Genome data of the incense tree Aquilaria sinensis.

Genome data of the incense tree Aquilaria sinensis.

Genome data of the incense tree Aquilaria sinensis.

Abstract
Background Homeobox-containing genes encode crucial transcription factors in animal and plant development, and changes to these genes have been linked to the evolution of body plans and morphologies. In animals some homeobox genes are clustered in the genome, due to either coordinated gene regulation or as remnants from ancestral genomic arrangements. Analyses of homeobox gene organization across a range of species thus helps to better understand the evolution of genome organization and developmental gene control, and the possible interactions between the two. However, homeobox gene organization in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians, remains to be fully elucidated.
Results Here, we present a high-quality chromosome-level genome assembly of Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~758Mb, scaffold N50 = 72.3Mb). A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated for this genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data in other mollusc species. Our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.
Conclusions The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally.

The Lepidoptera, including butterflies and moths, is one of the most widespread insect orders in the world, playing important roles in the environment as pollinators and agricultural pests. Different sexes of the same species exhibit biological and physiological differences in addition to their sex organs, however, if and how these differences relate to climate change are poorly understood. In this study, we investigated the common yellow butterfly Eurema hecabe (Family Pieridae), a species that is widely distributed in Asia, Africa, and Australia. In addition to the establishment of high-quality genomic resources and transcriptomes from eight developmental stages, we subjected adult butterflies of different sexes to varying temperature to examine gene expression differences. Both mRNA and microRNA transcriptomes were obtained separately from head and body, and sex-specific responses were clearly identified, including differential expression of sesquiterpenoid biosynthetic pathway genes, neuropeptides, and a lepidopteran microRNA cluster. This study lays the foundation for further understanding of differential responses to environmental stress in a widespread lepidopteran model, and demonstrates the potential complexity of sex-specific responses of lepidopterans to climate change.

The Lepidoptera, including butterflies and moths, is one of the most widespread insect orders in the world, playing important roles in the environment as pollinators and agricultural pests. Different sexes of the same species exhibit biological and physiological differences in addition to their sex organs, however, if and how these differences relate to climate change are poorly understood. In this study, we investigated the common yellow butterfly Eurema hecabe (Family Pieridae), a species that is widely distributed in Asia, Africa, and Australia. In addition to the establishment of high-quality genomic resources and transcriptomes from eight developmental stages, we subjected adult butterflies of different sexes to varying temperature to examine gene expression differences. Both mRNA and microRNA transcriptomes were obtained separately from head and body, and sex-specific responses were clearly identified, including differential expression of sesquiterpenoid biosynthetic pathway genes, neuropeptides, and a lepidopteran microRNA cluster. This study lays the foundation for further understanding of differential responses to environmental stress in a widespread lepidopteran model, and demonstrates the potential complexity of sex-specific responses of lepidopterans to climate change.

Trees in the genus Aquilaria (Thymelaeaceae) are known as lign aloes, and are native to the forests of southeast Asia. Lign aloes produce agarwood as an antimicrobial defence. Agarwood has a long history of cultural and medicinal use, and is of considerable commercial value. However, due to habitat destruction and over collection, lign aloes are threatened in the wild. We present a chromosomal‐level assembly for Aquilaria sinensis, a lign aloe endemic to China known as the incense tree, based on Illumina short‐read, 10X Genomics linked‐read, and Hi‐C sequencing data. Our 783.8 Mbp A. sinensis genome assembly is of high physical contiguity, with a scaffold N50 of 87.6 Mbp, and high completeness, with a 95.8% BUSCO score for eudicotyledon genes. We include 17 transcriptomes from various plant tissues, providing a total of 35,965 gene models. We reveal the first complete set of genes involved in sesquiterpenoid production, plant defence, and agarwood production for the genus Aquilaria, including genes involved in the biosynthesis of sesquiterpenoids via the mevalonic acid (MVA), 1‐deoxy‐D‐xylulose‐5‐phosphate (DXP), and methylerythritol phosphate (MEP) pathways. We perform a detailed repeat content analysis, revealing that transposable elements account for ~61% of the genome, with major contributions from gypsy‐like and copia‐like LTR retroelements. We also provide a comparative analysis of repeat content across sequenced species in the order Malvales. Our study reveals the first chromosomal‐level genome assembly for a tree in the genus Aquilaria and provides an unprecedented opportunity to address a variety of applied, genomic and evolutionary questions in the Thymelaeaceae more widely.

