria, including Scrupocellaria macandrei, remains uncertain.

The complete mitochondrial genomes of the Fenton's wood white, Leptidea morsei, and the lemon emigrant, Catopsilia pomona

The complete mitochondrial genomes of Leptidea morsei Fenton (Lepidoptera: Pieridae: Dis-morphiinae) and Catopsilia pomona (F.) (Lepidoptera: Pieridae: Coliadinae) were determined to be 15,122 and 15,142 bp in length, respectively, with that of L. morsei being the smallest among all known butterflies. Both mitogenomes contained 37 genes and an A+T-rich region, with the gene order identical to those of other butterflies, except for the presence of a tRNA-like insertion, tRNA(Leu) (UUR), in C. pomona. The nucleotide compositions of both genomes were higher in A and T (80.2% for L. morsei and 81.3% for C. pomona) than C and G; the A+T bias had a significant effect on the codon usage and the amino acid composition. The protein-coding genes utilized the standard mitochondrial start codon ATN, except the COI gene using CGA as the initiation codon, as reported in other butterflies. The intergenic spacer sequence between the tRNA(Ser) (UCN) and ND1 genes contained the ATACTAA motif. The A+T-rich region harbored a poly-T stretch and a conserved ATAGA motif located at the end of the region. In addition, there was a triplicated 23 bp repeat and a microsatellite-like (TA)9(AT)3 element in the A+T-rich region of the L. morsei mitogenome, while in C. pomona, there was a duplicated 24 bp repeat element and a microsatellite-like (TA)9 element. The phylogenetic trees of the main butterfly lineages (Hesperiidae, Papilionidae, Pieridae, Nymphalidae, Lycaenidae, and Riodinidae) were reconstructed with maximum likelihood and Bayesian inference methods based on the 13 concatenated nucleotide sequences of protein-coding genes, and both trees showed that the Pieridae family is sister to Lycaenidae. Although this result contradicts the traditional morphologically based views, it agrees with other recent studies based on mitochondrial genomic data.

Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae)

We sequenced the complete mitochondrial genome of Phalera flavescens. The mitogenome is 15,659 bp in length, including 13 protein-coding genes (atp6, atp8, cox1-3, nad1-6, nad4L, cob), two ribosomal RNAs (rrnS and rrnL), 22 transfer RNAs and an AT-rich region, a putative control region (D-loop). Gene order and orientation were found to be identical to those of other completely sequenced lepidopteran mitogenomes. All 13 protein-coding genes start with the common codon ATN, except for the cox1 gene, which uses CGA as the initial codon. Nine of the 13 protein-coding genes stop with codon TAA, while the cox1, cox2, nad5, and nad4 genes stop with the single nucleotide T. All tRNA genes can be folded into canonical cloverleaf secondary structure, except for trnS1, which loses the ''DHU'' arm. Six overlapping sequences totaling 20 bp (1-8 bp for each sequence) and 16 intergenic spacer sequences, totaling 276 bp (1-58 bp for each sequence) are scattered throughout the genome; the largest intergenic spacer is located between the trnQ and nad2 genes. A microsatellite-like structure (AT)(6)ACC(AT)(6) and 16-bp poly-T elements preceded by the ATTTA motif are present in the D-loop region. Additionally, unexpectedly, an extra 190-bp insertion, with unknown function, was found in the small subunit rRNA gene (rrnS); this gene is the longest known (1020 bp) among all of the Lepidoptera.

A molecular phylogeny of bryozoans

We present the most comprehensive molecular phylogeny of bryozoans to date. Our concatenated alignment of two nuclear ribosomal and five mitochondrial genes includes 95 taxa and 13,292 nucleotide sites, of which 8297 were included. The number of new sequences generated during this project are for each gene:ssrDNA (32), lsrDNA (22), rrnL (38), rrnS (35), cox1 (37), cox3 (34), and cytb (44). Our multi-gene analysis provides a largely stable topology across the phylum. The major groups were unambiguously resolved as (Phylactolaemata (Cyclostomata (Ctenostomata, Cheilostomata))), with Ctenostomata paraphyletic. Within Phylactolaemata, (Stephanellidae, Lophopodidae) form the earliest divergent clade. Fredericellidae is not resolved as a monophyletic family and forms a clade together with Plumatellidae, Cristatellidae and Pectinatellidae, with the latter two as sister taxa. Hyalinella and Gelatinella nest within the genus Plumatella. Cyclostome taxa fall into three major clades: i. (Favosipora (Plagioecia, Rectangulata)); ii. (Entalophoroecia ((Diplosolen, Cardioecia) (Frondipora, Cancellata))); and iii. (Articulata ((Annectocyma, Heteroporidae) (Tubulipora (Tennysonia, Idmidronea)))), with suborders Tubuliporina and Cerioporina, and family Plagioeciidae each being polyphyletic. Ctenostomata is composed of three paraphyletic clades to the inclusion of Cheilostomata: ((Alcyonidium, Flustrellidra) (Paludicella (Anguinella, Triticella)) (Hislopia (Bowerbankia, Amathia)) Cheilostomata); Flustrellidra nests within the genus Alcyonidium, and Amathia nests within the genus Bowerbankia. Suborders Carnosa and Stolonifera are not monophyletic. Within the cheilostomes, Malacostega is paraphyletic to the inclusion of all other cheilostomes. Conopeum is the most early divergent cheilostome, forming the sister group to ((Malacostega, Scrupariina, Inovicellina) ((Hippothoomorpha, Flustrina) (Lepraliomorpha, Umbonulomorpha))); Flustrina is paraphyletic to the inclusion of the hippothoomorphs; neither Lepraliomorpha nor Umbonulomorpha is monophyletic. Ascophorans are polyphyletic, with hippothoomorphs grouping separately from lepraliomorphs and umbonulomorphs; no cribrimorphs were included in the analysis. Results are discussed in the light of molecular and morphological evidence. Ancestral state reconstruction of larval strategy in Gymnolaemata revealed planktotrophy and lecithotrophy as equally parsimonious solutions for the ancestral condition. More comprehensive taxon sampling is expected to clarify this result. We discuss the extent of non-bryozoan contaminant sequences deposited in GenBank and their impact on the reconstruction of metazoan phylogenies and those of bryozoan interrelationships.

The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa

The complete mitochondrial genome of Flustrellidra hispida (Bryozoa, Ctenostomata, Flustrellidridae) was sequenced using a transposon-mediated approach. All but one of the 36 genes were identified (trnS2). The genome is 13,026 bp long, being one of the smallest metazoan mitochondrial genomes sequenced to date with a unique gene order when compared to other Metazoa. The genome has an overall AT richness of 59.4%. We found seven regions of overlaps between tRNAs and protein-coding genes ranging from 2 to 11 nt, and seven regions of overlap between tRNAs, ranging from 1 to 8 nt, resulting in a total number of 46 overlapping nucleotides. Genes nad4, cox2, atp8, and nad3 are terminated by the abbreviated stop codon T and cytb is suggested to terminate on (ACT)AA; we postulate that mRNA editing is required to remove AC for TAA to be functional in terminating translation. Phylogenetic analysis of nucleotide and amino acid data place Flustrellidra in the Lophotrochozoa. DNA for this study originated from two populations resulting in a contig consisting of multiple haplotypes. Twenty-seven SNP sites were detected, the majority occurring in cox1 and nad5. With cox1 already established as a marker in bryozoan studies, we advocate the further testing of nad5.