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Root-knot nematodes (RKNs) are among the most devastating pests in agriculture. Solanum torvum Sw. (Turkey berry) has been used as a rootstock for eggplant (aubergine) cultivation because of its resistance to RKNs, including Meloidogyne incognita and M. arenaria. We previously found that a pathotype of M. arenaria, A2-J, is able to infect and propagate in S. torvum. In vitro infection assays showed that S. torvum induced the accumulation of brown pigments during avirulent pathotype A2-O infection, but not during virulent A2-J infection. This experimental system is advantageous because resistant and susceptible responses can be distinguished within a few days, and because a single plant genome can yield information about both resistant and susceptible responses. Comparative RNA-sequencing analysis of S. torvum inoculated with A2-J and A2-O at early stages of infection was used to parse the specific resistance and susceptible responses. Infection with A2-J did not induce statistically significant changes in gene expression within one day post-inoculation (DPI), but afterward, A2-J specifically induced the expression of chalcone synthase, spermidine synthase, and genes related to cell wall modification and transmembrane transport. Infection with A2-O rapidly induced the expression of genes encoding class III peroxidases, sesquiterpene synthases, and fatty acid desaturases at 1 DPI, followed by genes involved in defense, hormone signaling, and the biosynthesis of lignin at 3 DPI. Both isolates induced the expression of suberin biosynthetic genes, which may be triggered by wounding during nematode infection. Histochemical analysis revealed that A2-O, but not A2-J, induced lignin accumulation at the root tip, suggesting that physical reinforcement of cell walls with lignin is an important defense response against nematodes. The S. torvum-RKN system can provide a molecular basis for understanding plant-nematode interactions.

Trilocha varians is a member of the bombycid moths. Since T. varians has a considerably shorter generation period than the prevailing model species, Bombyx mori, this species would be a novel model insect in Lepidoptera. To facilitate further use of T. varians, we developed genome annotation information on the chromosome-scale assembly of T. varians previously published by our group. 9 RNA-seq datasets and 2 Iso-seq datasets were submitted for transcriptome-based gene prediction. As a result, 16,266 protein-coding genes were predicted on the latest genome assembly, and 98.6% of BUSCO sequences were present in our gene models. ATAC-seq was also conducted to determine chromatin accessibility across the genome. Finally, piRNA-targeted small RNA-seq revealed T. varians genome harbours 517 piRNA clusters (piCs). This information will encourage and facilitate potential users who plan to use this species. [ABSTRACT FROM AUTHOR]

The wild silk moth, Bombyx mandarina, is the closest relative of the domesticated silk moth, Bombyx mori. National BioResource Project of Japan (NBRP) maintains a B. mandarina strain derived from individuals captured at Sakado (Saitama, Japan) in 1982. Now, NBRP has developed chromosome replacement strains of B. mori. In each strain, one autosome of B. mori was replaced with the corresponding chromosome of B. mandarina. To facilitate the use of chromosome replacement strains and B. mandarina itself, we constructed a chromosome-level genome assembly of B. mandarina. Furthermore, we performed functional annotations of the genome assembly, i.e., transcriptome-based gene prediction, Assay for Transposase-Accessible Chromatin (ATAC)-seq, and PIWI-interacting RNA (piRNA)-targeted small RNA-seq. The assembly harbors 14,859 protein-coding genes and 628 piRNA clusters across three tissues: ovaries, testis, and embryos. ATAC-seq data comprehensively detected open chromosome regions, which will benefit when CRISPR/Cas9-mediated genome editing is conducted. [ABSTRACT FROM AUTHOR]

Membrane proteins targeted to the plasma membrane are first transported from the endoplasmic reticulum (ER) to the Golgi apparatus. This study explored the mechanisms controlling plasma membrane trafficking of the boric acid channel AtNIP5;1 from the ER. Imaging-based screening using transgenic Arabidopsis identified six mutants in which GFP-NIP5;1 was localized in the ER in addition to the plasma membrane. Genetic mapping and whole-genome resequencing identified the responsible gene in four among the six mutants as KAONASHI3 (KNS3)/SPOTTY1/IMPERFECTIVE EXINE FORMATION. Among the plasma membrane-localized proteins tested, NIP5;1 and its homolog NIP6;1 were retained in the ER of the kns3 mutants. Our genetic analysis further discovered that two homologs of KNS3, KNSTH1 and KNSTH2, were also involved in the ER exit of NIP5;1. In Arabidopsis protoplasts and tobacco leaves, mCherry-fused KNS3 localized to the ER and Golgi, whereas KNSTH2 localized to the ER. The cytosolic C-terminal tail of KNS3 contains amino acids important for Golgi-to-ER trafficking. Furthermore, the ER-to-Golgi trafficking of KNS3 depended on KNSTH1 and KNSTH2, and the accumulation of these three proteins in Arabidopsis roots depended on each other. We propose that KNS3, KNSTH1, and KNSTH2 function as a cargo-receptor complex mediating the ER exit of NIP5;1. [ABSTRACT FROM AUTHOR]

Populations in extreme environments at the margins of a species' range are often the most vulnerable to climate change, but they may also experience novel evolutionary processes, such as secondary contact and hybridization with their relatives. The range overlap resulting from secondary contact with related species that have adapted to different climatic zones may act as corridors for adaptive introgression. To test this hypothesis, we examined the hybrid zones along the altitude of two closely related Rubus species, one temperate and the other subtropical species, at their southern and northern limits on Yakushima Island, Japan. Genomic cline analysis revealed non‐neutral introgression throughout the genome in both directions in the two species. Some of these genomic regions involve gene ontology terms related to the regulation of several biological processes. Our niche modeling suggests that, assuming niche conservatism, the temperate species are likely to lose their suitable habitat, and the backcrossed hybrids with the subtropical species are already expanding upslope on the island. Adaptive introgression through the hybrid zone may contribute to the persistence and expansion of the species in the southernmost and northernmost populations. [ABSTRACT FROM AUTHOR]

Fem is a W‐linked gene that encodes a piRNA precursor, and its product, Fem piRNA, is a master factor of female determination in Bombyx mori. Fem has low similarity to any known sequences, and the origin of Fem remains unclear. So far, two hypotheses have been proposed for the origin of Fem: The first hypothesis is that Fem is an allele of Masc, which assumes that the W chromosome was originally a homologous chromosome of the Z chromosome. The second hypothesis is that Fem arose by the transposition of Masc to the W chromosome. To explore the origin of Fem, we determined the W chromosome sequences of B. mori and, as a comparison, a closely relative bombycid species of Trilocha varians with a Fem‐independent sex determination system. To our surprise, although the sequences of W and Z chromosomes show no homology to each other, a few pairs of homologues are shared by W and Z chromosomes, indicating the W chromosome of both species originated from Z chromosome. In addition, the W chromosome of T. varians lacks Fem, while the W chromosome of B. mori has over 100 copies of Fem. The high‐quality assembly of the W chromosome of B. mori arose the third hypothesis about the origin of Fem: Fem is a chimeric sequence of multiple transposons. More than half of one transcriptional unit of Fem shows a significant homology to RTE‐BovB. Moreover, the Fem piRNA‐producing region could correspond to the boundary of the two transposons, gypsy and satellite DNA. [ABSTRACT FROM AUTHOR]