The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes

Rambutan (Nephelium lappaceum var. lappaceum), a tropical fruit tree native to southeastern Asia, belongs to the family Sapindaceae. Rambutan is a popular table fruit and is also processed into preserves, juices, wines, and sorbets [1]. At present, only three Sapindaceae genomes are publicly available: Xanthoceras sorbifolium [2], Dimocarpus longan (longan) [3], and Acer yangbiense [4]. During the process of submitting this manuscript, the genome paper for the rambutan cultivar Baoyan7 became available online, but its genome sequence has not yet been released [5]

The Physiological Race of the first Hemileia vastatrix (Coffee Leaf Rust) discovered in Hawaii

29th Conference of Association for the Science and Information on Coffee, 11 Sept. - 14 Sept. 2023 Hanoi, Vietnaminfo:eu-repo/semantics/publishedVersio

First report of the physiological race (XXIV) of Hemileia vastatrix (Coffee Leaf Rust) in Hawaii

This research was funded by the Foundation for Science and Technology (FCT) UNIT (UID/AGR/04129/2020) of LEAF- -Linking Landscape, Environment, Agriculture and Food, Research Unit.info:eu-repo/semantics/publishedVersio

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis.

The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode

The bracteatus pineapple genome and domestication of clonally propagated crops

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Identification of yeast and plant salt stress tolerance determinants

The detrimental effects of high concentrations of salts (mainly Na +) on plants remains a major limitation to agricultural productivity in arid, semi-arid and irrigated agriculture. Currently, the use of genetic molecular systems is become an increasingly important tool in understanding basic cellular functions. Here the yeast, Saccharomyces cerevisiae , has been used as a molecular genetic system to identify salt tolerance determinants by gain-of-function complementation of salt sensitive yeast mutants with yeast or plant genes. In addition, genomic microarray analysis has been used to dissect components of pivotal salt stress signal transduction cascades in the model organism by monitoring global mRNA level changes, in response to salt treatment, between wild type cells and salt sensitive yeast mutants. Functional complementation of the salt sensitive yeast mutant, nls2, identified two categories of suppressors, SPK1 (Salt Protein Kinase) and SCP1 (Salt C-2 domain Protein), albeit neither is NLS2. SPK1 expression also increased Na+/Li+ tolerance of wild type yeast cells, suggesting it is a limiting factor in salt adaptation. A spk1 knockout resulted in reduced growth of yeast strains in the presence of salt. The salt sensitive phenotype of a spk1 and calcineurin null (cnb1) double mutant was additive, relative to either individual mutant, indicating that Spk1 functions independent of calcineurin to regulate ion homeostasis and salt tolerance. Expression of a tobacco cDNA library (constructed in a single copy yeast expression vector) in cnb1 resulted in the isolation of NtSLT1 (Nicotiana tabacum Sodium Lithium Tolerant) by functional complementation of salt sensitivity. NtSLT1 suppressed salt sensitivity of the yeast mutant only if a N-terminally truncated protein was produced. Truncation was also a conserved property for functional complementation by the Arabidopsis thaliana homolog AtSLT1, and is indicative that the N-terminus contains an auto-inhibitor. NtSLT1 increased salt tolerance of wild type yeast, and suppression of salt sensitivity was restricted to mutants that are defective specifically in components of the calcineurin signal pathway (cnb1, tcn1, ena1-4). Microarray analysis of wild type and yeast mutants (cnb1, hog1, spk1) cells revealed numerous genes that were regulated uniquely by each of the major hyper-saline stress signal pathway

Evaluation of <i>Coffea arabica</i> Cultivars for Resistance to <i>Meloidogyne konaensis</i>

Coffee is an important agricultural crop for the State of Hawaii. Developing new coffee cultivars with resistance to damaging pests and diseases is crucial for improving production and maintaining the profitability of the industry. With the recent discovery of Hemileia vastatrix, coffee leaf rust (CLR), to Hawaii there is a strong interest in replanting with CLR-resistant germplasm. However, when selecting an appropriate cultivar for replanting, susceptibility to other pathogens, such as plant-parasitic nematodes, should be taken into consideration. Meloidogyne konaensis, the Kona coffee root-knot nematode, causes severe destruction of the root system, reducing the yield and causing the mortality of susceptible Coffea arabica cv. Typica trees. Fortunately, resistance to root-knot nematodes has been found in some C. arabica germplasm. In this study, accessions of wild Ethiopian C. arabica and two CLR-resistant C. arabica cultivars, Tupi-HI and Obata, were evaluated for resistance to M. konaensis in a greenhouse bioassay. All Ethiopian accessions retained high levels of resistance, resulting in reproductive factors (Rfs) lower than 1.0, and low root-rot ratings. Tupi-HI was highly susceptible to M. konanensis, with an Rf value of 7.12, whereas Obata was slightly susceptible, with an Rf value of 2.33. Both cultivars had high root-rot ratings, suggesting intolerance to the nematode. Hybridizing Ethiopian C. arabica with Tupi-HI or Obata may result in new elite cultivars, resistant to both H. vastatrix and M. konaensis