Genome-wide identification, structural and gene expression analysis of the nitrate transporters (NRTs) family in potato (Solanum tuberosum L.)

Nitrogen (N2) is the most important source of mineral N for plant growth, which was mainly transported by nitrate transporters (NRTs). However, little is known about the NRT gene family in potato. In this study, StNRT gene family members were identified in potato. In addition, we performed StNRT subfamily classification, gene structure and distribution analysis, and conserved domain prediction using various bioinformatics tools. Totally, 39 StNRT gene members were identified in potato genome, including 33, 4 and 2 member belong to NRT1, NRT2, and NRT3, respectively. These 39 StNRT genes were randomly distributed on all chromosomes. The collinearity results show that StNRT members in potato are closely related to Solanum lycopersicum and Solanum melongena. For the expression, different members of StNRT play different roles in leaves and roots. Especially under sufficient nitrogen conditions, different members have a clear distribution in different tissues. These results provide valuable information for identifying the members of the StNRT family in potato and could provide functional characterization of StNRT genes in further research.

Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)

Robber flies or assassin flies (Diptera: Asilidae) are a diverse family of venomous predators. The most recent classification organizes Asilidae into 14 subfamilies based on a comprehensive morphological phylogeny, but many of these have not been supported in a subsequent molecular study using traditional molecular markers. To address questions of monophyly in Asilidae, we leveraged the recently developed Diptera-wide UCE baitset to compile seven datasets comprising 151 robber flies and 146 - 2,508 loci, varying in the extent of missing data. We also studied the behavior of different nodal support metrics, as the non-parametric bootstrap is known to perform poorly with large genomic datasets. Our ML phylogeny was fully resolved and well-supported, but partially incongruent with the coalescent phylogeny. Further examination of the datasets suggested the possibility that GC bias had influenced gene tree inference and subsequent species tree analysis. The subfamilies Brachyrhopalinae, Dasypogoninae, Dioctriinae, Stenopogoninae, Tillobromatinae, Trigonomiminae, and Willistonininae were not recovered as monophyletic in either analysis, consistent with a previous molecular study. The inter-subfamily relationships are summarized as follows: Laphriinae and Dioctriinae (in part) are successively sister to the remaining subfamilies, which form two clades; the first consists of a grade of Stenopogoninae (in part), Willistonininae (in part), Bathypogoninae+Phellinae, Stichopogoninae, Leptogastrinae, Ommatiinae, and Asilinae; the second clade consists of a thoroughly paraphyletic assemblage of genera from Dioctriinae (in part), Trigonomiminae, Stenopogoninae (in part), Tillobromatinae, Brachyrhopalinae, and Dasypogoninae. We find that nodal support does not significantly vary with missing data. Furthermore, the bootstrap appears to overestimate nodal support, as has been reported from many recent studies. Gene concordance and site concordance factors seem to perform better, but may actually underestimate support. We instead recommend quartet concordance as a more appropriate estimator of nodal support. Our comprehensive phylogeny demonstrates that the higher classification of Asilidae is far from settled, and it will provide a much-needed foundation for a thorough revision of the subfamily classification.

Supralittoral pseudoscorpions of the genus Garypus (Pseudoscorpiones : Garypidae) from the Indo-West Pacific region, with a review of the subfamily classification of Garypidae