Abstract
Background Homeobox-containing genes encode crucial transcription factors in animal and plant development, and changes to these genes have been linked to the evolution of body plans and morphologies. In animals some homeobox genes are clustered in the genome, due to either coordinated gene regulation or as remnants from ancestral genomic arrangements. Analyses of homeobox gene organization across a range of species thus helps to better understand the evolution of genome organization and developmental gene control, and the possible interactions between the two. However, homeobox gene organization in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians, remains to be fully elucidated.
Results Here, we present a high-quality chromosome-level genome assembly of Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~758Mb, scaffold N50 = 72.3Mb). A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated for this genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data in other mollusc species. Our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.
Conclusions The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally.

Animals have fascinating diversity of life forms. Analyses of the available genome sequence reveals dynamic evolution of gene gain and loss at different lineages in the animal tree of life (e.g. Albalat and Canestro 2016; Sharma et al 2018; Fernandez and Gabaldon 2020; Guijarro-Clarke et al 2020; Jebb et al 2020). Gene gain via another kingdom as well as the evolutionary consequence of gene loss are generally ignored and difficult to interpret. Here we sequenced six new myriapod genomes at key phylogenetic positions of this understudied arthropod lineage (three millipedes and three centipedes). Comparison of myriapod genomes revealed multiple horizontal gene transfer (HGT) of genes shared between centipedes, including glucose/arabinose dehydrogenase that happened at the last common of ancestor of centipedes, while there was no detectable HGT shared between the millipedes. In all millipede lineages, the loss of juvenile hormone O-methyltransferase, a key enzyme in catalysing the last step of sesquiterpenoid hormone methyl farnesoate production in arthropods was revealed. These findings provided the first evidence of shared HGT in the last common ancestor of centipede ancestor, while gene loss event could indeed happen in endocrine system in contrary to the conventional view of stepwise gene gain resulting in diversity of animal physiology for adaptation to environment.

The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a true oyster species that native to the estuary-coast of Pearl River Delta in southern China. The species has long been farmed for hundreds of years, and with scientific, ecological, cultural and nutritional importance. However, there is only limited information on the genetic background and stress adaptation mechanism of M. hongkongensis, restricting the sustainable production and utilisation of the local oyster resources. Here, we presented the population structure analysis on oysters collected from Deep Bay (Shenzhen Bay) and Lantau Island in Hong Kong, the transcriptome analysis on heat shock responses and the gut microbiota profile of M. hongkongensis. A conserved genetic background of local oysters was uncovered by the whole genome resequencing on 49 individuals, and the results indicated a close relationship and adaptation process in local oyster populations. Genetic variants in homeobox and heat shock protein genes were identified and predicted with regulatory function. Oysters had also been incubated under temperate (25 °C) and heat shock (32 °C) conditions for 24 hours to investigate the stress responses. Transcriptome profiles revealed the heat-induced regulation on heat shock protein, protein binding genes and signal transduction genes. We also found the differential expression of two splicing factors might be regulated by alternative splicing, and their expression levels were higher under heat stress. In addition, the gut microbe community were detected by 16S rRNA sequencing, and Cyanobacteria, Proteobacteria and Spirochaetes were the top phyla found in local oysters. Our results provided the knowledge on transcriptomic responses to heat shock in local oyster and implied the molecular basis for the divergent adaptation to the changeable aquatic environment. We also suggested that gut microbiota might participate in the regulation of stress response in M. hongkongensis. These findings give new insights on different mechanisms of local adaptation in Hong Kong oysters and other molluscs.