The pseudoscorpions of the genus Garypus L. Koch are restricted to seashore habitats where they occupy supralittoral and littoral zones primarily in tropical and subtropical areas. Few species have been recorded from the Indo-West Pacific region, and this project was devised to produce a review of the species found in museum collections and to test the relationships of the various garypid genera using a molecular analysis and an assessment of their morphology. A new subfamily classification is proposed with the subfamilies Garypinae, including Garypus and the new genus Anchigarypus Harvey (type species Garypus californicus Banks), and the Synsphyroninae for the other genera (Ammogarypus Beier, Anagarypus Chamberlin, Elattogarypus Beier, Eremogarypus Beier, Meiogarypus Beier, Neogarypus Vachon, Paragarypus Vachon, Neogarypus Vachon, Synsphyronus Chamberlin, and Thaumastogarypus Beier). The species-level revision of Garypus provides evidence for at least 14 species, most of which are known from only single localities. The following species are redescribed: G. insularis Tullgren from the Seychelles, G. krusadiensis Murthy & Ananthakrishnan from India and Sri Lanka, G. longidigitus Hoff from Queensland, Australia, G. maldivensis Pocock from the Maldives, G. nicobarensis Beier from the Nicobar Islands and G. ornatus Beier from the Marshall Islands. The holotype of G. insularis is a tritonymph, and not therefore readily identifiable. Nine new species are described: G. latens Harvey, sp. nov., G. malgaryungu Harvey, sp. nov., G. necopinus Harvey, sp. nov., G. postlei Harvey, sp. nov., G. ranalliorum Harvey, sp. nov. and G. weipa Harvey, sp. nov. from northern Australia, G. dissitus Harvey, sp. nov. from Cocos-Keeling Island, G. reong Harvey, sp. nov. and G. yeni Harvey, sp. nov. from Indonesia. A further possible new species from Queensland is described but not named, as it is represented by a single tritonymph. The subspecies of the Caribbean species G. bonairensis Beier are elevated to full species status: G. bonairensis, G. realini Hummelinck and G. withi Hoff. We supplement the descriptions with sequence data from five specimens from four species of Garypus and two species of Anchigarypus, and find COI divergence levels of 7–19% between Garypus species. http://zoobank.org/References/16463E29-6F13-4392-9E41-46A4312C852B

A molecular phylogeny of the cicadas (Hemiptera: Cicadidae) with a review of tribe and subfamily classification

A molecular phylogeny and a review of family-group classification are presented for 137 species (ca. 125 genera) of the insect family Cicadidae, the true cicadas, plus two species of hairy cicadas (Tettigarctidae) and two outgroup species from Cercopidae. Five genes, two of them mitochondrial, comprise the 4992 base-pair molecular dataset. Maximum-likelihood and Bayesian phylogenetic results are shown, including analyses to address potential base composition bias. Tettigarcta is confirmed as the sister-clade of the Cicadidae and support is found for three subfamilies identified in an earlier morphological cladistic analysis. A set of paraphyletic deep-level clades formed by African genera are together named as Tettigomyiinae n. stat. Taxonomic reassignments of genera and tribes are made where morphological examination confirms incorrect placements suggested by the molecular tree, and 11 new tribes are defined (Arenopsaltriini n. tribe, Durangonini n. tribe, Katoini n. tribe, Lacetasini n. tribe, Macrotristriini n. tribe, Malagasiini n. tribe, Nelcyndanini n. tribe, Pagiphorini n. tribe, Pictilini n. tribe, Psaltodini n. tribe, and Selymbriini n. tribe). Tribe Tacuini n. syn. is synonymized with Cryptotympanini, and Tryellina n. syn. is synonymized with an expanded Tribe Lamotialnini. Tribe Hyantiini n. syn. is synonymized with Fidicinini. Tribe Sinosenini is transferred to Cicadinae from Cicadettinae, Cicadatrini is moved to Cicadettinae from Cicadinae, and Ydiellini and Tettigomyiini are transferred to Tettigomyiinae n. stat from Cicadettinae. While the subfamily Cicadinae, historically defined by the presence of timbal covers, is weakly supported in the molecular tree, high taxonomic rank is not supported for several earlier clades based on unique morphology associated with sound production.

Molecular phylogenetic relationships of halacarid mites suggest the reevaluation of traditional subfamily classification

Molecular phylogenetic relationships were examined for marine mites in the subfamilies Halacarinae, Copidognathinae, Rhombognathinae and Halixodinae from the aquatic mite family Halacaridae by using nuclear 18S and 28S ribosomal RNA gene sequences. The analysis revealed incongruences between the clustering obtained in the phylogenetic trees and the current morphological classification in the subfamilies Halacarinae and Rhombognathinae (based on 18S sequences) and in the Rhombognathinae (based on both 28S and combined 18S and 28S sequences). By contrast, the tree clustering was consistent with the morphological taxonomic positions in the Copidognathinae and Halixodinae subfamilies. It can be concluded that molecular phylogenetic analysis challenges the current classifications of Halacarinae and Rhombognathinae subfamilies. Accordingly diagnostic characters for their classification should be reevaluated.